10 20 30 40 50 60 70 80 3FGW - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE 08-DEC-08 3FGW
TITLE ONE CHAIN FORM OF THE 66.3 KDA PROTEIN
COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE PHOSPHOLIPASE B-LIKE 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 66.3 KDA PROTEIN, LAMINA ANCESTOR HOMOLOG 2, LAMA-LIKE COMPND 5 PROTEIN 2, 76 KDA PROTEIN, P76, PUTATIVE PHOSPHOLIPASE B-LIKE 2 28 COMPND 6 KDA FORM, PUTATIVE PHOSPHOLIPASE B-LIKE 2 40 KDA FORM, PUTATIVE COMPND 7 PHOSPHOLIPASE B-LIKE 2 15 KDA FORM; COMPND 8 EC: 3.1.1.-; COMPND 9 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(+)
KEYWDS ALPHA BETA, GLYCOSYLATED, DISULPHIDE BONDS, N-TERMINAL HYDROLASE KEYWDS 2 FOLD, OCCUPIED POCKET, ONE CHAIN FORM, GLYCOPROTEIN, HYDROLASE, KEYWDS 3 LIPID DEGRADATION, LYSOSOME
EXPDTA X-RAY DIFFRACTION
AUTHOR K.LAKOMEK,A.DICKMANNS,R.FICNER
REVDAT 2 13-JUL-11 3FGW 1 VERSN REVDAT 1 15-SEP-09 3FGW 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. 2.80 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.07 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 20907 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) : 0.224 REMARK 3 R VALUE (WORKING SET) : 0.223 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1072 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) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1431 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.54 REMARK 3 BIN R VALUE (WORKING SET) : 0.3640 REMARK 3 BIN FREE R VALUE SET COUNT : 69 REMARK 3 BIN FREE R VALUE : 0.4120 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4220 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 107 REMARK 3 SOLVENT ATOMS : 160 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.21 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.92000 REMARK 3 B22 (A**2) : -5.06000 REMARK 3 B33 (A**2) : 6.04000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.08000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.539 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.342 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.227 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.500 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.908 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.877 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4446 ; 0.005 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6059 ; 0.983 ; 1.971 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 527 ; 5.207 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 207 ;34.745 ;24.155 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 684 ;15.437 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 23 ;15.319 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 654 ; 0.069 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3396 ; 0.002 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2215 ; 0.187 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3001 ; 0.304 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 216 ; 0.122 ; 0.200 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): 59 ; 0.134 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 7 ; 0.097 ; 0.200 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED 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; CNS 1.21 WAS ALSO USED IN REFINEMENT
