HEADER HYDROLASE 07-MAR-07 2P27 TITLE CRYSTAL STRUCTURE OF HUMAN PYRIDOXAL PHOSPHATE PHOSPHATASE WITH MG2+ TITLE 2 AT 1.9 A RESOLUTION CAVEAT 2P27 CHIRALITY ERRORS AT RESIDUE A 102 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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PHOSPHATASE, STRUCTURAL GENOMICS, NYSGXRC, NEW YORK STRUCTURAL KEYWDS 2 GENOMICS RESEARCH CONSORTIUM, NYSGRC, NEW YORK SGX RESEARCH CENTER KEYWDS 3 FOR STRUCTURAL GENOMICS, PSI-2, PROTEIN STRUCTURE INITIATIVE, KEYWDS 4 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 2P27 1 REMARK REVDAT 8 15-NOV-23 2P27 1 REMARK REVDAT 7 30-AUG-23 2P27 1 REMARK REVDAT 6 03-FEB-21 2P27 1 AUTHOR JRNL REMARK SEQADV REVDAT 6 2 1 LINK REVDAT 5 14-NOV-18 2P27 1 AUTHOR REVDAT 4 18-OCT-17 2P27 1 REMARK REVDAT 3 01-APR-08 2P27 1 SEQADV REVDAT 2 25-MAR-08 2P27 1 JRNL VERSN REVDAT 1 13-MAR-07 2P27 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. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.34 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 26182 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) : 0.213 REMARK 3 R VALUE (WORKING SET) : 0.211 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1332 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1798 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2370 REMARK 3 BIN FREE R VALUE SET COUNT : 91 REMARK 3 BIN FREE R VALUE : 0.2690 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2170 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 116 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.29000 REMARK 3 B22 (A**2) : 0.29000 REMARK 3 B33 (A**2) : -0.59000 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): 0.159 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.149 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.100 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.356 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.932 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2284 ; 0.011 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3106 ; 1.454 ; 1.982 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 301 ; 7.347 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 104 ;31.997 ;21.731 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 359 ;15.049 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 31 ;17.508 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 343 ; 0.088 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1796 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 999 ; 0.203 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1556 ; 0.300 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 117 ; 0.160 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.022 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 51 ; 0.130 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 6 ; 0.143 ; 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): 1509 ; 0.906 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2340 ; 1.538 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 853 ; 2.199 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 766 ; 3.453 ; 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 2P27 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-MAR-07. REMARK 100 THE DEPOSITION ID IS D_1000041873. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-FEB-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 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 : 26274 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 8.300 REMARK 200 R MERGE (I) : 0.06800 REMARK 200 R SYM (I) : 0.05200 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.20 REMARK 200 R MERGE FOR SHELL (I) : 0.62400 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 (%): 47.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM TRIS-HCL PH 8.5, 17% PEG 20000, REMARK 280 100MM MAGNESIUM CHLORIDE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 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 106.59100 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 27.12250 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 27.12250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 159.88650 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 27.12250 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 27.12250 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 53.29550 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 27.12250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 27.12250 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 159.88650 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 27.12250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 27.12250 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 53.29550 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 106.59100 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 MOLECULE APPEARS TO BE DIMER GENERATED FROM REMARK 300 THE MONOMER IN THE ASYMMETRIC UNIT BY OPERATION X,Y,Z-1 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 213.18200 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 423 LIES ON A SPECIAL POSITION. 