HEADER OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR 21-JUN-10 3NKS TITLE STRUCTURE OF HUMAN PROTOPORPHYRINOGEN IX OXIDASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTOPORPHYRINOGEN OXIDASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROTOPORPHYRINOGEN IX OXIDASE, PPO; COMPND 5 EC: 1.3.3.4; 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: PPOX; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS KEYWDS FAD CONTAINING PROTEIN, PPO, VARIEGATE PORPHYRIA DISEASE, VP, KEYWDS 2 OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.SHEN REVDAT 2 01-NOV-23 3NKS 1 REMARK REVDAT 1 20-APR-11 3NKS 0 JRNL AUTH X.QIN,Y.TAN,L.WANG,Z.WANG,B.WANG,X.WEN,G.YANG,Z.XI,Y.SHEN JRNL TITL STRUCTURAL INSIGHT INTO HUMAN VARIEGATE PORPHYRIA DISEASE JRNL REF FASEB J. V. 25 653 2011 JRNL REFN ISSN 0892-6638 JRNL PMID 21048046 JRNL DOI 10.1096/FJ.10-170811 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.71 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 97002.540 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.4 REMARK 3 NUMBER OF REFLECTIONS : 42448 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) : 0.206 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2120 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 79.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 5587 REMARK 3 BIN R VALUE (WORKING SET) : 0.2590 REMARK 3 BIN FREE R VALUE : 0.2480 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 294 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.014 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3460 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 89 REMARK 3 SOLVENT ATOMS : 269 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.84000 REMARK 3 B22 (A**2) : -2.84000 REMARK 3 B33 (A**2) : 5.68000 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) : 0.23 REMARK 3 ESD FROM SIGMAA (A) : 0.17 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) : 0.25 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.13 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 2.110 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) : 1.370 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.250 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.040 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.070 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 56.79 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 : FAD.PARAM REMARK 3 PARAMETER FILE 4 : ACJ.PARAM REMARK 3 PARAMETER FILE 5 : GOL.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : FAD.TOP REMARK 3 TOPOLOGY FILE 4 : ACJ.TOP REMARK 3 TOPOLOGY FILE 5 : GOL.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 3NKS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-JUL-10. REMARK 100 THE DEPOSITION ID IS D_1000059953. 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 : 10.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44210 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 10.00 REMARK 200 R MERGE (I) : 0.08500 REMARK 200 R SYM (I) : 0.08500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 25.9000 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 (%) : 88.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 0.45800 REMARK 200 R SYM FOR SHELL (I) : 0.45800 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASES REMARK 200 STARTING MODEL: PDB ENTRY 2IVE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM CITRATE DIBASIC, PEG3350, PH REMARK 280 10.