HEADER HYDROLASE 11-NOV-14 4D6H
TITLE CRYSTAL STRUCTURE OF A FAMILY 98 GLYCOSIDE HYDROLASE CATALYTIC MODULE
TITLE 2 (SP3GH98) IN COMPLEX WITH THE TYPE 1 BLOOD GROUP A-TETRASACCHARIDE
TITLE 3 (E558A X02 MUTANT)
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: GLYCOSIDE HYDROLASE;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: CATALYTIC DOMAIN, RESIDUES 423-1005;
COMPND 5 EC: 3.2.1.102;
COMPND 6 ENGINEERED: YES;
COMPND 7 MUTATION: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PNEUMONIAE;
SOURCE 3 ORGANISM_TAXID: 406556;
SOURCE 4 STRAIN: SP3-BS71;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET29
KEYWDS HYDROLASE, BLOOD GROUP ANTIGEN
EXPDTA X-RAY DIFFRACTION
AUTHOR D.H.KWAN,I.CONSTANTINESCU,R.CHAPANIAN,M.A.HIGGINS,E.SAMAIN,
AUTHOR 2 A.B.BORASTON,J.N.KIZHAKKEDATHU,S.G.WITHERS
REVDAT 6 20-DEC-23 4D6H 1 HETSYN ATOM
REVDAT 5 29-JUL-20 4D6H 1 COMPND REMARK HETNAM LINK
REVDAT 5 2 1 SITE ATOM
REVDAT 4 05-JUL-17 4D6H 1 REMARK
REVDAT 3 20-MAY-15 4D6H 1 JRNL
REVDAT 2 29-APR-15 4D6H 1 JRNL
REVDAT 1 26-NOV-14 4D6H 0
JRNL AUTH D.H.KWAN,I.CONSTANTINESCU,R.CHAPANIAN,M.A.HIGGINS,
JRNL AUTH 2 M.KOETZLER,E.SAMAIN,A.B.BORASTON,J.N.KIZHAKKEDATHU,
JRNL AUTH 3 S.G.WITHERS
JRNL TITL TOWARDS EFFICIENT ENZYMES FOR THE GENERATION OF UNIVERSAL
JRNL TITL 2 BLOOD THROUGH STRUCTURE-GUIDED DIRECTED EVOLUTION.
JRNL REF J.AM.CHEM.SOC. V. 137 5695 2015
JRNL REFN ISSN 0002-7863
JRNL PMID 25870881
JRNL DOI 10.1021/JA5116088
REMARK 2
REMARK 2 RESOLUTION. 1.65 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) : 1.65
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.16
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 3 NUMBER OF REFLECTIONS : 79310
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) : 0.147
REMARK 3 R VALUE (WORKING SET) : 0.145
REMARK 3 FREE R VALUE : 0.186
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 4167
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) : 1.65
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.69
REMARK 3 REFLECTION IN BIN (WORKING SET) : 5707
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.78
REMARK 3 BIN R VALUE (WORKING SET) : 0.4210
REMARK 3 BIN FREE R VALUE SET COUNT : 305
REMARK 3 BIN FREE R VALUE : 0.4600
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 4775
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 78
REMARK 3 SOLVENT ATOMS : 819
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.26
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.01000
REMARK 3 B22 (A**2) : 0.02000
REMARK 3 B33 (A**2) : -0.01000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.00000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.113
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.084
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.047
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.095
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.953
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5141 ; 0.010 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): 3459 ; 0.001 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6997 ; 1.294 ; 1.947
REMARK 3 BOND ANGLES OTHERS (DEGREES): 8430 ; 0.874 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 620 ; 6.006 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 256 ;35.964 ;25.078
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 864 ;12.016 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;17.715 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 724 ; 0.082 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5768 ; 0.005 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): 1051 ; 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): 3022 ; 0.916 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1223 ; 0.264 ; 1.500
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4899 ; 1.520 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2119 ; 2.590 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2098 ; 3.875 ; 4.500
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): 8600 ; 1.026 ; 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 : NULL
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.
