HEADER TRANSFERASE 10-AUG-06 2DWC TITLE CRYSTAL STRUCTURE OF PROBABLE PHOSPHORIBOSYLGLYCINAMIDE FORMYL TITLE 2 TRANSFERASE FROM PYROCOCCUS HORIKOSHII OT3 COMPLEXED WITH ADP COMPND MOL_ID: 1; COMPND 2 MOLECULE: 433AA LONG HYPOTHETICAL PHOSPHORIBOSYLGLYCINAMIDE FORMYL COMPND 3 TRANSFERASE; COMPND 4 CHAIN: A, B; COMPND 5 SYNONYM: PH0318; COMPND 6 EC: 2.1.2.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS HORIKOSHII; SOURCE 3 ORGANISM_TAXID: 70601; SOURCE 4 STRAIN: OT3; SOURCE 5 GENE: PH0318; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)-CODONPLUS-RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS PURINE RIBONUCLEOTIDE BIOSYNTHESIS, PHOSPHORIBOSYLGLYCINAMIDE KEYWDS 2 FORMYLTRANSFERASE, PURT, STRUCTURAL GENOMICS, NPPSFA, NATIONAL KEYWDS 3 PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES, RIKEN KEYWDS 4 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.YOSHIKAWA,R.ARAI,T.KAMO-UCHIKUBO,M.SHIROUZU,S.YOKOYAMA,RIKEN AUTHOR 2 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 5 25-OCT-23 2DWC 1 REMARK REVDAT 4 13-JUL-11 2DWC 1 VERSN REVDAT 3 24-FEB-09 2DWC 1 VERSN REVDAT 2 27-FEB-07 2DWC 1 REMARK REVDAT 1 10-FEB-07 2DWC 0 JRNL AUTH S.YOSHIKAWA,R.ARAI,T.KAMO-UCHIKUBO,M.SHIROUZU,S.YOKOYAMA JRNL TITL CRYSTAL STRUCTURE OF PROBABLE PHOSPHORIBOSYLGLYCINAMIDE JRNL TITL 2 FORMYL TRANSFERASE FROM PYROCOCCUS HORIKOSHII OT3 COMPLEXED JRNL TITL 3 WITH ADP JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.33 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 219423.640 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.2 REMARK 3 NUMBER OF REFLECTIONS : 134239 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 SET) : 0.181 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 13365 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.002 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.81 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 79.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 17280 REMARK 3 BIN R VALUE (WORKING SET) : 0.2430 REMARK 3 BIN FREE R VALUE : 0.2620 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 1918 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.006 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6467 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 74 REMARK 3 SOLVENT ATOMS : 519 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.00000 REMARK 3 B22 (A**2) : 0.81000 REMARK 3 B33 (A**2) : -2.81000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.17 REMARK 3 ESD FROM SIGMAA (A) : 0.12 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.20 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.13 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.015 REMARK 3 BOND ANGLES (DEGREES) : 1.700 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.630 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 3.210 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.980 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 5.500 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 6.930 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.38 REMARK 3 BSOL : 53.32 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : SO4.PARAM REMARK 3 PARAMETER FILE 4 : ADP.