HEADER HYDROLASE/HYDROLASE INHIBITOR 09-FEB-12 4DO4
TITLE PHARMACOLOGICAL CHAPERONES FOR HUMAN ALPHA-N-ACETYLGALACTOSAMINIDASE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: ALPHA-N-ACETYLGALACTOSAMINIDASE;
COMPND 3 CHAIN: A, B;
COMPND 4 FRAGMENT: UNP RESIDUES 18-411;
COMPND 5 SYNONYM: ALPHA-GALACTOSIDASE B;
COMPND 6 EC: 3.2.1.49;
COMPND 7 ENGINEERED: YES;
COMPND 8 MUTATION: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: NAGA;
SOURCE 6 EXPRESSION_SYSTEM: TRICHOPLUSIA NI;
SOURCE 7 EXPRESSION_SYSTEM_COMMON: CABBAGE LOOPER;
SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7111;
SOURCE 9 EXPRESSION_SYSTEM_STRAIN: HI-FIVE;
SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PIB/V5-HIS-TOPO TA
KEYWDS PHARMACOLOGICAL CHAPERONE, (BETA/ALPHA)8 BARREL, GLYCOSIDASE,
KEYWDS 2 CARBOHYDRATE-BINDING PROTEIN, GLYCOPROTEIN, LYSOSOME, HYDROLASE-
KEYWDS 3 HYDROLASE INHIBITOR COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR N.E.CLARK,S.C.GARMAN
REVDAT 5 13-SEP-23 4DO4 1 HETSYN
REVDAT 4 29-JUL-20 4DO4 1 CAVEAT COMPND REMARK SEQADV
REVDAT 4 2 1 HETNAM HETSYN LINK SITE
REVDAT 4 3 1 ATOM
REVDAT 3 15-NOV-17 4DO4 1 REMARK
REVDAT 2 21-NOV-12 4DO4 1 JRNL
REVDAT 1 10-OCT-12 4DO4 0
JRNL AUTH N.E.CLARK,M.C.METCALF,D.BEST,G.W.FLEET,S.C.GARMAN
JRNL TITL PHARMACOLOGICAL CHAPERONES FOR HUMAN
JRNL TITL 2 ALPHA-N-ACETYLGALACTOSAMINIDASE
JRNL REF PROC.NATL.ACAD.SCI.USA V. 109 17400 2012
JRNL REFN ISSN 0027-8424
JRNL PMID 23045655
JRNL DOI 10.1073/PNAS.1203924109
REMARK 2
REMARK 2 RESOLUTION. 1.40 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.5.0109
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.63
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6
REMARK 3 NUMBER OF REFLECTIONS : 228268
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING + TEST SET) : 0.143
REMARK 3 R VALUE (WORKING SET) : 0.142
REMARK 3 FREE R VALUE : 0.178
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 11481
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 20
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.40
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.44
REMARK 3 REFLECTION IN BIN (WORKING SET) : 14980
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.35
REMARK 3 BIN R VALUE (WORKING SET) : 0.3570
REMARK 3 BIN FREE R VALUE SET COUNT : 775
REMARK 3 BIN FREE R VALUE : 0.3960
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 6279
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 363
REMARK 3 SOLVENT ATOMS : 991
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.11
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.02000
REMARK 3 B22 (A**2) : -0.05000
REMARK 3 B33 (A**2) : 0.04000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.05000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.046
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.048
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.041
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.560
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.982
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.974
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6920 ; 0.012 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): 4666 ; 0.001 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9436 ; 1.457 ; 2.004
REMARK 3 BOND ANGLES OTHERS (DEGREES): 11318 ; 0.927 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 809 ; 6.186 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 311 ;34.790 ;24.084