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 68.35100 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 39.46247 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 52.95900 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 68.35100 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 39.46247 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 52.95900 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 68.35100 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 39.46247 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 52.95900 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 68.35100 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 39.46247 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 52.95900 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 68.35100 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 39.46247 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 52.95900 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 68.35100 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 39.46247 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 52.95900 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 78.92494 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 105.91800 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 78.92494 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 105.91800 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 78.92494 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 105.91800 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 78.92494 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 105.91800 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 78.92494 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 105.91800 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 78.92494 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 105.91800 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: MONOMERIC 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1710 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 39620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 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 -0.500000 -0.866025 0.000000 -68.35100 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 -39.46247 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 105.91800 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 LEU A 115 REMARK 465 LEU A 116 REMARK 465 ARG A 117 REMARK 465 ALA A 205 REMARK 465 GLY A 206 REMARK 465 ARG A 207 REMARK 465 THR A 208 REMARK 465 PRO A 209 REMARK 465 PRO A 475 REMARK 465 ASN A 476 REMARK 465 SER A 477 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 3 CG CD NE CZ NH1 NH2 REMARK 470 THR A 110 OG1 CG2 REMARK 470 LEU A 112 CG CD1 CD2 REMARK 470 ARG A 113 CG CD NE CZ NH1 NH2 REMARK 470 PRO A 118 CG CD REMARK 470 SER A 380 OG REMARK 470 GLU A 474 CG CD OE1 OE2 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 PRO A 125 C - N - CA ANGL. DEV. = -12.9 DEGREES REMARK 500 PRO A 125 C - N - CD ANGL. DEV. = 12.9 DEGREES REMARK 500 PRO A 125 N - CA - C ANGL. DEV. = 17.5 DEGREES REMARK 500 LEU A 126 CA - CB - CG ANGL. DEV. = -15.6 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 ASP A 90 40.36 -97.55 REMARK 500 THR A 110 -80.51 -96.61 REMARK 500 SER A 119 97.39 -163.30 REMARK 500 LYS A 124 -47.01 -140.72 REMARK 500 PRO A 125 -93.25 -95.70 REMARK 500 LEU A 126 -6.10 83.94 REMARK 500 PHE A 127 -60.53 -99.17 REMARK 500 ALA A 162 -63.01 -91.97 REMARK 500 ARG A 195 1.28 88.35 REMARK 500 PRO A 211 -175.70 -61.28 REMARK 500 GLN A 263 -153.70 -147.90 REMARK 500 ASP A 340 104.71 -166.48 REMARK 500 TYR A 451 -77.02 -112.88 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 ACJ A 478 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FAD A 479 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 968 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 969 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3I6D RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PPO FROM BACILLUS SUBTILIS WITH AF DBREF 3NKS A 1 477 UNP P50336 PPOX_HUMAN 1 477 SEQRES 1 A 477 MET GLY ARG THR VAL VAL VAL LEU GLY GLY GLY ILE SER SEQRES 2 A 477 GLY LEU ALA ALA