REMARK 4
REMARK 4 4D6H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-NOV-14.
REMARK 100 THE DEPOSITION ID IS D_1290062282.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : NULL
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : N
REMARK 200 RADIATION SOURCE : ROTATING ANODE
REMARK 200 BEAMLINE : NULL
REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-002
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.54187
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : OSMIC BLUE
REMARK 200
REMARK 200 DETECTOR TYPE : IMAGE PLATE
REMARK 200 DETECTOR MANUFACTURER : RIGAKU R-AXIS 4
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM
REMARK 200 DATA SCALING SOFTWARE : AIMLESS
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 83578
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650
REMARK 200 RESOLUTION RANGE LOW (A) : 30.700
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 200 DATA REDUNDANCY : 3.800
REMARK 200 R MERGE (I) : 0.07000
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.2000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.74
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3
REMARK 200 DATA REDUNDANCY IN SHELL : 3.40
REMARK 200 R MERGE FOR SHELL (I) : 0.50000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.200
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: NULL
REMARK 200 STARTING MODEL: PDB ENTRY 2WMI
REMARK 200
REMARK 200 REMARK: NONE
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 51.18
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG 3350, 0.2M AMMONIUM SULFATE,
REMARK 280 0.1M SODIUM ACETATE PH 4.8
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,-Y,Z+1/2
REMARK 290 3555 -X,Y,-Z+1/2
REMARK 290 4555 X,-Y,-Z
REMARK 290 5555 X+1/2,Y+1/2,Z
REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2
REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2
REMARK 290 8555 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 48.58000
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.58000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 46.13000
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 77.37500
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 46.13000
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 77.37500
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 48.58000
REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 46.13000
REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 77.37500
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 48.58000
REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 46.13000
REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 77.37500
REMARK 290 SMTRY3 8 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: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B
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 ARG A 1008
REMARK 465 ALA A 1009
REMARK 465 PRO A 1010
REMARK 465 PRO A 1011
REMARK 465 PRO A 1012
REMARK 465 PRO A 1013
REMARK 465 PRO A 1014
REMARK 465 LEU A 1015
REMARK 465 ARG A 1016
REMARK 465 SER A 1017
REMARK 465 GLY A 1018
REMARK 465 CYS A 1019
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 470 I=INSERTION CODE):
REMARK 470 M RES CSSEQI ATOMS
REMARK 470 GLU A 421 CG CD OE1 OE2
REMARK 470 LYS A 508 CG CD CE NZ
REMARK 470 GLU A 804 CG CD OE1 OE2
REMARK 470 LYS A 983 CG CD CE NZ
REMARK 470 THR A1007 OG1 CG2
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 O HOH A 3642 O HOH A 3650 1.24
REMARK 500 OE2 GLU A 879 O HOH A 3654 1.97
REMARK 500 ND2 ASN A 762 O HOH A 3265 2.01
REMARK 500 O HOH A 3053 O HOH A 3107 2.08
REMARK 500 O HOH A 3544 O HOH A 3601 2.13
REMARK 500 O HOH A 3077 O HOH A 3425 2.14
REMARK 500 OD1 ASN A 762 O HOH A 3266 2.17
REMARK 500 O HOH A 3333 O HOH A 3349 2.17
REMARK 500 O HOH A 3376 O HOH A 3377 2.18
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15
REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A
REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375
REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE
REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.