REMARK 4 REMARK 4 3FGW 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 RCSB ID CODE IS RCSB050575.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-FEB-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 : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.8 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21117 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 46.070 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 6.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.13900 REMARK 200 R SYM (I) : 0.13900 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 5.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.43000 REMARK 200 R SYM FOR SHELL (I) : 0.43000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 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 (%): 65.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12% (W/V) PEG 4000, 100MM 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 73.34500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.05500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 73.34500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 44.05500 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: 8220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 39580 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 146.69000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 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 GLY A 595 REMARK 465 ARG A 596 REMARK 465 GLY A 597 REMARK 465 SER A 598 REMARK 465 HIS A 599 REMARK 465 HIS A 600 REMARK 465 HIS A 601 REMARK 465 HIS A 602 REMARK 465 HIS A 603 REMARK 465 HIS A 604 REMARK 465 GLY A 605
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 SER A 75 -16.97 -148.49 REMARK 500 THR A 142 -69.12 -102.72 REMARK 500 GLU A 151 126.41 -35.06 REMARK 500 THR A 206 88.28 -164.47 REMARK 500 SER A 246 -61.43 177.39 REMARK 500 SER A 248 76.10 45.92 REMARK 500 CYS A 249 156.54 91.74 REMARK 500 MET A 275 41.80 -84.25 REMARK 500 THR A 310 105.07 -51.60 REMARK 500 ASP A 316 83.24 83.17 REMARK 500 TYR A 379 74.16 53.41 REMARK 500 ASN A 394 -11.88 67.02 REMARK 500 ARG A 401 -21.53 90.24 REMARK 500 TYR A 431 -157.36 -150.23 REMARK 500 ASN A 487 108.83 -161.56 REMARK 500 ARG A 513 58.12 -145.53 REMARK 500 GLN A 561 -33.70 -132.27 REMARK 500 HIS A 577 63.54 -153.02 REMARK 500 TRP A 593 95.09 70.07 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 A 672 DISTANCE = 5.34 ANGSTROMS
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 A 610 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A 379 OH REMARK 620 2 HOH A 712 O 73.6 REMARK 620 N 1
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAG A 11 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAG A 12 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BMA A 13 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAG A 21 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAG A 31 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAG A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 4 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 8 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 606 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IOD A 607 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IOD A 15 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IOD A 16 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IOD A 17 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IOD A 608 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IOD A 609 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 610
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 REMARK 900 MOUSE SOLVED BY S-SAD REMARK 900 RELATED ID: 3FGR RELATED DB: PDB REMARK 900 TWO CHAIN FORM OF THE 66.3 KDA PROTEIN AT 1.8 ANGSTROEM REMARK 900 RELATED ID: 3FGT RELATED DB: PDB REMARK 900 TWO CHAIN FORM OF THE 66.3 KDA PROTEIN FROM MOUSE LACKING REMARK 900 THE LINKER PEPTIDE
DBREF 3FGW A 47 594 UNP Q3TCN2 PLBL2_MOUSE 47 594