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1077 ;12.647 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 40 ;18.715 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1036 ; 0.085 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7475 ; 0.007 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): 1359 ; 0.001 ; 0.020
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 3980 ; 5.886 ;12.000
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1600 ; 2.365 ;12.000
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6429 ; 7.373 ;16.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2940 ;10.819 ;20.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3001 ;13.901 ;24.000
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 RIGID-BOND RESTRAINTS (A**2): 11586 ; 2.780 ; 3.000
REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 NCS RESTRAINTS STATISTICS
REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 4
REMARK 3
REMARK 3 TLS GROUP : 1
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 18 A 310
REMARK 3 ORIGIN FOR THE GROUP (A): 56.7151 -1.1719 10.1644
REMARK 3 T TENSOR
REMARK 3 T11: 0.0758 T22: 0.0627
REMARK 3 T33: 0.0260 T12: -0.0064
REMARK 3 T13: -0.0111 T23: -0.0104
REMARK 3 L TENSOR
REMARK 3 L11: 0.9212 L22: 0.2145
REMARK 3 L33: 0.3245 L12: 0.0822
REMARK 3 L13: -0.1260 L23: -0.1021
REMARK 3 S TENSOR
REMARK 3 S11: 0.0380 S12: 0.0249 S13: 0.0973
REMARK 3 S21: 0.0203 S22: 0.0123 S23: 0.0078
REMARK 3 S31: -0.0187 S32: 0.0314 S33: -0.0503
REMARK 3
REMARK 3 TLS GROUP : 2
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 311 A 404
REMARK 3 ORIGIN FOR THE GROUP (A): 26.0927 3.2089 11.0002
REMARK 3 T TENSOR
REMARK 3 T11: 0.0568 T22: 0.0668
REMARK 3 T33: 0.0949 T12: 0.0198
REMARK 3 T13: 0.0159 T23: 0.0425
REMARK 3 L TENSOR
REMARK 3 L11: 1.0910 L22: 1.3464
REMARK 3 L33: 0.5842 L12: -0.0439
REMARK 3 L13: -0.2090 L23: -0.3245
REMARK 3 S TENSOR
REMARK 3 S11: 0.0466 S12: 0.0375 S13: 0.1107
REMARK 3 S21: 0.0776 S22: 0.0683 S23: 0.2526
REMARK 3 S31: -0.0786 S32: -0.1131 S33: -0.1149
REMARK 3
REMARK 3 TLS GROUP : 3
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : B 18 B 310
REMARK 3 ORIGIN FOR THE GROUP (A): 21.7878 -31.6515 21.9579
REMARK 3 T TENSOR
REMARK 3 T11: 0.1038 T22: 0.0830
REMARK 3 T33: 0.1301 T12: -0.0043
REMARK 3 T13: 0.0010 T23: 0.0503
REMARK 3 L TENSOR
REMARK 3 L11: 1.0073 L22: 0.8673
REMARK 3 L33: 0.5771 L12: 0.3230
REMARK 3 L13: -0.4705 L23: -0.3412
REMARK 3 S TENSOR
REMARK 3 S11: -0.0446 S12: 0.0793 S13: -0.0001
REMARK 3 S21: 0.1227 S22: 0.1280 S23: 0.2757
REMARK 3 S31: -0.0028 S32: -0.0394 S33: -0.0834
REMARK 3
REMARK 3 TLS GROUP : 4
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : B 311 B 404
REMARK 3 ORIGIN FOR THE GROUP (A): 51.6276 -37.0146 16.6568
REMARK 3 T TENSOR
REMARK 3 T11: 0.0866 T22: 0.0919
REMARK 3 T33: 0.1769 T12: 0.0172
REMARK 3 T13: -0.0134 T23: 0.0224
REMARK 3 L TENSOR
REMARK 3 L11: 1.4598 L22: 1.6788
REMARK 3 L33: 0.6512 L12: -0.1561
REMARK 3 L13: -0.4924 L23: 0.1996
REMARK 3 S TENSOR
REMARK 3 S11: -0.0987 S12: -0.0598 S13: -0.2751
REMARK 3 S21: 0.0133 S22: -0.0048 S23: -0.3822
REMARK 3 S31: 0.0866 S32: 0.1400 S33: 0.1034
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : MASK
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.40
REMARK 3 ION PROBE RADIUS : 0.80
REMARK 3 SHRINKAGE RADIUS : 0.80
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING
REMARK 3 POSITIONS U VALUES : WITH TLS ADDED
REMARK 4
REMARK 4 4DO4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-FEB-12.