REMARK 500
REMARK 500 DISTANCE CUTOFF:
REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS
REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE
REMARK 500 O HOH A 3650 O HOH A 3650 4555 1.72
REMARK 500
REMARK 500 REMARK: NULL
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 ASP A 481 -114.73 36.21
REMARK 500 TRP A 535 42.22 -96.86
REMARK 500 ALA A 558 61.20 64.91
REMARK 500 ILE A 562 74.19 -150.28
REMARK 500 ASN A 591 45.67 -78.32
REMARK 500 TRP A 667 -126.26 -133.87
REMARK 500 PHE A 670 -0.61 72.97
REMARK 500 GLN A 679 52.92 -142.54
REMARK 500 ASN A 765 -128.82 53.99
REMARK 500 VAL A 772 -69.17 -105.84
REMARK 500 ASN A 788 -131.59 36.74
REMARK 500 ASN A 788 -138.61 52.54
REMARK 500 ASP A 849 -120.31 44.32
REMARK 500 ASN A 860 34.55 -141.93
REMARK 500 ASN A 872 -115.04 56.34
REMARK 500 THR A 926 163.06 72.16
REMARK 500 TYR A 938 -50.86 -123.74
REMARK 500
REMARK 500 REMARK: NULL
REMARK 525
REMARK 525 SOLVENT
REMARK 525
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525
REMARK 525 M RES CSSEQI
REMARK 525 HOH A3366 DISTANCE = 5.87 ANGSTROMS
REMARK 525 HOH A3421 DISTANCE = 6.45 ANGSTROMS
REMARK 525 HOH A3464 DISTANCE = 7.04 ANGSTROMS
REMARK 525 HOH A3468 DISTANCE = 7.04 ANGSTROMS
REMARK 525 HOH A3819 DISTANCE = 7.10 ANGSTROMS
REMARK 600
REMARK 600 HETEROGEN
REMARK 600
REMARK 600 BETA-D-GALACTOSE (GAL): PART OF THE BLOOD GROUP
REMARK 600 A-TETRASACCHARIDE SUBSTRATE.
REMARK 600 ALPHA-L-FUCOSE (FUC): PART OF THE BLOOD GROUP
REMARK 600 A-TETRASACCHARIDE SUBSTRATE.
REMARK 600 N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE (A2G): PART OF THE BLOOD
REMARK 600 GROUP A-TETRASACCHARIDE SUBSTRATE.
REMARK 600 N-ACETYL-D-GLUCOSAMINE (NAG): PART OF THE BLOOD GROUP
REMARK 600 A-TETRASACCHARIDE SUBSTRATE.
REMARK 700
REMARK 700 SHEET
REMARK 700 DETERMINATION METHOD: DSSP
REMARK 700 THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS
REMARK 700 BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY
REMARK 700 A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS
REMARK 700 ARE IDENTICAL.
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 4D6C RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF A FAMILY 98 GLYCOSIDE HYDROLASE CATALYTIC
REMARK 900 MODULE (SP3GH98)
REMARK 900 RELATED ID: 4D6D RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF A FAMILY 98 GLYCOSIDE HYDROLASE CATALYTIC