SEQADV 3FGW GLY A 595 UNP Q3TCN2 EXPRESSION TAG SEQADV 3FGW ARG A 596 UNP Q3TCN2 EXPRESSION TAG SEQADV 3FGW GLY A 597 UNP Q3TCN2 EXPRESSION TAG SEQADV 3FGW SER A 598 UNP Q3TCN2 EXPRESSION TAG SEQADV 3FGW HIS A 599 UNP Q3TCN2 EXPRESSION TAG SEQADV 3FGW HIS A 600 UNP Q3TCN2 EXPRESSION TAG SEQADV 3FGW HIS A 601 UNP Q3TCN2 EXPRESSION TAG SEQADV 3FGW HIS A 602 UNP Q3TCN2 EXPRESSION TAG SEQADV 3FGW HIS A 603 UNP Q3TCN2 EXPRESSION TAG SEQADV 3FGW HIS A 604 UNP Q3TCN2 EXPRESSION TAG SEQADV 3FGW GLY A 605 UNP Q3TCN2 EXPRESSION TAG
SEQRES 1 A 559 LEU PRO THR LEU GLY PRO GLY TRP GLN ARG GLN ASN PRO SEQRES 2 A 559 ASP PRO PRO VAL SER ARG THR ARG SER LEU LEU LEU ASP SEQRES 3 A 559 ALA ALA SER GLY GLN LEU ARG LEU GLU ASP GLY PHE HIS SEQRES 4 A 559 PRO ASP ALA VAL ALA TRP ALA ASN LEU THR ASN ALA ILE SEQRES 5 A 559 ARG GLU THR GLY TRP ALA TYR LEU ASP LEU SER THR ASN SEQRES 6 A 559 GLY ARG TYR ASN ASP SER LEU GLN ALA TYR ALA ALA GLY SEQRES 7 A 559 VAL VAL GLU ALA SER VAL SER GLU GLU LEU ILE TYR MET SEQRES 8 A 559 HIS TRP MET ASN THR VAL VAL ASN TYR CYS GLY PRO PHE SEQRES 9 A 559 GLU TYR GLU VAL GLY TYR CYS GLU LYS LEU LYS ASN PHE SEQRES 10 A 559 LEU GLU ALA ASN LEU GLU TRP MET GLN ARG GLU MET GLU SEQRES 11 A 559 LEU ASN PRO ASP SER PRO TYR TRP HIS GLN VAL ARG LEU SEQRES 12 A 559 THR LEU LEU GLN LEU LYS GLY LEU GLU ASP SER TYR GLU SEQRES 13 A 559 GLY ARG LEU THR PHE PRO THR GLY ARG PHE THR ILE LYS SEQRES 14 A 559 PRO LEU GLY PHE LEU LEU LEU GLN ILE SER GLY ASP LEU SEQRES 15 A 559 GLU ASP LEU GLU PRO ALA LEU ASN LYS THR ASN THR LYS SEQRES 16 A 559 PRO SER LEU GLY SER GLY SER CYS SER ALA LEU ILE LYS SEQRES 17 A 559 LEU LEU PRO GLY GLY HIS ASP LEU LEU VAL ALA HIS ASN SEQRES 18 A 559 THR TRP ASN SER TYR GLN ASN MET LEU ARG ILE ILE LYS SEQRES 19 A 559 LYS TYR ARG LEU GLN PHE ARG GLU GLY PRO GLN GLU GLU SEQRES 20 A 559 TYR PRO LEU VAL ALA GLY ASN ASN LEU VAL PHE SER SER SEQRES 21 A 559 TYR PRO GLY THR ILE PHE SER GLY ASP ASP PHE TYR ILE SEQRES 22 A 559 LEU GLY SER GLY LEU VAL THR LEU GLU THR THR ILE GLY SEQRES 23 A 559 ASN LYS ASN PRO ALA LEU TRP LYS TYR VAL GLN PRO GLN SEQRES 24 A 559 GLY CYS VAL LEU GLU TRP ILE ARG ASN VAL VAL ALA ASN SEQRES 25 A 559 ARG LEU ALA LEU ASP GLY ALA THR TRP ALA ASP VAL PHE SEQRES 26 A 559 LYS ARG PHE ASN SER GLY THR TYR ASN ASN GLN TRP MET SEQRES 27 A 559 ILE VAL ASP TYR LYS ALA PHE LEU PRO ASN GLY PRO SER SEQRES 28 A 559 PRO GLY SER ARG VAL LEU THR ILE LEU GLU GLN ILE PRO SEQRES 29 A 559 GLY MET VAL VAL VAL ALA ASP LYS THR ALA GLU LEU TYR SEQRES 30 A 559 LYS THR THR TYR TRP ALA SER TYR ASN ILE PRO TYR PHE SEQRES 31 A 559 GLU THR VAL PHE ASN ALA SER GLY LEU GLN ALA LEU VAL SEQRES 32 A 559 ALA GLN TYR GLY ASP TRP PHE SER TYR THR LYS ASN PRO SEQRES 33 A 559 ARG ALA LYS ILE PHE GLN ARG ASP GLN SER LEU VAL GLU SEQRES 34 A 559 ASP MET ASP ALA MET VAL ARG LEU MET ARG TYR ASN ASP SEQRES 35 A 559 PHE LEU HIS ASP PRO LEU SER LEU CYS GLU ALA CYS ASN SEQRES 36 A 559 PRO LYS PRO ASN ALA GLU ASN ALA ILE SER ALA ARG SER SEQRES 37 A 559 ASP LEU ASN PRO ALA ASN GLY SER TYR PRO PHE GLN ALA SEQRES 38 A 559 LEU HIS GLN ARG ALA HIS GLY GLY ILE ASP VAL LYS VAL SEQRES 39 A 559 THR SER PHE THR LEU ALA LYS TYR MET SER MET LEU ALA SEQRES 40 A 559 ALA SER GLY PRO THR TRP ASP GLN CYS PRO PRO PHE GLN SEQRES 41 A 559 TRP SER LYS SER PRO PHE HIS SER MET LEU HIS MET GLY SEQRES 42 A 559 GLN PRO ASP LEU TRP MET PHE SER PRO ILE ARG VAL PRO SEQRES 43 A 559 TRP ASP GLY ARG GLY SER HIS HIS HIS HIS HIS HIS GLY
MODRES 3FGW ASN A 93 ASN GLYCOSYLATION SITE MODRES 3FGW ASN A 115 ASN GLYCOSYLATION SITE MODRES 3FGW ASN A 236 ASN GLYCOSYLATION SITE MODRES 3FGW ASN A 441 ASN GLYCOSYLATION SITE