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : SO4.TOP REMARK 3 TOPOLOGY FILE 4 : ADP.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2DWC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-AUG-06. REMARK 100 THE DEPOSITION ID IS D_1000025923. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JAN-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : SI DOUBLE CRYSTAL REMARK 200 OPTICS : TWO DIMENSIONAL FOCUSING MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 142103 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 4.413 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04300 REMARK 200 FOR THE DATA SET : 30.7220 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 (%) : 93.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.43900 REMARK 200 FOR SHELL : 3.087 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 2CZG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.2M AMMONIUM SULFATE, 25% GLYCEROL, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 60.30250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 60.30250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 51.86700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 106.25900 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 51.86700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 106.25900 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 60.30250 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 51.86700 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 106.25900 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 60.30250 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 51.86700 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 106.25900 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -69.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 18330 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 55960 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -142.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 60.30250 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 MET A 1 REMARK 465 SER A 166 REMARK 465 SER A 167 REMARK 465 SER A 168 REMARK 465 GLY A 169 REMARK 465 LYS A 170 REMARK 465 GLY A 171 REMARK 465 ALA A 188 REMARK 465 LYS A 189 REMARK 465 THR A 190 REMARK 465 LYS A 191 REMARK 465 ALA A 192 REMARK 465 ARG A 193 REMARK 465 GLY A 194 REMARK 465 SER A 195 REMARK 465 ALA A 196 REMARK 465 GLN A 423 REMARK 465 ASN A 424 REMARK 465 TYR A 425 REMARK 465 GLU A 426 REMARK 465 LYS A 427 