REMARK 900 MODULE (SP3GH98) IN COMPLEX WITH THE BLOOD GROUP A-TRISACCHARIDE
REMARK 900 RELATED ID: 4D6E RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF A FAMILY 98 GLYCOSIDE HYDROLASE CATALYTIC
REMARK 900 MODULE (SP3GH98) IN COMPLEX WITH THE BLOOD GROUP A-TRISACCHARIDE
REMARK 900 RELATED ID: 4D6F RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF A FAMILY 98 GLYCOSIDE HYDROLASE CATALYTIC
REMARK 900 MODULE (SP3GH98) IN COMPLEX WITH THE BLOOD GROUP A-TETRASACCHARIDE
REMARK 900 (E558A, X01 MUTANT)
REMARK 900 RELATED ID: 4D6G RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF A FAMILY 98 GLYCOSIDE HYDROLASE CATALYTIC
REMARK 900 MODULE (SP3GH98) IN COMPLEX WITH THE BLOOD GROUP A-TRISACCHARIDE
REMARK 900 (L19 MUTANT)
REMARK 900 RELATED ID: 4D6I RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF A FAMILY 98 GLYCOSIDE HYDROLASE CATALYTIC
REMARK 900 MODULE (SP3GH98) IN COMPLEX WITH THE TYPE 1 BLOOD GROUP A-
REMARK 900 TETRASACCHARIDE (E558A L19 MUTANT)
REMARK 900 RELATED ID: 4D6J RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF A FAMILY 98 GLYCOSIDE HYDROLASE CATALYTIC
REMARK 900 MODULE (SP3GH98) IN COMPLEX WITH THE TYPE 2 BLOOD GROUP A-
REMARK 900 TETRASACCHARIDE (E558A X01 MUTANT)
DBREF 4D6H A 421 1003 UNP A5LBQ0 A5LBQ0_STREE 423 1005
SEQADV 4D6H ALA A 558 UNP A5LBQ0 GLU 560 ENGINEERED MUTATION
SEQADV 4D6H SER A 559 UNP A5LBQ0 ASN 561 ENGINEERED MUTATION
SEQADV 4D6H SER A 592 UNP A5LBQ0 ASN 594 ENGINEERED MUTATION
SEQADV 4D6H LEU A 1004 UNP A5LBQ0 EXPRESSION TAG
SEQADV 4D6H GLU A 1005 UNP A5LBQ0 EXPRESSION TAG
SEQADV 4D6H HIS A 1006 UNP A5LBQ0 EXPRESSION TAG
SEQADV 4D6H THR A 1007 UNP A5LBQ0 EXPRESSION TAG
SEQADV 4D6H ARG A 1008 UNP A5LBQ0 EXPRESSION TAG
SEQADV 4D6H ALA A 1009 UNP A5LBQ0 EXPRESSION TAG
SEQADV 4D6H PRO A 1010 UNP A5LBQ0 EXPRESSION TAG
SEQADV 4D6H PRO A 1011 UNP A5LBQ0 EXPRESSION TAG
SEQADV 4D6H PRO A 1012 UNP A5LBQ0 EXPRESSION TAG
SEQADV 4D6H PRO A 1013 UNP A5LBQ0 EXPRESSION TAG
SEQADV 4D6H PRO A 1014 UNP A5LBQ0 EXPRESSION TAG
SEQADV 4D6H LEU A 1015 UNP A5LBQ0 EXPRESSION TAG
SEQADV 4D6H ARG A 1016 UNP A5LBQ0 EXPRESSION TAG
SEQADV 4D6H SER A 1017 UNP A5LBQ0 EXPRESSION TAG
SEQADV 4D6H GLY A 1018 UNP A5LBQ0 EXPRESSION TAG
SEQADV 4D6H CYS A 1019 UNP A5LBQ0 EXPRESSION TAG