REMARK 100 THE DEPOSITION ID IS D_1000070571.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 10-JUN-10
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 3.4
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : NSLS
REMARK 200 BEAMLINE : X25
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.100
REMARK 200 MONOCHROMATOR : SI(111) DOUBLE CRYSTAL
REMARK 200 OPTICS : PT COATED MIRROR
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 228468
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9
REMARK 200 DATA REDUNDANCY : 5.100
REMARK 200 R MERGE (I) : 0.05800
REMARK 200 R SYM (I) : 0.05800
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.6000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.42
REMARK 200 COMPLETENESS FOR SHELL (%) : 94.9
REMARK 200 DATA REDUNDANCY IN SHELL : 4.00
REMARK 200 R MERGE FOR SHELL (I) : 0.84200
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS
REMARK 200 SOFTWARE USED: NULL
REMARK 200 STARTING MODEL: PDB ENTRY 3H53
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 62.80
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.31
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 8-16% PEG3350, 70MM CITRIC ACID, 30MM
REMARK 280 BIS-TRIS PROPANE, PH 3.4, VAPOR DIFFUSION, HANGING DROP,
REMARK 280 TEMPERATURE 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,Y,-Z
REMARK 290 3555 X+1/2,Y+1/2,Z
REMARK 290 4555 -X+1/2,Y+1/2,-Z
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 77.02750
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 57.31200
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 77.02750
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 57.31200
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 9320 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 32420 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 41.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 ASN A 405
REMARK 465 LEU A 406
REMARK 465 GLU A 407
REMARK 465 MET A 408
REMARK 465 SER A 409
REMARK 465 GLN A 410
REMARK 465 GLN A 411
REMARK 465 HIS A 412
REMARK 465 HIS A 413
REMARK 465 HIS A 414
REMARK 465 HIS A 415
REMARK 465 HIS A 416
REMARK 465 HIS A 417
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 ARG A 37 -132.69 50.89
REMARK 500 ASP A 78 -150.91 -112.21
REMARK 500 CYS A 80 19.48 86.96
REMARK 500 LYS A 149 35.90 71.00
REMARK 500 ASP A 252 -178.13 95.30
REMARK 500 ASN A 258 -144.20 -102.04
REMARK 500 LEU A 280 77.33 -108.14
REMARK 500 SER A 283 85.71 -159.82
