HEADER HYDROLASE 08-DEC-08 3FGR
TITLE TWO CHAIN FORM OF THE 66.3 KDA PROTEIN AT 1.8 ANGSTROEM
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PUTATIVE PHOSPHOLIPASE B-LIKE 2 28 KDA FORM;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: N-TERMINAL DOMAIN, RESIDUES 47-248;
COMPND 5 SYNONYM: LAMINA ANCESTOR HOMOLOG 2, LAMA-LIKE PROTEIN 2, 76 KDA
COMPND 6 PROTEIN, P76, 66.3 KDA PROTEIN;
COMPND 7 EC: 3.1.1.-;
COMPND 8 ENGINEERED: YES;
COMPND 9 MOL_ID: 2;
COMPND 10 MOLECULE: PUTATIVE PHOSPHOLIPASE B-LIKE 2 40 KDA FORM;
COMPND 11 CHAIN: B;
COMPND 12 FRAGMENT: C-TERMINAL DOMAIN, RESIDUES 249-594;
COMPND 13 SYNONYM: LAMINA ANCESTOR HOMOLOG 2, LAMA-LIKE PROTEIN 2, 76 KDA
COMPND 14 PROTEIN, P76, 66.3 KDA PROTEIN;
COMPND 15 EC: 3.1.1.-;
COMPND 16 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS;
SOURCE 3 ORGANISM_COMMON: MOUSE;
SOURCE 4 ORGANISM_TAXID: 10090;
SOURCE 5 STRAIN: C3H/RV;
SOURCE 6 GENE: AAG44101;
SOURCE 7 EXPRESSION_SYSTEM: HOMO SAPIENS;
SOURCE 8 EXPRESSION_SYSTEM_COMMON: HUMAN;
SOURCE 9 EXPRESSION_SYSTEM_TAXID: 9606;
SOURCE 10 EXPRESSION_SYSTEM_CELL_LINE: HT1080;
SOURCE 11 EXPRESSION_SYSTEM_CELL: FIBROSARCOMA CELL;
SOURCE 12 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 13 EXPRESSION_SYSTEM_PLASMID: PCDNA3.1/HYGRO(+);
SOURCE 14 MOL_ID: 2;
SOURCE 15 ORGANISM_SCIENTIFIC: MUS MUSCULUS;
SOURCE 16 ORGANISM_COMMON: MOUSE;
SOURCE 17 ORGANISM_TAXID: 10090;
SOURCE 18 STRAIN: C3H/RV;
SOURCE 19 GENE: AAG44101;
SOURCE 20 EXPRESSION_SYSTEM: HOMO SAPIENS;
SOURCE 21 EXPRESSION_SYSTEM_COMMON: HUMAN;
SOURCE 22 EXPRESSION_SYSTEM_TAXID: 9606;
SOURCE 23 EXPRESSION_SYSTEM_CELL_LINE: HT1080;
SOURCE 24 EXPRESSION_SYSTEM_CELL: FIBROSARCOMA CELL;
SOURCE 25 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 26 EXPRESSION_SYSTEM_PLASMID: PCDNA3.1/HYGRO(+)
KEYWDS ALPHA BETA, GLYCOSYLATED, DISULPHIDE BONDS, N-TERMINAL NUCLEOPHILE
KEYWDS 2 HYDROLASE FOLD, TWO CHAIN FORM, GLYCOPROTEIN, HYDROLASE, LIPID
KEYWDS 3 DEGRADATION, LYSOSOME
EXPDTA X-RAY DIFFRACTION
AUTHOR K.LAKOMEK,A.DICKMANNS,R.FICNER
REVDAT 6 22-NOV-23 3FGR 1 REMARK
REVDAT 5 01-NOV-23 3FGR 1 HETSYN
REVDAT 4 29-JUL-20 3FGR 1 COMPND REMARK SEQADV HETNAM
REVDAT 4 2 1 LINK SITE ATOM
REVDAT 3 01-NOV-17 3FGR 1 REMARK
REVDAT 2 13-JUL-11 3FGR 1 VERSN
REVDAT 1 15-SEP-09 3FGR 0
JRNL AUTH K.LAKOMEK,A.DICKMANNS,M.KETTWIG,H.URLAUB,R.FICNER,T.LUEBKE
JRNL TITL INITIAL INSIGHT INTO THE FUNCTION OF THE LYSOSOMAL 66.3 KDA
JRNL TITL 2 PROTEIN FROM MOUSE BY MEANS OF X-RAY CRYSTALLOGRAPHY
JRNL REF BMC STRUCT.BIOL. V. 9 56 2009
JRNL REFN ESSN 1472-6807
JRNL PMID 19706171
JRNL DOI 10.1186/1472-6807-9-56
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH K.LAKOMEK,A.DICKMANNS,U.MUELLER,K.KOLLMANN,F.DEUSCHL,
REMARK 1 AUTH 2 A.BERNDT,T.LUEBKE,R.FICNER
REMARK 1 TITL DE NOVO SULFUR SAD PHASING OF THE LYSOSOMAL 66.3 KDA PROTEIN
REMARK 1 TITL 2 FROM MOUSE
REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 65 220 2009
REMARK 1 REFN ISSN 0907-4449
REMARK 1 PMID 19237744