SEQRES 1 A 599 GLU VAL ASP LYS ARG ARG GLU ILE ASN ASN GLU HIS PRO
SEQRES 2 A 599 LEU LEU MET MET PRO LEU TYR ALA ASN GLY GLU GLU PHE
SEQRES 3 A 599 ASN GLN GLY LYS TYR THR PHE TRP GLY GLY ASP THR LEU
SEQRES 4 A 599 THR GLY LYS TRP GLU ASN ILE PRO ASP ASP LEU LYS PRO
SEQRES 5 A 599 TYR THR VAL ILE GLN LEU HIS PRO ASP ASP LEU PRO LYS
SEQRES 6 A 599 ARG ASP GLY ALA ALA ARG ASP PHE TYR GLU HIS MET LEU
SEQRES 7 A 599 GLU GLU ALA ALA LYS TYR VAL ASN PRO LYS THR GLY LYS
SEQRES 8 A 599 ASN GLU PRO ILE PRO VAL ILE LEU THR VAL TYR THR ALA
SEQRES 9 A 599 GLY ASN MET PRO TYR TYR THR SER ALA HIS TRP LEU SER
SEQRES 10 A 599 THR SER TRP ILE ASP LYS MET TYR GLN LYS TYR PRO ASN
SEQRES 11 A 599 LEU HIS GLY ILE PHE SER THR ALA SER TYR TRP ILE TRP
SEQRES 12 A 599 ALA ASN ASP ILE GLU ASN LYS ALA ALA ASP TYR LEU LYS
SEQRES 13 A 599 VAL SER ALA LYS ASN GLY GLY TYR PHE ILE TRP ALA GLU
SEQRES 14 A 599 GLN ASN SER GLY SER ALA ILE GLU LYS ALA PHE GLY LYS
SEQRES 15 A 599 ASN GLY LYS ILE ALA PHE GLN LYS SER VAL ASP LYS TYR
SEQRES 16 A 599 TRP LYS ASN LEU ILE PHE MET PHE LYS ASN THR PRO ALA
SEQRES 17 A 599 ALA GLU GLY ASN ASP SER THR THR GLU SER TYR MET LYS
SEQRES 18 A 599 GLY LEU TRP LEU SER ASN HIS THR TYR GLN TRP GLY GLY
SEQRES 19 A 599 LEU MET ASP THR TRP LYS TRP TYR GLU THR GLY LYS TRP
SEQRES 20 A 599 LYS LEU PHE ALA SER GLY ASN ILE GLY LYS SER GLN GLY
SEQRES 21 A 599 ASP ARG GLN TRP LEU THR GLU PRO GLU SER MET LEU GLY
SEQRES 22 A 599 GLU GLU ALA LEU GLY VAL TYR LEU ASN GLY GLY VAL VAL
SEQRES 23 A 599 TYR ASN PHE GLU HIS PRO ALA TYR THR TYR GLY VAL ASN
SEQRES 24 A 599 ASN LYS GLU SER LEU LEU PHE SER GLU VAL ILE LYS GLU
SEQRES 25 A 599 PHE PHE ARG TYR VAL ILE ALA HIS PRO ALA PRO SER LYS
SEQRES 26 A 599 GLU LYS VAL LEU GLU ASP THR LYS VAL PHE ILE HIS GLY
SEQRES 27 A 599 ASP TYR SER ASN LYS GLY ASN GLY LYS PHE PHE VAL ASN
SEQRES 28 A 599 VAL ASN THR ASP ARG GLU GLN THR PRO LEU TYR MET THR
SEQRES 29 A 599 GLY ARG TYR ASN VAL ILE PRO ALA ILE PRO GLY VAL LEU
SEQRES 30 A 599 LYS THR ASP LYS LEU LYS GLU SER VAL SER SER SER ARG
SEQRES 31 A 599 ILE GLN ILE LYS GLU ILE THR SER PRO GLU PHE SER SER
SEQRES 32 A 599 THR GLN ALA ARG LYS GLU TYR LEU ASN LYS LEU TYR PRO
SEQRES 33 A 599 MET ASN TYR GLU GLY ASP ILE PHE ALA GLN LYS LEU ASP
SEQRES 34 A 599 ASN ARG TRP PHE VAL TYR ASN TYR LYS VAL ASN GLU ASN
SEQRES 35 A 599 VAL LYS GLN THR GLY LYS LEU LYS PHE ASN SER LEU GLU