REMARK 465 ARG A 428 REMARK 465 LYS A 429 REMARK 465 HIS A 430 REMARK 465 LEU A 431 REMARK 465 LEU A 432 REMARK 465 ARG A 433 REMARK 465 MET B 1 REMARK 465 SER B 167 REMARK 465 SER B 168 REMARK 465 GLY B 169 REMARK 465 LYS B 170 REMARK 465 ALA B 188 REMARK 465 LYS B 189 REMARK 465 THR B 190 REMARK 465 LYS B 191 REMARK 465 ALA B 192 REMARK 465 ARG B 193 REMARK 465 GLY B 194 REMARK 465 SER B 195 REMARK 465 ALA B 196 REMARK 465 ASN B 424 REMARK 465 TYR B 425 REMARK 465 GLU B 426 REMARK 465 LYS B 427 REMARK 465 ARG B 428 REMARK 465 LYS B 429 REMARK 465 HIS B 430 REMARK 465 LEU B 431 REMARK 465 LEU B 432 REMARK 465 ARG B 433 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 MET A 68 CB MET A 68 CG 0.192 REMARK 500 REMARK 500 REMARK: NULL 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 ARG A 62 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 319 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 414 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 414 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG B 295 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 ARG B 295 NE - CZ - NH2 ANGL. DEV. = -4.6 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 THR A 15 -5.45 77.17 REMARK 500 ILE A 238 53.43 -91.24 REMARK 500 ASP A 239 105.86 55.52 REMARK 500 THR B 15 -3.95 76.05 REMARK 500 ASN B 290 -65.29 -105.40 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP B 502 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2CZG RELATED DB: PDB REMARK 900 THE SAME PROTEIN, APO-FORM. REMARK 900 RELATED ID: PHO001000318.2 RELATED DB: TARGETDB DBREF 2DWC A 1 433 UNP O58056 O58056_PYRHO 1 433 DBREF 2DWC B 1 433 UNP O58056 O58056_PYRHO 1 433 SEQRES 1 A 433 MET VAL VAL MET ILE LYS LEU ARG ASP GLU LEU GLY THR SEQRES 2 A 433 ALA THR THR ASP SER ALA GLN LYS ILE LEU LEU LEU GLY SEQRES 3 A 433 SER GLY GLU LEU GLY LYS GLU ILE ALA ILE GLU ALA GLN SEQRES 4 A 433 ARG LEU GLY VAL GLU VAL VAL ALA VAL ASP ARG TYR ALA SEQRES 5 A 433 ASN ALA PRO ALA MET GLN VAL ALA HIS ARG SER TYR VAL SEQRES 6 A 433 GLY ASN MET MET ASP LYS ASP PHE LEU TRP SER VAL VAL SEQRES 7 A 433 GLU ARG GLU LYS PRO ASP ALA ILE ILE PRO GLU ILE GLU SEQRES 8 A 433 ALA ILE ASN LEU ASP ALA LEU PHE GLU PHE GLU LYS ASP SEQRES 9 A 433 GLY TYR PHE VAL VAL PRO ASN ALA ARG ALA THR TRP ILE SEQRES 10 A 433 ALA MET HIS ARG GLU ARG LEU ARG GLU THR LEU VAL LYS SEQRES 11 A 433 GLU ALA LYS VAL PRO THR SER ARG TYR MET TYR ALA THR SEQRES 12 A 433 THR LEU ASP GLU LEU TYR GLU ALA CYS GLU LYS ILE GLY SEQRES 13 A 433 TYR PRO CYS HIS THR LYS ALA ILE MET SER SER SER GLY SEQRES 14 A 433 LYS GLY SER TYR PHE VAL LYS GLY PRO GLU ASP ILE PRO SEQRES 15 A 433 LYS ALA TRP GLU GLU ALA LYS THR LYS ALA ARG GLY SER SEQRES 16 A 433 ALA GLU LYS ILE ILE VAL GLU GLU HIS ILE ASP PHE ASP SEQRES 17 A 433 VAL GLU VAL THR GLU LEU ALA VAL ARG HIS PHE ASP GLU SEQRES 18 A 