REMARK 500 ASP A 346 -71.09 -113.82
REMARK 500 SER A 363 -10.04 70.42
REMARK 500 ARG B 37 -134.18 52.72
REMARK 500 ASP B 45 59.41 -142.54
REMARK 500 ASP B 78 -149.60 -114.19
REMARK 500 CYS B 80 21.14 80.84
REMARK 500 LYS B 149 33.31 73.95
REMARK 500 ASP B 252 -177.26 92.47
REMARK 500 ASN B 258 -142.65 -98.70
REMARK 500 LEU B 280 78.14 -111.67
REMARK 500 SER B 283 85.76 -157.24
REMARK 500 ASP B 346 -70.17 -116.73
REMARK 500 SER B 363 47.98 -103.35
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3H53 RELATED DB: PDB
REMARK 900 COMPLEX WITH GLYCEROL
REMARK 900 RELATED ID: 3H54 RELATED DB: PDB
REMARK 900 COMPLEX WITH GALNAC
REMARK 900 RELATED ID: 3H55 RELATED DB: PDB
REMARK 900 COMPLEX WITH GALACTOSE
REMARK 900 RELATED ID: 3IGU RELATED DB: PDB
REMARK 900 COVALENT COMPLEX
REMARK 900 RELATED ID: 4DO5 RELATED DB: PDB
REMARK 900 COMPLEX WITH DGJ
REMARK 900 RELATED ID: 4DO6 RELATED DB: PDB
REMARK 900 GLUCOSE SOAK
DBREF 4DO4 A 18 411 UNP P17050 NAGAB_HUMAN 18 411
DBREF 4DO4 B 18 411 UNP P17050 NAGAB_HUMAN 18 411
SEQADV 4DO4 GLN A 201 UNP P17050 ASN 201 ENGINEERED MUTATION
SEQADV 4DO4 HIS A 412 UNP P17050 EXPRESSION TAG
SEQADV 4DO4 HIS A 413 UNP P17050 EXPRESSION TAG
SEQADV 4DO4 HIS A 414 UNP P17050 EXPRESSION TAG
SEQADV 4DO4 HIS A 415 UNP P17050 EXPRESSION TAG
SEQADV 4DO4 HIS A 416 UNP P17050 EXPRESSION TAG
SEQADV 4DO4 HIS A 417 UNP P17050 EXPRESSION TAG
SEQADV 4DO4 GLN B 201 UNP P17050 ASN 201 ENGINEERED MUTATION
SEQADV 4DO4 HIS B 412 UNP P17050 EXPRESSION TAG
SEQADV 4DO4 HIS B 413 UNP P17050 EXPRESSION TAG
SEQADV 4DO4 HIS B 414 UNP P17050 EXPRESSION TAG
SEQADV 4DO4 HIS B 415 UNP P17050 EXPRESSION TAG
SEQADV 4DO4 HIS B 416 UNP P17050 EXPRESSION TAG
SEQADV 4DO4 HIS B 417 UNP P17050 EXPRESSION TAG
SEQRES 1 A 400 LEU ASP ASN GLY LEU LEU GLN THR PRO PRO MET GLY TRP
SEQRES 2 A 400 LEU ALA TRP GLU ARG PHE ARG CYS ASN ILE ASN CYS ASP
SEQRES 3 A 400 GLU ASP PRO LYS ASN CYS ILE SER GLU GLN LEU PHE MET
SEQRES 4 A 400 GLU MET ALA ASP ARG MET ALA GLN ASP GLY TRP ARG ASP
SEQRES 5 A 400 MET GLY TYR THR TYR LEU ASN ILE ASP ASP CYS TRP ILE
SEQRES 6 A 400 GLY GLY ARG ASP ALA SER GLY ARG LEU MET PRO ASP PRO
SEQRES 7 A 400 LYS ARG PHE PRO HIS GLY ILE PRO PHE LEU ALA ASP TYR
SEQRES 8 A 400 VAL HIS SER LEU GLY LEU LYS LEU GLY ILE TYR ALA ASP
SEQRES 9 A 400 MET GLY ASN PHE THR CYS MET GLY TYR PRO GLY THR THR
SEQRES 10 A 400 LEU ASP LYS VAL VAL GLN ASP ALA GLN THR PHE ALA GLU
SEQRES 11 A 400 TRP LYS VAL ASP MET LEU LYS LEU ASP GLY CYS PHE SER
