HEADER HYDROLASE 21-FEB-07 2OYC TITLE CRYSTAL STRUCTURE OF HUMAN PYRIDOXAL PHOSPHATE PHOSPHATASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PYRIDOXAL PHOSPHATE PHOSPHATASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PLP PHOSPHATASE; COMPND 5 EC: 3.1.3.74; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PDXP, PLP, PLPP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: BC-PSGX3(BC) KEYWDS PHOSPHATASE, STRUCTURAL GENOMICS, NYSGXRC, NEW YORK SGX RESEARCH KEYWDS 2 CENTER FOR STRUCTURAL GENOMICS, PSI-2, PROTEIN STRUCTURE INITIATIVE, KEYWDS 3 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR U.A.RAMAGOPAL,J.FREEMAN,M.IZUKA,R.TORO,J.M.SAUDER,S.K.BURLEY, AUTHOR 2 S.C.ALMO,NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS AUTHOR 3 (NYSGXRC) REVDAT 9 16-OCT-24 2OYC 1 REMARK REVDAT 8 15-NOV-23 2OYC 1 REMARK REVDAT 7 30-AUG-23 2OYC 1 REMARK REVDAT 6 03-FEB-21 2OYC 1 AUTHOR JRNL REMARK SEQADV REVDAT 6 2 1 LINK REVDAT 5 14-NOV-18 2OYC 1 AUTHOR REVDAT 4 18-OCT-17 2OYC 1 REMARK REVDAT 3 01-APR-08 2OYC 1 SEQADV REVDAT 2 25-MAR-08 2OYC 1 JRNL VERSN REVDAT 1 13-MAR-07 2OYC 0 JRNL AUTH S.C.ALMO,J.B.BONANNO,J.M.SAUDER,S.EMTAGE,T.P.DILORENZO, JRNL AUTH 2 V.MALASHKEVICH,S.R.WASSERMAN,S.SWAMINATHAN,S.ESWARAMOORTHY, JRNL AUTH 3 R.AGARWAL,D.KUMARAN,M.MADEGOWDA,S.RAGUMANI,Y.PATSKOVSKY, JRNL AUTH 4 J.ALVARADO,U.A.RAMAGOPAL,J.FABER-BARATA,M.R.CHANCE,A.SALI, JRNL AUTH 5 A.FISER,Z.Y.ZHANG,D.S.LAWRENCE,S.K.BURLEY JRNL TITL STRUCTURAL GENOMICS OF PROTEIN PHOSPHATASES. JRNL REF J.STRUCT.FUNCT.GENOM. V. 8 121 2007 JRNL REFN ISSN 1345-711X JRNL PMID 18058037 JRNL DOI 10.1007/S10969-007-9036-1 REMARK 2 REMARK 2 RESOLUTION. 1.72 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 1.72 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 34933 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) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1755 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) : 1.72 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.77 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2391 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.70 REMARK 3 BIN R VALUE (WORKING SET) : 0.2600 REMARK 3 BIN FREE R VALUE SET COUNT : 111 REMARK 3 BIN FREE R VALUE : 0.3200 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2199 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 168 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.27000 REMARK 3 B22 (A**2) : 0.27000 REMARK 3 B33 (A**2) : -0.55000 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): 0.111 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.107 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.077 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.360 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.947 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2392 ; 0.009 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3259 ; 1.151 ; 1.984 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 319 ;13.186 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 108 ;32.668 ;20.741 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 383 ;15.719 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 38 ;19.771 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 358 ; 0.108 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1891 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1055 ; 0.225 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1630 ; 0.313 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 153 ; 0.150 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 4 ; 0.142 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 66 ; 0.225 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 14 ; 0.226 ; 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): 1533 ; 1.350 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2446 ; 2.319 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 874 ; 3.659 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 813 ; 5.931 ; 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 2OYC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-FEB-07. REMARK 100 THE DEPOSITION ID IS D_1000041736. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-FEB-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 31-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97900 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 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35004 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.720 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : 0.05800 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 26.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.72 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.78 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 6.00 REMARK 200 R MERGE FOR SHELL (I) : 0.59700 REMARK 200 R SYM FOR SHELL (I) : 0.63300 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.160 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 1ZJJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40% PEG4000, 0.1M SODIUM CITRATE PH REMARK 280 5.6, 20% ISOPROPANOL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 106.60000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 27.16450 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 27.16450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 159.90000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 27.16450 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 27.16450 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 53.30000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 27.16450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 27.16450 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 159.90000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 27.16450 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 27.16450 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 53.30000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 106.60000 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: PROBABLE DIMER 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 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 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 213.20000 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 MSE A -1 REMARK 465 ASP A 137 REMARK 465 GLY A 138 REMARK 465 ALA A 139 REMARK 465 GLU A 295 REMARK 465 ASP A 296 REMARK 465 GLU A 297 REMARK 465 GLY A 298 REMARK 465 HIS A 299 REMARK 465 HIS A 300 REMARK 465 HIS A 301 REMARK 465 HIS A 302 REMARK 465 HIS A 303 REMARK 465 HIS A 304 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 NH2 ARG A 63 O3 WO4 A 401 2.05 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 CYS A 26 -65.31 -108.95 REMARK 500 CYS A 26 -65.42 -100.00 REMARK 500 VAL A 29 -54.60 -123.94 REMARK 500 THR A 242 -59.19 -126.51 REMARK 500 THR A 242 -69.46 -107.52 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 PRO A 104 ASP A 105 -140.18 REMARK 500 ASP A 105 ALA A 106 110.06 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 A 305 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 25 OD2 REMARK 620 2 ASP A 27 O 106.7 REMARK 620 3 ASP A 238 OD1 110.6 94.6 REMARK 620 4 HOH A 506 O 65.4 169.9 83.0 REMARK 620 5 HOH A 519 O 152.5 91.2 87.8 98.4 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE WO4 A 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: NYSGXRC-8744A RELATED DB: TARGETDB DBREF 2OYC A 2 296 UNP Q96GD0 PLPP_HUMAN 2 296 SEQADV 2OYC MSE A -1 UNP Q96GD0 EXPRESSION TAG SEQADV 2OYC SER A 0 UNP Q96GD0 EXPRESSION TAG SEQADV 2OYC LEU A 1 UNP Q96GD0 EXPRESSION TAG SEQADV 2OYC GLU A 297 UNP Q96GD0 EXPRESSION TAG SEQADV 2OYC GLY A 298 UNP Q96GD0 EXPRESSION TAG SEQADV 2OYC HIS A 299 UNP Q96GD0 EXPRESSION TAG SEQADV 2OYC HIS A 300 UNP Q96GD0 EXPRESSION TAG SEQADV 2OYC HIS A 301 UNP Q96GD0 EXPRESSION TAG SEQADV 2OYC HIS A 302 UNP Q96GD0 EXPRESSION TAG SEQADV 2OYC HIS A 303 UNP Q96GD0 EXPRESSION TAG SEQADV 2OYC HIS A 304 UNP Q96GD0 EXPRESSION TAG SEQRES 1 A 306 MSE SER LEU ALA ARG CYS GLU ARG LEU ARG GLY ALA ALA SEQRES 2 A 306 LEU ARG ASP VAL LEU GLY ARG ALA GLN GLY VAL LEU PHE SEQRES 3 A 306 ASP