433 ASN GLY GLU ILE VAL THR THR PHE PRO LYS PRO VAL GLY SEQRES 19 A 433 HIS TYR GLN ILE ASP GLY ASP TYR HIS ALA SER TRP GLN SEQRES 20 A 433 PRO ALA GLU ILE SER GLU LYS ALA GLU ARG GLU VAL TYR SEQRES 21 A 433 ARG ILE ALA LYS ARG ILE THR ASP VAL LEU GLY GLY LEU SEQRES 22 A 433 GLY ILE PHE GLY VAL GLU MET PHE VAL LYS GLY ASP LYS SEQRES 23 A 433 VAL TRP ALA ASN GLU VAL SER PRO ARG PRO HIS ASP THR SEQRES 24 A 433 GLY MET VAL THR LEU ALA SER HIS PRO PRO GLY PHE SER SEQRES 25 A 433 GLU PHE ALA LEU HIS LEU ARG ALA VAL LEU GLY LEU PRO SEQRES 26 A 433 ILE PRO GLY GLU TRP VAL ASP GLY TYR ARG LEU PHE PRO SEQRES 27 A 433 MET LEU ILE PRO ALA ALA THR HIS VAL ILE LYS ALA LYS SEQRES 28 A 433 VAL SER GLY TYR SER PRO ARG PHE ARG GLY LEU VAL LYS SEQRES 29 A 433 ALA LEU SER VAL PRO ASN ALA THR VAL ARG LEU PHE GLY SEQRES 30 A 433 LYS PRO GLU ALA TYR VAL GLY ARG ARG LEU GLY ILE ALA SEQRES 31 A 433 LEU ALA TRP ASP LYS ASP VAL GLU VAL ALA LYS ARG LYS SEQRES 32 A 433 ALA GLU MET VAL ALA HIS MET ILE GLU LEU ARG THR ARG SEQRES 33 A 433 SER SER ASP TRP HIS ASP GLN ASN TYR GLU LYS ARG LYS SEQRES 34 A 433 HIS LEU LEU ARG SEQRES 1 B 433 MET VAL VAL MET ILE LYS LEU ARG ASP GLU LEU GLY THR SEQRES 2 B 433 ALA THR THR ASP SER ALA GLN LYS ILE LEU LEU LEU GLY SEQRES 3 B 433 SER GLY GLU LEU GLY LYS GLU ILE ALA ILE GLU ALA GLN SEQRES 4 B 433 ARG LEU GLY VAL GLU VAL VAL ALA VAL ASP ARG TYR ALA SEQRES 5 B 433 ASN ALA PRO ALA MET GLN VAL ALA HIS ARG SER TYR VAL SEQRES 6 B 433 GLY ASN MET MET ASP LYS ASP PHE LEU TRP SER VAL VAL SEQRES 7 B 433 GLU ARG GLU LYS PRO ASP ALA ILE ILE PRO GLU ILE GLU SEQRES 8 B 433 ALA ILE ASN LEU ASP ALA LEU PHE GLU PHE GLU LYS ASP SEQRES 9 B 433 GLY TYR PHE VAL VAL PRO ASN ALA ARG ALA THR TRP ILE SEQRES 10 B 433 ALA MET HIS ARG GLU ARG LEU ARG GLU THR LEU VAL LYS SEQRES 11 B 433 GLU ALA LYS VAL PRO THR SER ARG TYR MET TYR ALA THR SEQRES 12 B 433 THR LEU ASP GLU LEU TYR GLU ALA CYS GLU LYS ILE GLY SEQRES 13 B 433 TYR PRO CYS HIS THR LYS ALA ILE MET SER SER SER GLY SEQRES 14 B 433 LYS GLY SER TYR PHE VAL LYS GLY PRO GLU ASP ILE PRO SEQRES 15 B 433 LYS ALA TRP GLU GLU ALA LYS THR LYS ALA ARG GLY SER SEQRES 16 B 433 ALA GLU LYS ILE ILE VAL GLU GLU HIS ILE ASP PHE ASP SEQRES 17 B 433 VAL GLU VAL THR GLU LEU ALA VAL ARG HIS PHE ASP GLU SEQRES 18 B 433 ASN GLY GLU ILE VAL THR THR PHE PRO LYS PRO VAL GLY SEQRES 19 B 433 HIS TYR GLN ILE ASP GLY ASP TYR HIS ALA SER TRP GLN SEQRES 20 B 433 PRO ALA GLU ILE SER GLU LYS ALA GLU ARG GLU VAL TYR SEQRES 21 B 433 ARG ILE ALA LYS ARG ILE THR ASP VAL LEU GLY GLY LEU SEQRES 22 B 433 GLY ILE PHE GLY VAL GLU MET PHE VAL LYS GLY ASP LYS SEQRES 23 B 433 VAL TRP ALA ASN GLU VAL SER PRO ARG PRO HIS ASP THR SEQRES 24 B 433 GLY MET VAL THR LEU ALA SER HIS PRO PRO GLY PHE SER SEQRES 25 B 433 GLU PHE ALA LEU HIS LEU ARG ALA VAL LEU GLY LEU PRO SEQRES 26 B 433 ILE PRO GLY GLU TRP VAL ASP GLY