REMARK 1 DOI 10.1107/S0907444908041814
REMARK 2
REMARK 2 RESOLUTION. 1.80 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC
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) : 1.80
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.26
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 3 NUMBER OF REFLECTIONS : 77685
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) : 0.153
REMARK 3 R VALUE (WORKING SET) : 0.152
REMARK 3 FREE R VALUE : 0.182
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900
REMARK 3 FREE R VALUE TEST SET COUNT : 3839
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) : 1.80
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85
REMARK 3 REFLECTION IN BIN (WORKING SET) : 5489
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.79
REMARK 3 BIN R VALUE (WORKING SET) : 0.2030
REMARK 3 BIN FREE R VALUE SET COUNT : 259
REMARK 3 BIN FREE R VALUE : 0.2870
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 4180
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 174
REMARK 3 SOLVENT ATOMS : 576
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.26
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.51000
REMARK 3 B22 (A**2) : -0.51000
REMARK 3 B33 (A**2) : 0.89000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : -0.44000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.085
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.087
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.052
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.607
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.956
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4607 ; 0.015 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6282 ; 1.533 ; 1.984
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 567 ; 5.707 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 213 ;34.654 ;23.944
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 723 ;13.418 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 27 ;21.962 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 681 ; 0.121 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3506 ; 0.007 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2360 ; 0.228 ; 0.300
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3157 ; 0.323 ; 0.500
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 853 ; 0.207 ; 0.500
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): 40 ; 0.177 ; 0.300
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 29 ; 0.170 ; 0.500
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): 2688 ; 0.955 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4353 ; 1.777 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2019 ; 2.926 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1906 ; 4.534 ; 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): NULL ; NULL ; NULL
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 : 1.20
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 3FGR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-DEC-08.