SEQRES 36 A 599 MET ASN VAL GLU PHE GLU PRO HIS THR TYR GLY ILE PHE
SEQRES 37 A 599 GLU ARG ILE SER ASN GLY LEU LYS VAL ASN LEU ASN ASN
SEQRES 38 A 599 PHE ARG THR ASN LYS ASP SER LEU TRP SER ASN ALA GLN
SEQRES 39 A 599 ASP ALA ASN GLN ALA LYS LYS LEU PRO GLN LEU THR LYS
SEQRES 40 A 599 LYS GLY ALA ILE LYS TRP ILE GLU GLU HIS TYR ILE LYS
SEQRES 41 A 599 ASP THR GLN PHE GLY GLU LYS ARG VAL THR LYS ILE VAL
SEQRES 42 A 599 LEU ARG GLY ILE ASP LYS LEU PRO THR ILE HIS SER LEU
SEQRES 43 A 599 SER GLY THR ASN ASN SER TYR ASP GLN PRO SER LEU ASN
SEQRES 44 A 599 PHE ASP GLN LYS ASN HIS MET VAL THR ILE THR ILE ASN
SEQRES 45 A 599 SER ASN GLY ASN LEU GLU PHE GLU LEU HIS PHE LEU GLU
SEQRES 46 A 599 HIS THR ARG ALA PRO PRO PRO PRO PRO LEU ARG SER GLY
SEQRES 47 A 599 CYS
HET NAG B 1 15
HET GAL B 2 11
HET FUC B 3 10
HET A2G B 4 14
HET EDO A2012 4
HET SO4 A2013 5
HET SO4 A2014 5
HET SO4 A2015 5
HET SO4 A2016 5
HET EDO A2017 4
HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE
HETNAM GAL BETA-D-GALACTOPYRANOSE
HETNAM FUC ALPHA-L-FUCOPYRANOSE
HETNAM A2G 2-ACETAMIDO-2-DEOXY-ALPHA-D-GALACTOPYRANOSE
HETNAM EDO 1,2-ETHANEDIOL
HETNAM SO4 SULFATE ION
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 GAL BETA-D-GALACTOSE; D-GALACTOSE; GALACTOSE
HETSYN FUC ALPHA-L-FUCOSE; 6-DEOXY-ALPHA-L-GALACTOPYRANOSE; L-
HETSYN 2 FUC FUCOSE; FUCOSE
HETSYN A2G N-ACETYL-ALPHA-D-GALACTOSAMINE; 2-ACETAMIDO-2-DEOXY-
HETSYN 2 A2G ALPHA-D-GALACTOSE; 2-ACETAMIDO-2-DEOXY-D-GALACTOSE; 2-
HETSYN 3 A2G ACETAMIDO-2-DEOXY-GALACTOSE; N-ACETYL-2-DEOXY-2-AMINO-
HETSYN 4 A2G GALACTOSE
HETSYN EDO ETHYLENE GLYCOL
FORMUL 2 NAG C8 H15 N O6
FORMUL 2 GAL C6 H12 O6
FORMUL 2 FUC C6 H12 O5
FORMUL 2 A2G C8 H15 N O6
FORMUL 3 EDO 2(C2 H6 O2)
FORMUL 4 SO4 4(O4 S 2-)
FORMUL 9 HOH *819(H2 O)
HELIX 1 1 ASN A 442 GLN A 448 1 7
HELIX 2 2 THR A 458 ILE A 466 1 9
HELIX 3 3 LEU A 470 PRO A 472 5 3
HELIX 4 4 GLY A 488 TYR A 504 1 17
HELIX 5 5 GLY A 525 MET A 527 5 3
HELIX 6 6 THR A 531 LEU A 536 5 6
HELIX 7 7 SER A 537 TYR A 548 1 12
HELIX 8 8 ASP A 566 ASN A 581 1 16
HELIX 9 9 ASN A 591 GLY A 593 5 3
HELIX 10 10 SER A 594 PHE A 600 1 7
HELIX 11 11 ILE A 606 TRP A 616 1 11
HELIX 12 12 PRO A 627 GLY A 631 5 5
HELIX 13 13 ASN A 632 SER A 646 1 15
HELIX 14 14 TRP A 659 THR A 664 1 6
HELIX 15 15 GLN A 679 GLU A 687 1 9