TYR ARG LEU PHE PRO SEQRES 27 B 433 MET LEU ILE PRO ALA ALA THR HIS VAL ILE LYS ALA LYS SEQRES 28 B 433 VAL SER GLY TYR SER PRO ARG PHE ARG GLY LEU VAL LYS SEQRES 29 B 433 ALA LEU SER VAL PRO ASN ALA THR VAL ARG LEU PHE GLY SEQRES 30 B 433 LYS PRO GLU ALA TYR VAL GLY ARG ARG LEU GLY ILE ALA SEQRES 31 B 433 LEU ALA TRP ASP LYS ASP VAL GLU VAL ALA LYS ARG LYS SEQRES 32 B 433 ALA GLU MET VAL ALA HIS MET ILE GLU LEU ARG THR ARG SEQRES 33 B 433 SER SER ASP TRP HIS ASP GLN ASN TYR GLU LYS ARG LYS SEQRES 34 B 433 HIS LEU LEU ARG HET SO4 A 602 5 HET SO4 A 604 5 HET ADP A 501 27 HET SO4 B 601 5 HET SO4 B 603 5 HET ADP B 502 27 HETNAM SO4 SULFATE ION HETNAM ADP ADENOSINE-5'-DIPHOSPHATE FORMUL 3 SO4 4(O4 S 2-) FORMUL 5 ADP 2(C10 H15 N5 O10 P2) FORMUL 9 HOH *519(H2 O) HELIX 1 1 GLY A 28 LEU A 41 1 14 HELIX 2 2 ALA A 54 ALA A 60 1 7 HELIX 3 3 ASP A 70 LYS A 82 1 13 HELIX 4 4 ASN A 94 ASP A 104 1 11 HELIX 5 5 ASN A 111 HIS A 120 1 10 HELIX 6 6 HIS A 120 GLU A 131 1 12 HELIX 7 7 THR A 144 GLY A 156 1 13 HELIX 8 8 GLY A 177 GLU A 179 5 3 HELIX 9 9 ASP A 180 GLU A 187 1 8 HELIX 10 10 SER A 252 GLY A 271 1 20 HELIX 11 11 HIS A 297 MET A 301 5 5 HELIX 12 12 VAL A 302 HIS A 307 1 6 HELIX 13 13 SER A 312 GLY A 323 1 12 HELIX 14 14 GLY A 361 LEU A 366 1 6 HELIX 15 15 ASP A 396 MET A 410 1 15 HELIX 16 16 GLY B 28 LEU B 41 1 14 HELIX 17 17 ALA B 54 ALA B 60 1 7 HELIX 18 18 ASP B 70 LYS B 82 1 13 HELIX 19 19 ASN B 94 ASP B 104 1 11 HELIX 20 20 ASN B 111 MET B 119 1 9 HELIX 21 21 HIS B 120 GLU B 131 1 12 HELIX 22 22 THR B 144 GLY B 156 1 13 HELIX 23 23 GLY B 177 GLU B 179 5 3 HELIX 24 24 ASP B 180 GLU B 186 1 7 HELIX 25 25 SER B 252 GLY B 271 1 20 HELIX 26 26 HIS B 297 MET B 301 5 5 HELIX 27 27 VAL B 302 HIS B 307 1 6 HELIX 28 28 SER B 312 GLY B 323 1 12 HELIX 29 29 GLY B 361 LEU B 366 1 6 HELIX 30 30 ASP B 396 MET B 410 1 15 SHEET 1 A 4 GLU A 10 LEU A 11 0 SHEET 2 A 4 ARG B 358 ARG B 360 -1 O PHE B 359 N LEU A 11 SHEET 3 A 4 GLU B 412 ARG B 414 -1 O GLU B 412 N ARG B 360 SHEET 4 A 4 HIS B 421 ASP B 422 -1 O HIS B 421 N LEU B 413 SHEET 1 B 4 ARG A 62 VAL A 65 0 SHEET 2 B 4 GLU A 44 ASP A 49 1 N ALA A 47 O ARG A 62 SHEET 3 B 4 LYS A 21 LEU A 25 1 N LEU A 24 O VAL A 46 SHEET 4 B 4 ALA A 85 PRO A 88 1 O ILE A 87 N LEU A 23 SHEET 1 C 4 TYR A 139 ALA A 142 0 SHEET 2 C 4 ILE A 199 GLU A 203 -1 O VAL A 201 N MET A 140 SHEET 3 C 4 CYS A 159 ALA A 163 -1 N HIS A 160 O GLU A 202 SHEET 4 C 4 TYR A 173 VAL A 175 -1 O TYR A 173 N THR A 161 SHEET 1 D 8 LYS A 286 SER A 293 0 SHEET 2 D 8 GLY A 277 LYS A 283 -1 N GLU A 279 O ASN A 290 SHEET 3 D 8 VAL A 209 GLU A 213 -1 N GLU A 213 O VAL A 278 SHEET 4 D 8 VAL A 233 GLN A 237 -1 O VAL A 233 N THR A 212 SHEET 5 D 8 TYR A 242 GLN A 247 -1 O HIS A 243 N TYR A 236 SHEET 6 D 8 ALA A 343 LYS A 349 -1 O THR A 345 N SER A 245 SHEET 7 D 8 ARG A 386 TRP A 393 -1 O ALA A 390 N HIS A 346 SHEET 8 D 