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 SER A 2 REMARK 465 LEU A 3 REMARK 465 GLY A 138 REMARK 465 ASP A 139 REMARK 465 GLY A 140 REMARK 465 ALA A 141 REMARK 465 GLU A 297 REMARK 465 ASP A 298 REMARK 465 GLU A 299 REMARK 465 GLY A 300 REMARK 465 HIS A 301 REMARK 465 HIS A 302 REMARK 465 HIS A 303 REMARK 465 HIS A 304 REMARK 465 HIS A 305 REMARK 465 HIS A 306 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 ARG A 5 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 51 CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LEU A 102 CA - CB - CG ANGL. DEV. = 16.6 DEGREES REMARK 500 PRO A 106 C - N - CD ANGL. DEV. = -13.9 DEGREES REMARK 500 ARG A 208 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES 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 28 -64.72 -100.98 REMARK 500 CYS A 28 -65.76 -100.98 REMARK 500 VAL A 31 -61.10 -128.62 REMARK 500 LEU A 102 61.22 32.93 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 GLY A 53 LYS A 54 -44.68 REMARK 500 ARG A 101 LEU A 102 134.38 REMARK 500 PRO A 106 ASP A 107 139.44 REMARK 500 ASP A 107 ALA A 108 45.05 REMARK 500 PRO A 109 GLY A 110 -34.38 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 MG A 307 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 27 OD2 REMARK 620 2 ASP A 29 O 95.2 REMARK 620 3 ASP A 29 O 90.0 5.4 REMARK 620 4 ASP A 240 OD1 87.7 91.1 89.6 REMARK 620 5 HOH A 308 O 94.5 92.9 94.6 175.3 REMARK 620 6 HOH A 309 O 173.3 86.2 91.3 85.8 91.9 REMARK 620 7 HOH A 310 O 89.7 174.5 178.9 91.4 84.4 89.2 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 MG A 307 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: NYSGXRC-8744A RELATED DB: TARGETDB DBREF 2P27 A 4 298 UNP Q96GD0 PLPP_HUMAN 2 296 SEQADV 2P27 MSE A 1 UNP Q96GD0 EXPRESSION TAG SEQADV 2P27 SER A 2 UNP Q96GD0 EXPRESSION TAG SEQADV 2P27 LEU A 3 UNP Q96GD0 EXPRESSION TAG SEQADV 2P27 GLU A 299 UNP Q96GD0 EXPRESSION TAG SEQADV 2P27 GLY A 300 UNP Q96GD0 EXPRESSION TAG SEQADV 2P27 HIS A 301 UNP Q96GD0 EXPRESSION TAG SEQADV 2P27 HIS A 302 UNP Q96GD0 EXPRESSION TAG SEQADV 2P27 HIS A 303 UNP Q96GD0 EXPRESSION TAG SEQADV 2P27 HIS A 304 UNP Q96GD0 EXPRESSION TAG SEQADV 2P27 HIS A 305 UNP Q96GD0 EXPRESSION TAG SEQADV 2P27 HIS A 306 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 2P27 MSE A 220 MET SELENOMETHIONINE MODRES 2P27 MSE A 237 MET SELENOMETHIONINE MODRES 2P27 MSE A 254 MET SELENOMETHIONINE HET MSE A 220 8 HET MSE A 237 8 HET MSE A 254 8 HET MG A 307 1 HETNAM MSE SELENOMETHIONINE HETNAM MG MAGNESIUM ION FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 2 MG MG 2+ FORMUL 3 HOH *116(H2 O) HELIX 1 1 ARG A 10 ALA A 21 1 12 HELIX 2 2 GLY A 41 GLY A 53 1 13 HELIX 3 3 ALA A 66 LEU A 77 1 12 HELIX 4 4 ARG A 83 GLU A 85 5 3 HELIX 5 5 SER A 90 LEU A 102 1 13 HELIX 6 6 GLY A 117 ALA A 127 1 11 HELIX 7 7 SER A 157 ARG A 169 1 13 HELIX 8 8 GLY A 194 GLY A 207 1 14 HELIX 9 9 PRO A 218 PHE A 228 1 11 HELIX 10 10 ASP A 231 ALA A 233 5 3 HELIX 11 11 THR A 244 GLY A 253 1 10 HELIX 12 12 ARG A 265 ALA A 275 1 11 HELIX 13 13 GLN A 277 VAL A 281 5 5 HELIX 14 14 SER A 288 LEU A 296 5 9 SHEET 1 A 7 GLU A 7 ARG A 8 0 SHEET 2 A 7 TYR A 284 VAL A 286 1 O TYR A 285 N GLU A 7 SHEET 3 A 7 THR A 255 THR A 259 1 N LEU A 258 O TYR A 284 SHEET 4 A 7 THR A 235 GLY A 239 1 N MSE A 237 O THR A 255 SHEET 5 A 7 GLY A 23 PHE A 26 1 N LEU A 25 O LEU A 236 SHEET 6 A 7 ALA A 55 SER A 60 1 O VAL A 59 N PHE A 26 SHEET 7 A 7 LEU A 87 SER A 89 1 O PHE A 88 N SER A 60 SHEET 1 B 2 TRP A 33 ASN A 34 0 SHEET 2 B 2 ARG A 37 ALA A 38 -1 O ARG A 37 N ASN A 34 SHEET 1 C 5 ARG A 130 LEU A 131 0 SHEET 2 C 5 ALA A 111 LEU A 115 1 N VAL A 112 O ARG A 130 SHEET 3 C 5 VAL A 145 VAL A 150 1 O ALA A 147 N PHE A 113 SHEET 4 C 5 LEU A 174 ALA A 177 1 O VAL A 176 N VAL A 150 SHEET 5 C 5 LEU A 211 VAL A 212 1 O LEU A 211 N LEU A 175 SHEET 1 D 2 TRP A 183 PRO A 185 0 SHEET 2 D 2 ARG A 191 PRO A 193 -1 O THR A 192 N HIS A 184 SSBOND 1 CYS A 93 CYS A 223 1555 1555 2.58 LINK C TYR A 219 N MSE A 220 1555 1555 1.33 LINK C MSE A 220 N PHE A 221 1555 1555 1.33 LINK C LEU A 236 N MSE A 237 1555 1555 1.33 LINK C MSE A 237 N VAL A 238 1555 1555 1.33 LINK C GLY A 253 N MSE A 254 1555 1555 1.33 LINK C MSE A 254 N THR A 255 1555 1555 1.32 LINK OD2 ASP A 27 MG MG A 307 1555 1555 1.97 LINK O AASP A 29 MG MG A 307 1555 1555 2.10 LINK O BASP A 29 MG MG A 307 1555 1555 2.14 LINK OD1 ASP A 240 MG MG A 307 1555 1555 2.05 LINK MG MG A 307 O HOH A 308 1555 1555 2.09 LINK MG MG A 307 O HOH A 309 1555 1555 2.21 LINK MG MG A 307 O HOH A 310 1555 1555 2.13 CISPEP 1 LYS A 215 PRO A 216 0 4.33 SITE 1 AC1 6 ASP A 27 ASP A 29 ASP A 240 HOH A 308 SITE 2 AC1 6 HOH A 309 HOH A 310 CRYST1 54.245 54.245 213.182 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 0.018435 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018435 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004691 0.00000