HELIX 16 16 PRO A 688 LEU A 701 1 14
HELIX 17 17 HIS A 711 TYR A 716 1 6
HELIX 18 18 SER A 723 VAL A 729 1 7
HELIX 19 19 VAL A 729 HIS A 740 1 12
HELIX 20 20 SER A 744 THR A 752 1 9
HELIX 21 21 ASP A 759 LYS A 763 5 5
HELIX 22 22 GLY A 764 VAL A 770 5 7
HELIX 23 23 THR A 799 SER A 805 1 7
HELIX 24 24 VAL A 806 SER A 809 5 4
HELIX 25 25 SER A 818 SER A 822 5 5
HELIX 26 26 SER A 823 TYR A 835 1 13
HELIX 27 27 LYS A 906 SER A 911 5 6
HELIX 28 28 ASP A 915 LYS A 921 1 7
HELIX 29 29 THR A 926 TYR A 938 1 13
SHEET 1 AA 9 LEU A 434 TYR A 440 0
SHEET 2 AA 9 VAL A 706 GLU A 710 1 O TYR A 707 N MET A 436
SHEET 3 AA 9 GLN A 651 ASP A 657 1 O GLY A 654 N ASN A 708
SHEET 4 AA 9 LEU A 619 LYS A 624 1 O PHE A 621 N GLY A 653
SHEET 5 AA 9 TYR A 584 ALA A 588 1 O PHE A 585 N ILE A 620
SHEET 6 AA 9 LEU A 551 THR A 557 1 O HIS A 552 N TYR A 584
SHEET 7 AA 9 VAL A 517 THR A 523 1 O VAL A 517 N HIS A 552
SHEET 8 AA 9 THR A 474 HIS A 479 1 O ILE A 476 N ILE A 518
SHEET 9 AA 9 LEU A 434 TYR A 440 1 O LEU A 435 N VAL A 475
SHEET 1 AB 2 GLY A 717 VAL A 718 0
SHEET 2 AB 2 LYS A 721 GLU A 722 -1 O LYS A 721 N VAL A 718
SHEET 1 AC 3 ALA A 792 ILE A 793 0
SHEET 2 AC 3 VAL A 754 HIS A 757 1 O ILE A 756 N ILE A 793
SHEET 3 AC 3 GLN A 812 GLU A 815 1 O GLN A 812 N PHE A 755
SHEET 1 AD 6 PHE A 844 LEU A 848 0
SHEET 2 AD 6 ARG A 851 TYR A 855 -1 O ARG A 851 N LEU A 848
SHEET 3 AD 6 TYR A 885 ILE A 891 -1 O GLY A 886 N VAL A 854
SHEET 4 AD 6 GLY A 894 ASN A 900 -1 O GLY A 894 N ILE A 891
SHEET 5 AD 6 ASN A 996 HIS A1002 -1 O LEU A 997 N LEU A 899
SHEET 6 AD 6 THR A 962 GLY A 968 -1 O THR A 962 N HIS A1002
SHEET 1 AE 5 GLN A 865 PHE A 871 0
SHEET 2 AE 5 LEU A 874 PHE A 880 -1 O LEU A 874 N PHE A 871
SHEET 3 AE 5 ARG A 948 ARG A 955 -1 O LYS A 951 N GLU A 879
SHEET 4 AE 5 MET A 986 SER A 993 -1 O VAL A 987 N LEU A 954
SHEET 5 AE 5 SER A 977 ASP A 981 -1 O SER A 977 N THR A 990
LINK O3 NAG B 1 C1 GAL B 2 1555 1555 1.45
LINK O2 GAL B 2 C1 FUC B 3 1555 1555 1.45
LINK O3 GAL B 2 C1 A2G B 4 1555 1555 1.76
CISPEP 1 GLU A 710 HIS A 711 0 -6.55
CRYST1 92.260 154.750 97.160 90.00 90.00 90.00 C 2 2 21 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 0.010839 0.000000 0.000000 0.00000
SCALE2 0.000000 0.006462 0.000000 0.00000
SCALE3 0.000000 0.000000 0.010292 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