8 ALA A 371 LEU A 375 -1 N THR A 372 O LEU A 391 SHEET 1 E 5 GLY A 274 ILE A 275 0 SHEET 2 E 5 VAL A 216 PHE A 219 -1 N ARG A 217 O GLY A 274 SHEET 3 E 5 ILE A 225 PRO A 230 -1 O VAL A 226 N HIS A 218 SHEET 4 E 5 TYR A 334 PHE A 337 1 O ARG A 335 N PHE A 229 SHEET 5 E 5 GLU A 329 VAL A 331 -1 N GLU A 329 O LEU A 336 SHEET 1 F 2 GLY A 354 TYR A 355 0 SHEET 2 F 2 GLU A 380 ALA A 381 -1 O ALA A 381 N GLY A 354 SHEET 1 G 3 GLU A 412 ARG A 414 0 SHEET 2 G 3 ARG A 358 ARG A 360 -1 N ARG A 358 O ARG A 414 SHEET 3 G 3 GLU B 10 LEU B 11 -1 O LEU B 11 N PHE A 359 SHEET 1 H 4 ARG B 62 VAL B 65 0 SHEET 2 H 4 GLU B 44 ASP B 49 1 N ALA B 47 O ARG B 62 SHEET 3 H 4 LYS B 21 LEU B 25 1 N LEU B 24 O VAL B 46 SHEET 4 H 4 ALA B 85 PRO B 88 1 O ILE B 87 N LEU B 23 SHEET 1 I 4 TYR B 139 ALA B 142 0 SHEET 2 I 4 ILE B 199 GLU B 203 -1 O VAL B 201 N MET B 140 SHEET 3 I 4 CYS B 159 ALA B 163 -1 N HIS B 160 O GLU B 202 SHEET 4 I 4 TYR B 173 VAL B 175 -1 O VAL B 175 N CYS B 159 SHEET 1 J 8 LYS B 286 SER B 293 0 SHEET 2 J 8 GLY B 277 LYS B 283 -1 N GLY B 277 O SER B 293 SHEET 3 J 8 VAL B 209 GLU B 213 -1 N GLU B 213 O VAL B 278 SHEET 4 J 8 VAL B 233 ILE B 238 -1 O VAL B 233 N THR B 212 SHEET 5 J 8 ASP B 241 GLN B 247 -1 O TRP B 246 N GLY B 234 SHEET 6 J 8 ALA B 343 LYS B 349 -1 O VAL B 347 N HIS B 243 SHEET 7 J 8 ARG B 386 TRP B 393 -1 O ALA B 390 N HIS B 346 SHEET 8 J 8 ALA B 371 LEU B 375 -1 N THR B 372 O LEU B 391 SHEET 1 K 5 GLY B 274 ILE B 275 0 SHEET 2 K 5 VAL B 216 PHE B 219 -1 N ARG B 217 O GLY B 274 SHEET 3 K 5 ILE B 225 PRO B 230 -1 O VAL B 226 N HIS B 218 SHEET 4 K 5 TYR B 334 PHE B 337 1 O ARG B 335 N PHE B 229 SHEET 5 K 5 GLU B 329 VAL B 331 -1 N VAL B 331 O TYR B 334 SHEET 1 L 2 GLY B 354 TYR B 355 0 SHEET 2 L 2 GLU B 380 ALA B 381 -1 O ALA B 381 N GLY B 354 CISPEP 1 VAL A 109 PRO A 110 0 -0.94 CISPEP 2 TYR A 157 PRO A 158 0 -0.26 CISPEP 3 GLN A 247 PRO A 248 0 0.06 CISPEP 4 VAL B 109 PRO B 110 0 -1.00 CISPEP 5 TYR B 157 PRO B 158 0 -0.40 CISPEP 6 GLN B 247 PRO B 248 0 -0.16 SITE 1 AC1 5 LYS B 378 TYR B 382 ARG B 385 HOH B 982 SITE 2 AC1 5 HOH B1200 SITE 1 AC2 3 ARG A 414 TRP A 420 HOH A 942 SITE 1 AC3 4 ARG B 414 TRP B 420 HOH B 904 HOH B1004 SITE 1 AC4 4 LYS A 378 TYR A 382 ARG A 385 HOH A1074 SITE 1 AC5 13 ARG A 121 HIS A 160 LYS A 162 GLU A 202 SITE 2 AC5 13 GLU A 203 HIS A 204 ILE A 205 PHE A 207 SITE 3 AC5 13 GLU A 210 GLN A 237 PHE A 281 ASN A 290 SITE 4 AC5 13 GLU A 291 SITE 1 AC6 14 ARG B 121 HIS B 160 LYS B 162 GLU B 202 SITE 2 AC6 14 GLU B 203 HIS B 204 ILE B 205 PHE B 207 SITE 3 AC6 14 GLU B 210 GLN B 237 PHE B 281 ASN B 290 SITE 4 AC6 14 GLU B 291 HOH B1003 CRYST1 103.734 212.518 120.605 90.00 90.00 90.00 C 2 2 21 16 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 0.009640 0.000000 0.000000 0.00000 SCALE2 0.000000 0.004705 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008292 0.00000