SEQRES 12 A 400 THR PRO GLU GLU ARG ALA GLN GLY TYR PRO LYS MET ALA
SEQRES 13 A 400 ALA ALA LEU ASN ALA THR GLY ARG PRO ILE ALA PHE SER
SEQRES 14 A 400 CYS SER TRP PRO ALA TYR GLU GLY GLY LEU PRO PRO ARG
SEQRES 15 A 400 VAL GLN TYR SER LEU LEU ALA ASP ILE CYS ASN LEU TRP
SEQRES 16 A 400 ARG ASN TYR ASP ASP ILE GLN ASP SER TRP TRP SER VAL
SEQRES 17 A 400 LEU SER ILE LEU ASN TRP PHE VAL GLU HIS GLN ASP ILE
SEQRES 18 A 400 LEU GLN PRO VAL ALA GLY PRO GLY HIS TRP ASN ASP PRO
SEQRES 19 A 400 ASP MET LEU LEU ILE GLY ASN PHE GLY LEU SER LEU GLU
SEQRES 20 A 400 GLN SER ARG ALA GLN MET ALA LEU TRP THR VAL LEU ALA
SEQRES 21 A 400 ALA PRO LEU LEU MET SER THR ASP LEU ARG THR ILE SER
SEQRES 22 A 400 ALA GLN ASN MET ASP ILE LEU GLN ASN PRO LEU MET ILE
SEQRES 23 A 400 LYS ILE ASN GLN ASP PRO LEU GLY ILE GLN GLY ARG ARG
SEQRES 24 A 400 ILE HIS LYS GLU LYS SER LEU ILE GLU VAL TYR MET ARG
SEQRES 25 A 400 PRO LEU SER ASN LYS ALA SER ALA LEU VAL PHE PHE SER
SEQRES 26 A 400 CYS ARG THR ASP MET PRO TYR ARG TYR HIS SER SER LEU
SEQRES 27 A 400 GLY GLN LEU ASN PHE THR GLY SER VAL ILE TYR GLU ALA
SEQRES 28 A 400 GLN ASP VAL TYR SER GLY ASP ILE ILE SER GLY LEU ARG
SEQRES 29 A 400 ASP GLU THR ASN PHE THR VAL ILE ILE ASN PRO SER GLY
SEQRES 30 A 400 VAL VAL MET TRP TYR LEU TYR PRO ILE LYS ASN LEU GLU
SEQRES 31 A 400 MET SER GLN GLN HIS HIS HIS HIS HIS HIS
SEQRES 1 B 400 LEU ASP ASN GLY LEU LEU GLN THR PRO PRO MET GLY TRP
SEQRES 2 B 400 LEU ALA TRP GLU ARG PHE ARG CYS ASN ILE ASN CYS ASP
SEQRES 3 B 400 GLU ASP PRO LYS ASN CYS ILE SER GLU GLN LEU PHE MET
SEQRES 4 B 400 GLU MET ALA ASP ARG MET ALA GLN ASP GLY TRP ARG ASP
SEQRES 5 B 400 MET GLY TYR THR TYR LEU ASN ILE ASP ASP CYS TRP ILE
SEQRES 6 B 400 GLY GLY ARG ASP ALA SER GLY ARG LEU MET PRO ASP PRO
SEQRES 7 B 400 LYS ARG PHE PRO HIS GLY ILE PRO PHE LEU ALA ASP TYR
SEQRES 8 B 400 VAL HIS SER LEU GLY LEU LYS LEU GLY ILE TYR ALA ASP
SEQRES 9 B 400 MET GLY ASN PHE THR CYS MET GLY TYR PRO GLY THR THR
SEQRES 10 B 400 LEU ASP LYS VAL VAL GLN ASP ALA GLN THR PHE ALA GLU
SEQRES 11 B 400 TRP LYS VAL ASP MET LEU LYS LEU ASP GLY CYS PHE SER
SEQRES 12 B 400 THR PRO GLU GLU ARG ALA GLN GLY TYR PRO LYS MET ALA
SEQRES 13 B 400 ALA ALA LEU ASN ALA THR GLY ARG PRO ILE ALA PHE SER
SEQRES 14 B 400 CYS SER TRP PRO ALA TYR GLU GLY GLY LEU PRO PRO ARG
SEQRES 15 B 400 VAL GLN TYR SER LEU LEU ALA ASP ILE CYS ASN LEU TRP
SEQRES 16 B 400 ARG ASN TYR ASP ASP ILE GLN ASP SER TRP TRP SER VAL
SEQRES 17 B 400 LEU SER ILE LEU ASN TRP PHE VAL GLU HIS GLN ASP ILE