REMARK 100 THE DEPOSITION ID IS D_1000050570.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 07-MAR-08
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 4.6
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : BESSY
REMARK 200 BEAMLINE : 14.2
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.91841
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 91683
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700
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 (%) : 99.5
REMARK 200 DATA REDUNDANCY : 3.200
REMARK 200 R MERGE (I) : 0.03300
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 32.0750
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76
REMARK 200 COMPLETENESS FOR SHELL (%) : 96.2
REMARK 200 DATA REDUNDANCY IN SHELL : 2.60
REMARK 200 R MERGE FOR SHELL (I) : 0.41900
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: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: MOLREP
REMARK 200 STARTING MODEL: PDB ENTRY 3FBX
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 63.54
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.37
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 12% (W/V) PEG 4000, 200MM NH4AC, 100MM
REMARK 280 NAAC/HAC PH 4.6, VAPOR DIFFUSION, SITTING DROP, 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 74.36850
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.78000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 74.36850
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 44.78000
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 300 REMARK: AUTHOR STATES THAT THE BIOLOGICAL UNIT IS UNKNOWN
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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 11410 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 19920 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D
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 LEU A 47
REMARK 465 PRO A 48
REMARK 465 THR A 49
REMARK 465 LEU A 50
REMARK 465 GLY A 51
REMARK 465 PRO A 52
REMARK 465 GLY A 53
REMARK 465 TRP A 54
REMARK 465 GLN A 55
REMARK 465 ARG A 56
REMARK 465 GLN A 57
REMARK 465 ASN A 58
REMARK 465 PRO A 59
REMARK 465 ASP A 60
REMARK 465 PRO A 61
REMARK 465 PRO A 62
REMARK 465 ASN A 239
REMARK 465 THR A 240
REMARK 465 LYS A 241
REMARK 465 PRO A 242
REMARK 465 SER A 243
REMARK 465 LEU A 244
REMARK 465 TRP B 593
REMARK 465 ASP B 594
REMARK 465 GLY B 595
REMARK 465 ARG B 596
REMARK 465 GLY B 597
REMARK 465 SER B 598
REMARK 465 HIS B 599
REMARK 465 HIS B 600
REMARK 465 HIS B 601
REMARK 465 HIS B 602
REMARK 465 HIS B 603
REMARK 465 HIS B 604
REMARK 465 GLY B 605
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 OD1 ASP A 87 O HOH A 594 1.84
REMARK 500 ND2 ASN B 520 O5 NAG B 41 1.91
REMARK 500 OD2 ASP A 107 NH2 ARG B 283 2.01
REMARK 500 OG1 THR A 95 O7 NAG A 1 2.02
REMARK 500 O HOH B 651 O HOH B 755 2.03
REMARK 500 NH1 ARG A 65 O HOH A 756 2.06
REMARK 500 OE2 GLU A 132 O HOH A 757 2.15
