PDB Short entry for 2P69 HEADER HYDROLASE 16-MAR-07 2P69 TITLE CRYSTAL STRUCTURE OF HUMAN PYRIDOXAL PHOSPHATE PHOSPHATASE WITH PLP 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, PSI-2, PROTEIN STRUCTURE KEYWDS 2 INITIATIVE, NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS, KEYWDS 3 NYSGXRC, 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 8 30-AUG-23 2P69 1 REMARK REVDAT 7 03-FEB-21 2P69 1 AUTHOR JRNL REMARK SEQADV REVDAT 7 2 1 LINK REVDAT 6 14-NOV-18 2P69 1 AUTHOR REVDAT 5 18-OCT-17 2P69 1 REMARK REVDAT 4 13-JUL-11 2P69 1 VERSN REVDAT 3 01-APR-08 2P69 1 SEQADV REVDAT 2 25-MAR-08 2P69 1 JRNL VERSN REVDAT 1 03-APR-07 2P69 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. 2.25 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) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.27 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 16086 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) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 805 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) : 2.25 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.31 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1092 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.57 REMARK 3 BIN R VALUE (WORKING SET) : 0.3240 REMARK 3 BIN FREE R VALUE SET COUNT : 69 REMARK 3 BIN FREE R VALUE : 0.4610 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2175 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 17 REMARK 3 SOLVENT ATOMS : 53 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 52.82 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.11000 REMARK 3 B22 (A**2) : 0.11000 REMARK 3 B33 (A**2) : -0.23000 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): 0.288 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.221 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.169 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.968 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.940 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2261 ; 0.012 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3065 ; 1.361 ; 1.991 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 291 ; 5.854 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 101 ;31.468 ;21.089 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 359 ;15.575 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 33 ;15.625 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 339 ; 0.087 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1747 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 958 ; 0.202 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1515 ; 0.313 ; 0.300 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 163 ; 0.187 ; 0.500 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 4 ; 0.120 ; 0.500 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 31 ; 0.129 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 7 ; 0.124 ; 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): 1473 ; 2.712 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2279 ; 3.838 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 868 ; 6.560 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 785 ; 8.879 ; 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 2P69 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-MAR-07. REMARK 100 THE DEPOSITION ID IS D_1000042018. 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 : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A 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 : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16163 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250 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 : 13.00 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 12.60 REMARK 200 R MERGE FOR SHELL (I) : 0.82500 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 2YOC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M CITRIC ACID PH 5.5, 20% PEG REMARK 280 3000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 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 106.26850 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 27.27950 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 27.27950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 159.40275 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 27.27950 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 27.27950 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 53.13425 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 27.27950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 27.27950 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 159.40275 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 27.27950 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 27.27950 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 53.13425 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 106.26850 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: THE BIOLOGICAL UNIT IS A 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 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 MSE A -1 REMARK 465 ASP A 105 REMARK 465 ALA A 106 REMARK 465 PRO A 107 REMARK 465 GLY A 108 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 OE1 GLU A 116 O HOH A 355 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 CYS A 26 -67.34 -106.24 REMARK 500 VAL A 29 -62.05 -126.32 REMARK 500 THR A 242 -71.03 -120.20 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 CA A 305 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 25 OD1 REMARK 620 2 ASP A 25 OD2 50.0 REMARK 620 3 ASP A 27 O 98.1 97.5 REMARK 620 4 ASP A 238 OD1 122.6 72.7 84.8 REMARK 620 5 PLP A 306 O3P 77.5 127.1 95.9 159.6 REMARK 620 6 HOH A 335 O 165.0 144.6 78.9 72.0 88.2 REMARK 620 7 HOH A 343 O 92.1 80.0 164.3 79.7 97.8 94.1 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PLP A 306 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: NYSGXRC-8744A RELATED DB: TARGETDB DBREF 2P69 A 2 296 UNP Q96GD0 PLPP_HUMAN 2 296 SEQADV 2P69 MSE A -1 UNP Q96GD0 EXPRESSION TAG SEQADV 2P69 SER A 0 UNP Q96GD0 EXPRESSION TAG SEQADV 2P69 LEU A 1 UNP Q96GD0 EXPRESSION TAG SEQADV 2P69 GLU A 297 UNP Q96GD0 EXPRESSION TAG SEQADV 2P69 GLY A 298 UNP Q96GD0 EXPRESSION TAG SEQADV 2P69 HIS A 299 UNP Q96GD0 EXPRESSION TAG SEQADV 2P69 HIS A 300 UNP Q96GD0 EXPRESSION TAG SEQADV 2P69 HIS A 301 UNP Q96GD0 EXPRESSION TAG SEQADV 2P69 HIS A 302 UNP Q96GD0 EXPRESSION TAG SEQADV 2P69 HIS A 303 UNP Q96GD0 EXPRESSION TAG SEQADV 2P69 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 2P69 MSE A 218 MET SELENOMETHIONINE MODRES 2P69 MSE A 235 MET SELENOMETHIONINE MODRES 2P69 MSE A 252 MET SELENOMETHIONINE HET MSE A 218 8 HET MSE A 235 8 HET MSE A 252 8 HET CA A 305 1 HET PLP A 306 16 HETNAM MSE SELENOMETHIONINE HETNAM CA CALCIUM ION HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETSYN PLP VITAMIN B6 PHOSPHATE FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 2 CA CA 2+ FORMUL 3 PLP C8 H10 N O6 P FORMUL 4 HOH *53(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 ASP A 168 1 14 HELIX 8 8 GLY A 192 GLY A 205 1 14 HELIX 9 9 SER A 215 THR A 223 1 9 HELIX 10 10 ASP A 229 ALA A 231 5 3 HELIX 11 11 THR A 242 CYS A 250 1 9 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 THR A 253 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 LEU A 55 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 4 VAL A 110 LEU A 113 0 SHEET 2 C 4 ALA A 145 VAL A 148 1 O ALA A 145 N PHE A 111 SHEET 3 C 4 LEU A 172 ALA A 175 1 O VAL A 174 N VAL A 148 SHEET 4 C 4 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 SSBOND 1 CYS A 91 CYS A 221 1555 1555 2.99 LINK C TYR A 217 N MSE A 218 1555 1555 1.32 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 1.33 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 OD1 ASP A 25 CA CA A 305 1555 1555 2.75 LINK OD2 ASP A 25 CA CA A 305 1555 1555 2.37 LINK O ASP A 27 CA CA A 305 1555 1555 2.53 LINK OD1 ASP A 238 CA CA A 305 1555 1555 2.45 LINK CA CA A 305 O3P PLP A 306 1555 1555 2.20 LINK CA CA A 305 O HOH A 335 1555 1555 2.34 LINK CA CA A 305 O HOH A 343 1555 1555 2.40 CISPEP 1 LYS A 213 PRO A 214 0 2.61 SITE 1 AC1 6 ASP A 25 ASP A 27 ASP A 238 PLP A 306 SITE 2 AC1 6 HOH A 335 HOH A 343 SITE 1 AC2 13 ASP A 25 CYS A 26 ASP A 27 SER A 58 SITE 2 AC2 13 ASN A 59 ASN A 60 TYR A 150 ASP A 179 SITE 3 AC2 13 HIS A 182 LYS A 213 CA A 305 HOH A 326 SITE 4 AC2 13 HOH A 350 CRYST1 54.559 54.559 212.537 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 0.018329 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018329 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004705 0.00000