SEQRES 18 B 400 LEU GLN PRO VAL ALA GLY PRO GLY HIS TRP ASN ASP PRO
SEQRES 19 B 400 ASP MET LEU LEU ILE GLY ASN PHE GLY LEU SER LEU GLU
SEQRES 20 B 400 GLN SER ARG ALA GLN MET ALA LEU TRP THR VAL LEU ALA
SEQRES 21 B 400 ALA PRO LEU LEU MET SER THR ASP LEU ARG THR ILE SER
SEQRES 22 B 400 ALA GLN ASN MET ASP ILE LEU GLN ASN PRO LEU MET ILE
SEQRES 23 B 400 LYS ILE ASN GLN ASP PRO LEU GLY ILE GLN GLY ARG ARG
SEQRES 24 B 400 ILE HIS LYS GLU LYS SER LEU ILE GLU VAL TYR MET ARG
SEQRES 25 B 400 PRO LEU SER ASN LYS ALA SER ALA LEU VAL PHE PHE SER
SEQRES 26 B 400 CYS ARG THR ASP MET PRO TYR ARG TYR HIS SER SER LEU
SEQRES 27 B 400 GLY GLN LEU ASN PHE THR GLY SER VAL ILE TYR GLU ALA
SEQRES 28 B 400 GLN ASP VAL TYR SER GLY ASP ILE ILE SER GLY LEU ARG
SEQRES 29 B 400 ASP GLU THR ASN PHE THR VAL ILE ILE ASN PRO SER GLY
SEQRES 30 B 400 VAL VAL MET TRP TYR LEU TYR PRO ILE LYS ASN LEU GLU
SEQRES 31 B 400 MET SER GLN GLN HIS HIS HIS HIS HIS HIS
MODRES 4DO4 ASN A 177 ASN GLYCOSYLATION SITE
MODRES 4DO4 ASN B 177 ASN GLYCOSYLATION SITE
MODRES 4DO4 ASN A 124 ASN GLYCOSYLATION SITE
MODRES 4DO4 ASN B 385 ASN GLYCOSYLATION SITE
MODRES 4DO4 ASN A 385 ASN GLYCOSYLATION SITE
MODRES 4DO4 ASN B 124 ASN GLYCOSYLATION SITE
HET NAG C 1 14
HET NAG C 2 14
HET BMA C 3 11
HET NAG D 1 14
HET NAG D 2 14
HET BMA D 3 11
HET MAN D 4 11
HET MAN D 5 11
HET NAG E 1 14
HET NAG E 2 14
HET FUC E 3 10
HET NAG F 1 14
HET NAG F 2 14
HET BMA F 3 11
HET MAN F 4 11
HET MAN F 5 11
HET NAG A 509 14
HET DJN A 510 14
HET CIT A 511 13
HET GOL A 512 6
HET GOL A 513 6
HET GOL A 514 6
HET ACY A 515 4
HET GOL A 516 6
HET GOL A 517 6
HET GOL A 518 6
HET NAG B 509 14
HET DJN B 510 14
HET CIT B 511 13
HET GOL B 512 6
HET GOL B 513 6
HET GOL B 514 6
HET GOL B 515 6
HET GOL B 516 6
HET GOL B 517 6
HET GOL B 518 6
HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE
HETNAM BMA BETA-D-MANNOPYRANOSE
HETNAM MAN ALPHA-D-MANNOPYRANOSE
HETNAM FUC ALPHA-L-FUCOPYRANOSE
HETNAM DJN N-[(3S,4R,5S,6R)-4,5-DIHYDROXY-6-(HYDROXYMETHYL)
HETNAM 2 DJN PIPERIDIN-3-YL]ACETAMIDE
HETNAM CIT CITRIC ACID
HETNAM GOL GLYCEROL
HETNAM ACY ACETIC ACID
HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA-
HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO-
HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE
HETSYN BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE
HETSYN MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE
HETSYN FUC ALPHA-L-FUCOSE; 6-DEOXY-ALPHA-L-GALACTOPYRANOSE; L-
HETSYN 2 FUC FUCOSE; FUCOSE