REMARK 500 O HOH B 153 O HOH B 759 2.17
REMARK 500 O HOH A 271 O HOH A 712 2.18
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 MET B 275 40.10 -80.21
REMARK 500 SER B 306 -159.50 -155.45
REMARK 500 ASN B 394 -6.24 75.78
REMARK 500 ARG B 401 -27.94 83.92
REMARK 500 ARG B 401 -23.46 80.06
REMARK 500 TYR B 431 48.20 -162.81
REMARK 500 HIS B 577 48.42 -146.57
REMARK 500
REMARK 500 REMARK: NULL
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 NA B 607 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 OCS B 249 OD1
REMARK 620 2 OCS B 249 OD2 49.5
REMARK 620 3 ASP B 315 O 57.0 99.7
REMARK 620 4 GLU B 328 OE1 130.5 137.3 76.3
REMARK 620 5 THR B 330 OG1 125.2 78.2 168.5 97.5
REMARK 620 6 TYR B 379 OH 127.9 148.2 100.3 71.9 86.6
REMARK 620 N 1 2 3 4 5
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3FBX RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF THE LYSOSOMAL 66.3 KDA PROTEIN FROM MOUSE
REMARK 900 SOLVED BY S-SAD
REMARK 900 RELATED ID: 3FGT RELATED DB: PDB
REMARK 900 TWO CHAIN FORM OF THE 66.3 KDA PROTEIN FROM MOUSE LACKING THE
REMARK 900 LINKER PEPTIDE
REMARK 900 RELATED ID: 3FGW RELATED DB: PDB
REMARK 900 ONE CHAIN FORM OF THE 66.3 KDA PROTEIN
DBREF 3FGR A 47 248 UNP Q3TCN2 PLBL2_MOUSE 47 248
DBREF 3FGR B 249 594 UNP Q3TCN2 PLBL2_MOUSE 249 594
SEQADV 3FGR GLY B 595 UNP Q3TCN2 EXPRESSION TAG
SEQADV 3FGR ARG B 596 UNP Q3TCN2 EXPRESSION TAG
SEQADV 3FGR GLY B 597 UNP Q3TCN2 EXPRESSION TAG
SEQADV 3FGR SER B 598 UNP Q3TCN2 EXPRESSION TAG
SEQADV 3FGR HIS B 599 UNP Q3TCN2 EXPRESSION TAG
SEQADV 3FGR HIS B 600 UNP Q3TCN2 EXPRESSION TAG
SEQADV 3FGR HIS B 601 UNP Q3TCN2 EXPRESSION TAG
SEQADV 3FGR HIS B 602 UNP Q3TCN2 EXPRESSION TAG
SEQADV 3FGR HIS B 603 UNP Q3TCN2 EXPRESSION TAG
SEQADV 3FGR HIS B 604 UNP Q3TCN2 EXPRESSION TAG
SEQADV 3FGR GLY B 605 UNP Q3TCN2 EXPRESSION TAG
SEQRES 1 A 202 LEU PRO THR LEU GLY PRO GLY TRP GLN ARG GLN ASN PRO
SEQRES 2 A 202 ASP PRO PRO VAL SER ARG THR ARG SER LEU LEU LEU ASP
SEQRES 3 A 202 ALA ALA SER GLY GLN LEU ARG LEU GLU ASP GLY PHE HIS
SEQRES 4 A 202 PRO ASP ALA VAL ALA TRP ALA ASN LEU THR ASN ALA ILE
SEQRES 5 A 202 ARG GLU THR GLY TRP ALA TYR LEU ASP LEU SER THR ASN
SEQRES 6 A 202 GLY ARG TYR ASN ASP SER LEU GLN ALA TYR ALA ALA GLY
SEQRES 7 A 202 VAL VAL GLU ALA SER VAL SER GLU GLU LEU ILE TYR MET
SEQRES 8 A 202 HIS TRP MET ASN THR VAL VAL ASN TYR CYS GLY PRO PHE
SEQRES 9 A 202 GLU TYR GLU VAL GLY TYR CYS GLU LYS LEU LYS ASN PHE
SEQRES 10 A 202 LEU GLU ALA ASN LEU GLU TRP MET GLN ARG GLU MET GLU
SEQRES 11 A 202 LEU ASN PRO ASP SER PRO TYR TRP HIS GLN VAL ARG LEU
SEQRES 12 A 202 THR LEU LEU GLN LEU LYS GLY LEU GLU ASP SER TYR GLU
SEQRES 13 A 202 GLY ARG LEU THR PHE PRO THR GLY ARG PHE THR ILE LYS
SEQRES 14 A 202 PRO LEU GLY PHE LEU LEU LEU GLN ILE SER GLY ASP LEU
SEQRES 15 A 202 GLU ASP LEU GLU PRO ALA LEU ASN LYS THR ASN THR LYS
SEQRES 16 A 202 PRO SER LEU GLY SER GLY SER
SEQRES 1 B 357 OCS SER ALA LEU ILE LYS LEU LEU PRO GLY GLY HIS ASP