CYS ASP GLY VAL LEU TRP ASN GLY GLU ARG ALA VAL SEQRES 4 A 306 PRO GLY ALA PRO GLU LEU LEU GLU ARG LEU ALA ARG ALA SEQRES 5 A 306 GLY LYS ALA ALA LEU PHE VAL SER ASN ASN SER ARG ARG SEQRES 6 A 306 ALA ARG PRO GLU LEU ALA LEU ARG PHE ALA ARG LEU GLY SEQRES 7 A 306 PHE GLY GLY LEU ARG ALA GLU GLN LEU PHE SER SER ALA SEQRES 8 A 306 LEU CYS ALA ALA ARG LEU LEU ARG GLN ARG LEU PRO GLY SEQRES 9 A 306 PRO PRO ASP ALA PRO GLY ALA VAL PHE VAL LEU GLY GLY SEQRES 10 A 306 GLU GLY LEU ARG ALA GLU LEU ARG ALA ALA GLY LEU ARG SEQRES 11 A 306 LEU ALA GLY ASP PRO SER ALA GLY ASP GLY ALA ALA PRO SEQRES 12 A 306 ARG VAL ARG ALA VAL LEU VAL GLY TYR ASP GLU HIS PHE SEQRES 13 A 306 SER PHE ALA LYS LEU ARG GLU ALA CYS ALA HIS LEU ARG SEQRES 14 A 306 ASP PRO GLU CYS LEU LEU VAL ALA THR ASP ARG ASP PRO SEQRES 15 A 306 TRP HIS PRO LEU SER ASP GLY SER ARG THR PRO GLY THR SEQRES 16 A 306 GLY SER LEU ALA ALA ALA VAL GLU THR ALA SER GLY ARG SEQRES 17 A 306 GLN ALA LEU VAL VAL GLY LYS PRO SER PRO TYR MSE PHE SEQRES 18 A 306 GLU CYS ILE THR GLU ASN PHE SER ILE ASP PRO ALA ARG SEQRES 19 A 306 THR LEU MSE VAL GLY ASP ARG LEU GLU THR ASP ILE LEU SEQRES 20 A 306 PHE GLY HIS ARG CYS GLY MSE THR THR VAL LEU THR LEU SEQRES 21 A 306 THR GLY VAL SER ARG LEU GLU GLU ALA GLN ALA TYR LEU SEQRES 22 A 306 ALA ALA GLY GLN HIS ASP LEU VAL PRO HIS TYR TYR VAL SEQRES 23 A 306 GLU SER ILE ALA ASP LEU THR GLU GLY LEU GLU ASP GLU SEQRES 24 A 306 GLY HIS HIS HIS HIS HIS HIS MODRES 2OYC MSE A 218 MET SELENOMETHIONINE MODRES 2OYC MSE A 235 MET SELENOMETHIONINE MODRES 2OYC MSE A 252 MET SELENOMETHIONINE HET MSE A 218 8 HET MSE A 235 8 HET MSE A 252 8 HET NA A 305 1 HET WO4 A 401 5 HETNAM MSE SELENOMETHIONINE HETNAM NA SODIUM ION HETNAM WO4 TUNGSTATE(VI)ION FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 2 NA NA 1+ FORMUL 3 WO4 O4 W 2- FORMUL 4 HOH *168(H2 O) HELIX 1 1 ARG A 8 ALA A 19 1 12 HELIX 2 2 GLY A 39 ALA A 50 1 12 HELIX 3 3 ALA A 64 LEU A 75 1 12 HELIX 4 4 ARG A 81 GLU A 83 5 3 HELIX 5 5 SER A 88 LEU A 100 1 13 HELIX 6 6 GLY A 115 ALA A 125 1 11 HELIX 7 7 SER A 155 ARG A 167 1 13 HELIX 8 8 GLY A 192 GLY A 205 1 14 HELIX 9 9 PRO A 216 PHE A 226 1 11 HELIX 10 10 ASP A 229 ALA A 231 5 3 HELIX 11 11 THR A 242 GLY A 251 1 10 HELIX 12 12 ARG A 263 ALA A 273 1 11 HELIX 13 13 GLN A 275 VAL A 279 5 5 HELIX 14 14 SER A 286 LEU A 294 5 9 SHEET 1 A 7 GLU A 5 ARG A 6 0 SHEET 2 A 7 TYR A 282 VAL A 284 1 O TYR A 283 N GLU A 5 SHEET 3 A 7 THR A 253 THR A 257 1 N LEU A 256 O TYR A 282 SHEET 4 A 7 THR A 233 GLY A 237 1 N MSE A 235 O VAL A 255 SHEET 5 A 7 GLY A 21 PHE A 24 1 N LEU A 23 O LEU A 234 SHEET 6 A 7 ALA A 53 SER A 58 1 O VAL A 57 N PHE A 24 SHEET 7 A 7 LEU A 85 SER A 87 1 O PHE A 86 N SER A 58 SHEET 1 B 2 TRP A 31 ASN A 32 0 SHEET 2 B 2 ARG A 35 ALA A 36 -1 O ARG A 35 N ASN A 32 SHEET 1 C 5 ARG A 128 LEU A 129 0 SHEET 2 C 5 ALA A 109 LEU A 113 1 N VAL A 110 O ARG A 128 SHEET 3 C 5 VAL A 143 VAL A 148 1 O ARG A 144 N ALA A 109 SHEET 4 C 5 LEU A 172 ALA A 175 1 O VAL A 174 N VAL A 148 SHEET 5 C 5 LEU A 209 VAL A 210 1 O LEU A 209 N ALA A 175 SHEET 1 D 2 TRP A 181 PRO A 183 0 SHEET 2 D 2 ARG A 189 PRO A 191 -1 O THR A 190 N HIS A 182 LINK C TYR A 217 N MSE A 218 1555 1555 1.34 LINK C MSE A 218 N PHE A 219 1555 1555 1.33 LINK C LEU A 234 N MSE A 235 1555 1555 1.33 LINK C MSE A 235 N VAL A 236 1555 1555 1.34 LINK C GLY A 251 N MSE A 252 1555 1555 1.33 LINK C MSE A 252 N THR A 253 1555 1555 1.33 LINK OD2 ASP A 25 NA NA A 305 1555 1555 2.21 LINK O ASP A 27 NA NA A 305 1555 1555 2.42 LINK OD1 ASP A 238 NA NA A 305 1555 1555 2.27 LINK NA NA A 305 O HOH A 506 1555 1555 2.32 LINK NA NA A 305 O HOH A 519 1555 1555 2.30 CISPEP 1 LYS A 213 PRO A 214 0 12.48 SITE 1 AC1 5 ASP A 25 ASP A 27 ASP A 238 HOH A 506 SITE 2 AC1 5 HOH A 519 SITE 1 AC2 6 ARG A 6 ARG A 8 ARG A 63 ARG A 71 SITE 2 AC2 6 ARG A 74 HOH A 553 CRYST1 54.329 54.329 213.200 90.00 90.00 90.00 P 43 21 2 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 0.018406 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018406 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004690 0.00000