HETSYN DJN 2-ACETAMIDO-1,2-DIDEOXY-D-GALACTO-NOJIRIMYCIN; DGJNAC
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 3 NAG 10(C8 H15 N O6)
FORMUL 3 BMA 3(C6 H12 O6)
FORMUL 4 MAN 4(C6 H12 O6)
FORMUL 5 FUC C6 H12 O5
FORMUL 8 DJN 2(C8 H16 N2 O4)
FORMUL 9 CIT 2(C6 H8 O7)
FORMUL 10 GOL 13(C3 H8 O3)
FORMUL 13 ACY C2 H4 O2
FORMUL 27 HOH *991(H2 O)
HELIX 1 1 ALA A 32 ARG A 37 1 6
HELIX 2 2 SER A 51 ASP A 65 1 15
HELIX 3 3 GLY A 66 GLY A 71 1 6
HELIX 4 4 GLY A 101 LEU A 112 1 12
HELIX 5 5 THR A 134 ASP A 136 5 3
HELIX 6 6 LYS A 137 TRP A 148 1 12
HELIX 7 7 THR A 161 THR A 179 1 19
HELIX 8 8 TRP A 189 GLU A 193 5 5
HELIX 9 9 GLN A 201 CYS A 209 1 9
HELIX 10 10 SER A 221 HIS A 235 1 15
HELIX 11 11 HIS A 235 GLN A 240 1 6
HELIX 12 12 PRO A 241 ALA A 243 5 3
HELIX 13 13 SER A 262 LEU A 276 1 15
HELIX 14 14 SER A 290 GLN A 298 1 9
HELIX 15 15 ASN A 299 GLN A 307 1 9
HELIX 16 16 SER A 332 LYS A 334 5 3
HELIX 17 17 GLY A 356 ASN A 359 5 4
HELIX 18 18 ALA B 32 ARG B 37 1 6
HELIX 19 19 SER B 51 ASP B 65 1 15
HELIX 20 20 GLY B 66 GLY B 71 1 6
HELIX 21 21 GLY B 101 LEU B 112 1 12
HELIX 22 22 THR B 134 ASP B 136 5 3
HELIX 23 23 LYS B 137 LYS B 149 1 13
HELIX 24 24 THR B 161 GLY B 180 1 20
HELIX 25 25 TRP B 189 GLU B 193 5 5
HELIX 26 26 GLN B 201 CYS B 209 1 9
HELIX 27 27 SER B 221 HIS B 235 1 15
HELIX 28 28 HIS B 235 GLN B 240 1 6
HELIX 29 29 PRO B 241 ALA B 243 5 3
HELIX 30 30 SER B 262 LEU B 276 1 15
HELIX 31 31 SER B 290 GLN B 298 1 9
HELIX 32 32 ASN B 299 GLN B 307 1 9
HELIX 33 33 SER B 332 LYS B 334 5 3
HELIX 34 34 LEU B 355 ASN B 359 5 5
HELIX 35 35 ILE B 403 SER B 409 1 7
SHEET 1 A 8 TRP A 248 ASP A 250 0
SHEET 2 A 8 LEU A 211 ARG A 213 1 N TRP A 212 O ASP A 250
SHEET 3 A 8 ALA A 184 CYS A 187 1 N CYS A 187 O LEU A 211
SHEET 4 A 8 MET A 152 ASP A 156 1 N LEU A 153 O SER A 186
SHEET 5 A 8 LYS A 115 ASP A 121 1 N ALA A 120 O ASP A 156
SHEET 6 A 8 TYR A 74 ASN A 76 1 N LEU A 75 O LYS A 115
SHEET 7 A 8 MET A 28 LEU A 31 1 N TRP A 30 O ASN A 76
SHEET 8 A 8 LEU A 280 MET A 282 1 O MET A 282 N LEU A 31
SHEET 1 B 2 ILE A 82 ARG A 85 0
SHEET 2 B 2 LEU A 91 PRO A 93 -1 O MET A 92 N GLY A 83
SHEET 1 C 6 ARG A 315 LYS A 319 0
SHEET 2 C 6 ILE A 324 PRO A 330 -1 O VAL A 326 N ILE A 317
SHEET 3 C 6 SER A 336 SER A 342 -1 O PHE A 341 N GLU A 325
SHEET 4 C 6 VAL A 395 ILE A 403 -1 O VAL A 396 N PHE A 340
SHEET 5 C 6 ILE A 365 ASP A 370 -1 N ILE A 365 O ILE A 403
SHEET 6 C 6 ILE A 376 LEU A 380 -1 O ILE A 377 N ALA A 368
SHEET 1 D 2 TYR A 349 SER A 354 0