SEQRES 2 B 357 LEU LEU VAL ALA HIS ASN THR TRP ASN SER TYR GLN ASN
SEQRES 3 B 357 MET LEU ARG ILE ILE LYS LYS TYR ARG LEU GLN PHE ARG
SEQRES 4 B 357 GLU GLY PRO GLN GLU GLU TYR PRO LEU VAL ALA GLY ASN
SEQRES 5 B 357 ASN LEU VAL PHE SER SER TYR PRO GLY THR ILE PHE SER
SEQRES 6 B 357 GLY ASP ASP PHE TYR ILE LEU GLY SER GLY LEU VAL THR
SEQRES 7 B 357 LEU GLU THR THR ILE GLY ASN LYS ASN PRO ALA LEU TRP
SEQRES 8 B 357 LYS TYR VAL GLN PRO GLN GLY CYS VAL LEU GLU TRP ILE
SEQRES 9 B 357 ARG ASN VAL VAL ALA ASN ARG LEU ALA LEU ASP GLY ALA
SEQRES 10 B 357 THR TRP ALA ASP VAL PHE LYS ARG PHE ASN SER GLY THR
SEQRES 11 B 357 TYR ASN ASN GLN TRP MET ILE VAL ASP TYR LYS ALA PHE
SEQRES 12 B 357 LEU PRO ASN GLY PRO SER PRO GLY SER ARG VAL LEU THR
SEQRES 13 B 357 ILE LEU GLU GLN ILE PRO GLY MET VAL VAL VAL ALA ASP
SEQRES 14 B 357 LYS THR ALA GLU LEU TYR LYS THR THR TYR TRP ALA SER
SEQRES 15 B 357 TYR ASN ILE PRO TYR PHE GLU THR VAL PHE ASN ALA SER
SEQRES 16 B 357 GLY LEU GLN ALA LEU VAL ALA GLN TYR GLY ASP TRP PHE
SEQRES 17 B 357 SER TYR THR LYS ASN PRO ARG ALA LYS ILE PHE GLN ARG
SEQRES 18 B 357 ASP GLN SER LEU VAL GLU ASP MET ASP ALA MET VAL ARG
SEQRES 19 B 357 LEU MET ARG TYR ASN ASP PHE LEU HIS ASP PRO LEU SER
SEQRES 20 B 357 LEU CYS GLU ALA CYS ASN PRO LYS PRO ASN ALA GLU ASN
SEQRES 21 B 357 ALA ILE SER ALA ARG SER ASP LEU ASN PRO ALA ASN GLY
SEQRES 22 B 357 SER TYR PRO PHE GLN ALA LEU HIS GLN ARG ALA HIS GLY
SEQRES 23 B 357 GLY ILE ASP VAL LYS VAL THR SER PHE THR LEU ALA LYS
SEQRES 24 B 357 TYR MET SER MET LEU ALA ALA SER GLY PRO THR TRP ASP
SEQRES 25 B 357 GLN CYS PRO PRO PHE GLN TRP SER LYS SER PRO PHE HIS
SEQRES 26 B 357 SER MET LEU HIS MET GLY GLN PRO ASP LEU TRP MET PHE
SEQRES 27 B 357 SER PRO ILE ARG VAL PRO TRP ASP GLY ARG GLY SER HIS
SEQRES 28 B 357 HIS HIS HIS HIS HIS GLY
MODRES 3FGR ASN A 93 ASN GLYCOSYLATION SITE
MODRES 3FGR ASN A 115 ASN GLYCOSYLATION SITE
MODRES 3FGR ASN A 236 ASN GLYCOSYLATION SITE
MODRES 3FGR ASN B 441 ASN GLYCOSYLATION SITE
MODRES 3FGR ASN B 520 ASN GLYCOSYLATION SITE
MODRES 3FGR OCS B 249 CYS CYSTEINESULFONIC ACID
HET OCS B 249 9
HET NAG C 1 14
HET NAG C 2 14
HET NAG D 1 14
HET NAG D 2 14
HET NAG A 21 14
HET NAG A 1 14
HET GOL A 9 6
HET GOL A 10 6
HET ACT A 22 4
HET GOL A 3 6
HET NAG B 41 14
HET GOL B 11 6
HET GOL B 1 6
HET GOL B 2 6
HET GOL B 4 6
HET GOL B 5 6
HET GOL B 6 6
HET GOL B 7 6
HET GOL B 8 6
HET ACT B 21 4
HET XE B 606 1
HET NA B 607 1
HETNAM OCS CYSTEINESULFONIC ACID
HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE
HETNAM GOL GLYCEROL
HETNAM ACT ACETATE ION
HETNAM XE XENON
HETNAM NA SODIUM 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 GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 2 OCS C3 H7 N O5 S
FORMUL 3 NAG 7(C8 H15 N O6)
FORMUL 7 GOL 11(C3 H8 O3)
FORMUL 9 ACT 2(C2 H3 O2 1-)
FORMUL 21 XE XE
FORMUL 22 NA NA 1+
FORMUL 23 HOH *576(H2 O)
HELIX 1 1 ALA A 97 GLY A 102 1 6
HELIX 2 2 ASN A 115 VAL A 143 1 29
HELIX 3 3 GLU A 153 ASN A 178 1 26
HELIX 4 4 SER A 181 GLY A 203 1 23