HET NAG A 11 14 HET NAG A 12 14 HET BMA A 13 11 HET NAG A 21 14 HET NAG A 31 14 HET NAG A 1 14 HET GOL A 4 6 HET GOL A 8 6 HET GOL A 606 6 HET IOD A 607 1 HET IOD A 15 1 HET IOD A 16 1 HET IOD A 17 1 HET IOD A 20 1 HET IOD A 608 1 HET IOD A 609 1 HET NA A 610 1
HETNAM NAG N-ACETYL-D-GLUCOSAMINE HETNAM BMA BETA-D-MANNOSE HETNAM GOL GLYCEROL HETNAM IOD IODIDE ION HETNAM NA SODIUM ION
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 2 NAG 5(C8 H15 N O6) FORMUL 2 BMA C6 H12 O6 FORMUL 6 GOL 3(C3 H8 O3) FORMUL 9 IOD 7(I 1-) FORMUL 16 NA NA 1+ FORMUL 17 HOH *160(H2 O)
HELIX 1 1 ASN A 115 SER A 131 1 17 HELIX 2 2 SER A 131 THR A 142 1 12 HELIX 3 3 GLU A 153 ASN A 178 1 26 HELIX 4 4 SER A 181 GLU A 202 1 22 HELIX 5 5 ASP A 227 LEU A 235 1 9 HELIX 6 6 PRO A 257 HIS A 260 5 4 HELIX 7 7 GLN A 273 MET A 275 5 3 HELIX 8 8 ASN A 335 VAL A 342 5 8 HELIX 9 9 LEU A 349 ALA A 361 1 13 HELIX 10 10 ASP A 363 ARG A 373 1 11 HELIX 11 11 LYS A 418 THR A 426 1 9 HELIX 12 12 PHE A 436 SER A 443 1 8 HELIX 13 13 LEU A 445 GLY A 453 1 9 HELIX 14 14 ASP A 454 PHE A 456 5 3 HELIX 15 15 ASN A 461 GLN A 471 1 11 HELIX 16 16 SER A 472 VAL A 474 5 3 HELIX 17 17 ASP A 476 ARG A 485 1 10 HELIX 18 18 ASP A 492 LEU A 496 5 5 HELIX 19 19 ARG A 513 ASN A 517 5 5 HELIX 20 20 PHE A 525 HIS A 529 5 5 HELIX 21 21 SER A 542 TYR A 548 1 7
SHEET 1 A11 LEU A 78 ASP A 82 0 SHEET 2 A11 SER A 64 LEU A 71 -1 N SER A 68 O GLU A 81 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 TYR A 105 N THR A 95 SHEET 5 A11 ILE A 278 ARG A 283 1 O ARG A 283 N LEU A 108 SHEET 6 A11 ASN A 301 SER A 306 -1 O PHE A 304 N LYS A 280 SHEET 7 A11 PHE A 317 LEU A 320 -1 O ILE A 319 N VAL A 303 SHEET 8 A11 LEU A 324 THR A 330 -1 O LEU A 324 N LEU A 320 SHEET 9 A11 ASN A 381 ASP A 387 -1 O VAL A 386 N VAL A 325 SHEET 10 A11 LEU A 403 ILE A 409 -1 O LEU A 406 N TRP A 383 SHEET 11 A11 MET A 412 ASP A 417 -1 O MET A 412 N ILE A 409 SHEET 1 B 6 TYR A 427 SER A 430 0 SHEET 2 B 6 SER A 250 LEU A 255 -1 N ILE A 253 O TRP A 428 SHEET 3 B 6 LEU A 262 ASN A 267 -1 O ASN A 267 N SER A 250 SHEET 4 B 6 ASP A 537 THR A 541 -1 O LYS A 539 N HIS A 266 SHEET 5 B 6 MET A 551 SER A 555 -1 O LEU A 552 N VAL A 540 SHEET 6 B 6 ILE A 589 VAL A 591 -1 O ILE A 589 N ALA A 553 SHEET 1 C 2 TRP A 269 SER A 271 0 SHEET 2 C 2 HIS A 533 GLY A 535 -1 O GLY A 534 N ASN A 270
SSBOND 1 CYS A 147 CYS A 157 1555 1555 2.03 SSBOND 2 CYS A 497 CYS A 500 1555 1555 2.04
LINK ND2 ASN A 93 C1 NAG A 1 1555 1555 1.45 LINK ND2 ASN A 115 C1 NAG A 11 1555 1555 1.44 LINK ND2 ASN A 236 C1 NAG A 21 1555 1555 1.45 LINK OH TYR A 379 NA NA A 610 1555 1555 2.91 LINK ND2 ASN A 441 C1 NAG A 31 1555 1555 1.45 LINK O4 NAG A 11 C1 NAG A 12 1555 1555 1.44 LINK O4 NAG A 12 C1 BMA A 13 1555 1555 1.45 LINK NA NA A 610 O HOH A 712 1555 1555 2.97
CISPEP 1 ASN A 501 PRO A 502 0 3.50 CISPEP 2 VAL A 591 PRO A 592 0 6.61
SITE 1 AC1 4 NAG A 12 ASN A 115 SER A 117 PHE A 207 SITE 1 AC2 5 NAG A 11 BMA A 13 GLY A 76 PHE A 207 SITE 2 AC2 5 THR A 209 SITE 1 AC3 1 NAG A 12 SITE 1 AC4 2 LYS A 159 ASN A 236 SITE 1 AC5 6 GLU A 437 ASN A 441 GLN A 446 HOH A 651 SITE 2 AC5 6 HOH A 670 HOH A 676 SITE 1 AC6 3 SER A 64 ASN A 93 THR A 95 SITE 1 AC7 3 PHE A 436 GLU A 437 THR A 438 SITE 1 AC8 4 GLU A 293 TYR A 294 PRO A 493 HOH A 643 SITE 1 AC9 3 ARG A 469 HOH A 667 HOH A 697 SITE 1 BC1 3 HOH A 28 TRP A 170 GLU A 174 SITE 1 BC2 1 SER A 117 SITE 1 BC3 3 LYS A 161 LYS A 215 LEU A 217 SITE 1 BC4 1 HIS A 577 SITE 1 BC5 2 ARG A 373 HOH A 630 SITE 1 BC6 2 LEU A 78 PHE A 207 SITE 1 BC7 6 SER A 248 CYS A 249 GLU A 328 THR A 330 SITE 2 BC7 6 TYR A 379 HOH A 712
CRYST1 146.690 88.110 73.550 90.00 111.10 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 0.006817 0.000000 0.002630 0.00000
SCALE2 0.000000 0.011349 0.000000 0.00000
SCALE3 0.000000 0.000000 0.014573 0.00000