SHEET 2 D 2 ASN A 385 ILE A 390 -1 O VAL A 388 N TYR A 351
SHEET 1 E 8 TRP B 248 ASP B 250 0
SHEET 2 E 8 LEU B 211 ARG B 213 1 N TRP B 212 O ASP B 250
SHEET 3 E 8 ALA B 184 CYS B 187 1 N CYS B 187 O LEU B 211
SHEET 4 E 8 MET B 152 ASP B 156 1 N LEU B 153 O SER B 186
SHEET 5 E 8 LYS B 115 ASP B 121 1 N ALA B 120 O ASP B 156
SHEET 6 E 8 TYR B 74 ASN B 76 1 N LEU B 75 O LYS B 115
SHEET 7 E 8 MET B 28 LEU B 31 1 N TRP B 30 O ASN B 76
SHEET 8 E 8 LEU B 280 MET B 282 1 O MET B 282 N LEU B 31
SHEET 1 F 2 ILE B 82 ARG B 85 0
SHEET 2 F 2 LEU B 91 PRO B 93 -1 O MET B 92 N GLY B 83
SHEET 1 G 6 ARG B 315 LYS B 319 0
SHEET 2 G 6 ILE B 324 PRO B 330 -1 O VAL B 326 N ILE B 317
SHEET 3 G 6 SER B 336 SER B 342 -1 O PHE B 341 N GLU B 325
SHEET 4 G 6 GLY B 394 PRO B 402 -1 O VAL B 396 N PHE B 340
SHEET 5 G 6 TYR B 366 ASP B 370 -1 N GLU B 367 O TYR B 401
SHEET 6 G 6 ILE B 376 LEU B 380 -1 O LEU B 380 N TYR B 366
SHEET 1 H 2 TYR B 349 SER B 353 0
SHEET 2 H 2 PHE B 386 ILE B 390 -1 O VAL B 388 N TYR B 351
SSBOND 1 CYS A 38 CYS A 80 1555 1555 2.08
SSBOND 2 CYS A 42 CYS A 49 1555 1555 2.07
SSBOND 3 CYS A 127 CYS A 158 1555 1555 2.08
SSBOND 4 CYS A 187 CYS A 209 1555 1555 2.05
SSBOND 5 CYS B 38 CYS B 80 1555 1555 2.06
SSBOND 6 CYS B 42 CYS B 49 1555 1555 2.07
SSBOND 7 CYS B 127 CYS B 158 1555 1555 2.04
SSBOND 8 CYS B 187 CYS B 209 1555 1555 2.03
LINK ND2 ASN A 124 C1 NAG C 1 1555 1555 1.44
LINK ND2 ASN A 177 C1 NAG D 1 1555 1555 1.43
LINK ND2 ASN A 385 C1 NAG A 509 1555 1555 1.44
LINK ND2 ASN B 124 C1 NAG E 1 1555 1555 1.45
LINK ND2 ASN B 177 C1 NAG F 1 1555 1555 1.44
LINK ND2 ASN B 385 C1 NAG B 509 1555 1555 1.44
LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.46
LINK O4 NAG C 2 C1 BMA C 3 1555 1555 1.45
LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.44
LINK O4 NAG D 2 C1 BMA D 3 1555 1555 1.43
LINK O3 BMA D 3 C1 MAN D 4 1555 1555 1.45
LINK O6 BMA D 3 C1 MAN D 5 1555 1555 1.45
LINK O4 NAG E 1 C1 NAG E 2 1555 1555 1.44
LINK O6 NAG E 1 C1 FUC E 3 1555 1555 1.44
LINK O4 NAG F 1 C1 NAG F 2 1555 1555 1.43
LINK O4 NAG F 2 C1 BMA F 3 1555 1555 1.44
LINK O3 BMA F 3 C1 MAN F 4 1555 1555 1.45
LINK O6 BMA F 3 C1 MAN F 5 1555 1555 1.45
CISPEP 1 PRO A 197 PRO A 198 0 4.50
CISPEP 2 PRO B 197 PRO B 198 0 3.53
CRYST1 154.055 114.624 68.630 90.00 95.82 90.00 C 1 2 1 8
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.006491 0.000000 0.000662 0.00000
SCALE2 0.000000 0.008724 0.000000 0.00000
SCALE3 0.000000 0.000000 0.014646 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