HELIX 5 5 PHE A 219 ILE A 224 1 6
HELIX 6 6 ILE A 224 LEU A 235 1 12
HELIX 7 7 PRO B 257 HIS B 260 5 4
HELIX 8 8 GLN B 273 MET B 275 5 3
HELIX 9 9 ASN B 335 VAL B 342 5 8
HELIX 10 10 LEU B 349 ALA B 361 1 13
HELIX 11 11 ASP B 363 LYS B 372 1 10
HELIX 12 12 LYS B 389 PHE B 391 5 3
HELIX 13 13 LYS B 418 THR B 426 1 9
HELIX 14 14 PHE B 436 SER B 443 1 8
HELIX 15 15 GLY B 444 GLY B 453 1 10
HELIX 16 16 ASP B 454 SER B 457 5 4
HELIX 17 17 ASN B 461 GLN B 471 1 11
HELIX 18 18 SER B 472 VAL B 474 5 3
HELIX 19 19 ASP B 476 ARG B 485 1 10
HELIX 20 20 ASP B 492 LEU B 496 5 5
HELIX 21 21 ARG B 513 ASN B 517 5 5
HELIX 22 22 PHE B 525 HIS B 529 5 5
HELIX 23 23 SER B 542 TYR B 548 1 7
HELIX 24 24 SER B 568 SER B 570 5 3
SHEET 1 A11 GLN A 77 ASP A 82 0
SHEET 2 A11 SER A 64 ASP A 72 -1 N LEU A 70 O ARG A 79
SHEET 3 A11 ALA A 90 ASN A 96 -1 O ALA A 90 N LEU A 69
SHEET 4 A11 ALA A 104 THR A 110 -1 O SER A 109 N TRP A 91
SHEET 5 A11 ILE B 278 ARG B 283 1 O ILE B 279 N ALA A 104
SHEET 6 A11 ASN B 301 SER B 306 -1 O LEU B 302 N TYR B 282
SHEET 7 A11 PHE B 317 LEU B 320 -1 O ILE B 319 N VAL B 303
SHEET 8 A11 LEU B 324 THR B 330 -1 O LEU B 324 N LEU B 320
SHEET 9 A11 ASN B 381 ASP B 387 -1 O MET B 384 N LEU B 327
SHEET 10 A11 LEU B 403 ILE B 409 -1 O LEU B 406 N TRP B 383
SHEET 11 A11 MET B 412 ASP B 417 -1 O ALA B 416 N ILE B 405
SHEET 1 B 6 TYR B 427 SER B 430 0
SHEET 2 B 6 SER B 250 LEU B 255 -1 N ILE B 253 O TRP B 428
SHEET 3 B 6 LEU B 262 ASN B 267 -1 O ASN B 267 N SER B 250
SHEET 4 B 6 ASP B 537 THR B 541 -1 O THR B 541 N VAL B 264
SHEET 5 B 6 MET B 551 SER B 555 -1 O LEU B 552 N VAL B 540
SHEET 6 B 6 ILE B 589 VAL B 591 -1 O VAL B 591 N MET B 551
SHEET 1 C 2 TRP B 269 SER B 271 0
SHEET 2 C 2 HIS B 533 GLY B 535 -1 O GLY B 534 N ASN B 270
SHEET 1 D 2 PHE B 565 GLN B 566 0
SHEET 2 D 2 LEU B 583 TRP B 584 -1 O TRP B 584 N PHE B 565
SSBOND 1 CYS A 147 CYS A 157 1555 1555 2.11
SSBOND 2 CYS B 497 CYS B 500 1555 1555 2.12
LINK C1 NAG A 1 ND2 ASN A 93 1555 1555 1.50
LINK C1 NAG A 21 ND2 ASN A 236 1555 1555 1.30
LINK ND2 ASN A 115 C1 NAG C 1 1555 1555 1.34
LINK C1 NAG B 41 ND2 ASN B 520 1555 1555 1.25
LINK C OCS B 249 N SER B 250 1555 1555 1.33
LINK ND2 ASN B 441 C1 NAG D 1 1555 1555 1.32
LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.49
LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.34
LINK OD1 OCS B 249 NA NA B 607 1555 1555 3.00
LINK OD2 OCS B 249 NA NA B 607 1555 1555 2.76
LINK O ASP B 315 NA NA B 607 1555 1555 2.86
LINK OE1 GLU B 328 NA NA B 607 1555 1555 2.76
LINK OG1 THR B 330 NA NA B 607 1555 1555 2.82
LINK OH TYR B 379 NA NA B 607 1555 1555 2.84
CISPEP 1 ASP B 315 ASP B 316 0 -4.68
CISPEP 2 ASN B 501 PRO B 502 0 2.95
CISPEP 3 VAL B 591 PRO B 592 0 10.32
CRYST1 148.737 89.560 64.811 90.00 98.69 90.00 C 1 2 1 4
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 0.006723 0.000000 0.001028 0.00000
SCALE2 0.000000 0.011166 0.000000 0.00000
SCALE3 0.000000 0.000000 0.015609 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