SER TYR HIS LEU SER ARG ALA PRO CYS SEQRES 3 A 477 PRO PRO LYS VAL VAL LEU VAL GLU SER SER GLU ARG LEU SEQRES 4 A 477 GLY GLY TRP ILE ARG SER VAL ARG GLY PRO ASN GLY ALA SEQRES 5 A 477 ILE PHE GLU LEU GLY PRO ARG GLY ILE ARG PRO ALA GLY SEQRES 6 A 477 ALA LEU GLY ALA ARG THR LEU LEU LEU VAL SER GLU LEU SEQRES 7 A 477 GLY LEU ASP SER GLU VAL LEU PRO VAL ARG GLY ASP HIS SEQRES 8 A 477 PRO ALA ALA GLN ASN ARG PHE LEU TYR VAL GLY GLY ALA SEQRES 9 A 477 LEU HIS ALA LEU PRO THR GLY LEU ARG GLY LEU LEU ARG SEQRES 10 A 477 PRO SER PRO PRO PHE SER LYS PRO LEU PHE TRP ALA GLY SEQRES 11 A 477 LEU ARG GLU LEU THR LYS PRO ARG GLY LYS GLU PRO ASP SEQRES 12 A 477 GLU THR VAL HIS SER PHE ALA GLN ARG ARG LEU GLY PRO SEQRES 13 A 477 GLU VAL ALA SER LEU ALA MET ASP SER LEU CYS ARG GLY SEQRES 14 A 477 VAL PHE ALA GLY ASN SER ARG GLU LEU SER ILE ARG SER SEQRES 15 A 477 CYS PHE PRO SER LEU PHE GLN ALA GLU GLN THR HIS ARG SEQRES 16 A 477 SER ILE LEU LEU GLY LEU LEU LEU GLY ALA GLY ARG THR SEQRES 17 A 477 PRO GLN PRO ASP SER ALA LEU ILE ARG GLN ALA LEU ALA SEQRES 18 A 477 GLU ARG TRP SER GLN TRP SER LEU ARG GLY GLY LEU GLU SEQRES 19 A 477 MET LEU PRO GLN ALA LEU GLU THR HIS LEU THR SER ARG SEQRES 20 A 477 GLY VAL SER VAL LEU ARG GLY GLN PRO VAL CYS GLY LEU SEQRES 21 A 477 SER LEU GLN ALA GLU GLY ARG TRP LYS VAL SER LEU ARG SEQRES 22 A 477 ASP SER SER LEU GLU ALA ASP HIS VAL ILE SER ALA ILE SEQRES 23 A 477 PRO ALA SER VAL LEU SER GLU LEU LEU PRO ALA GLU ALA SEQRES 24 A 477 ALA PRO LEU ALA ARG ALA LEU SER ALA ILE THR ALA VAL SEQRES 25 A 477 SER VAL ALA VAL VAL ASN LEU GLN TYR GLN GLY ALA HIS SEQRES 26 A 477 LEU PRO VAL GLN GLY PHE GLY HIS LEU VAL PRO SER SER SEQRES 27 A 477 GLU ASP PRO GLY VAL LEU GLY ILE VAL TYR ASP SER VAL SEQRES 28 A 477 ALA PHE PRO GLU GLN ASP GLY SER PRO PRO GLY LEU ARG SEQRES 29 A 477 VAL THR VAL MET LEU GLY GLY SER TRP LEU GLN THR LEU SEQRES 30 A 477 GLU ALA SER GLY CYS VAL LEU SER GLN GLU LEU PHE GLN SEQRES 31 A 477 GLN ARG ALA GLN GLU ALA ALA ALA THR GLN LEU GLY LEU SEQRES 32 A 477 LYS GLU MET PRO SER HIS CYS LEU VAL HIS LEU HIS LYS SEQRES 33 A 477 ASN CYS ILE PRO GLN TYR THR LEU GLY HIS TRP GLN LYS SEQRES 34 A 477 LEU GLU SER ALA ARG GLN PHE LEU THR ALA HIS ARG LEU SEQRES 35 A 477 PRO LEU THR LEU ALA GLY ALA SER TYR GLU GLY VAL ALA SEQRES 36 A 477 VAL ASN ASP CYS ILE GLU SER GLY ARG GLN ALA ALA VAL SEQRES 37 A 477 SER VAL LEU GLY THR GLU PRO ASN SER HET ACJ A 478 24 HET FAD A 479 53 HET GOL A 968 6 HET GOL A 969 6 HETNAM ACJ 5-[2-CHLORO-4-(TRIFLUOROMETHYL)PHENOXY]-2-NITROBENZOIC HETNAM 2 ACJ ACID HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 ACJ C14 H7 CL F3 N O5 FORMUL 3 FAD C27 H33 N9 O15 P2 FORMUL 4 GOL 2(C3 H8 O3) FORMUL 6 HOH *269(H2 O) HELIX 1 1 GLY A 11 ARG A 23 1 13 HELIX 2 2 ALA A 64 LEU A 78 1 15 HELIX 3 3 LEU A 80 SER A 82 5 3 HELIX 4 4 HIS A 91 ASN A 96 1 6 HELIX 5 5 PHE A 127 ARG A 132 1 6 HELIX 6 6 THR A 145 GLY A 155 1 11 HELIX 7 7 GLY A 155 ALA A 162 1 8 HELIX 8 8 ALA A 162 ALA A 172 1 11 HELIX 9 9 SER A 179 PHE A 184 1 6 HELIX 10 10 PHE A 184 ARG A 195 1 12 HELIX 11 11 SER A 196 GLY A 204 1 9 HELIX 12 12 SER A 213 GLU A 222 1 10 HELIX 13 13 GLU A 234 ARG A 247 1 14 HELIX 14 14 ALA A 264 GLY A 266 5 3 HELIX 15 15 PRO A 287 LEU A 295 1 9 HELIX 16 16 PRO A 296 GLU A 298 5 3 HELIX 17 17 ALA A 299 ALA A 308 1 10 HELIX 18 18 TYR A 348 PHE A 353 1 6 HELIX 19 19 PRO A 354 ASP A 357 5 4 HELIX 20 20 GLY A 370 SER A 380 1 11 HELIX 21 21 SER A 385 GLY A 402 1 18 HELIX 22 22 GLY A 425 HIS A 440 1 16 HELIX 23 23 ALA A 455 THR A 473 1 19 SHEET 1 A 5 SER A 250 LEU A 252 0 SHEET 2 A 5 LYS A 29 VAL A 33 1 N LEU A 32 O SER A 250 SHEET 3 A 5 THR A 4 LEU A 8 1 N VAL A 5 O LYS A 29 SHEET 4 A 5 HIS A 281 SER A 284 1 O ILE A 283 N LEU A 8 SHEET 5 A 5 LEU A 444 LEU A 446 1 O THR A 445 N SER A 284 SHEET 1 B 2 SER A 45 ARG A 47 0 SHEET 2 B 2 ILE A 53 GLU A 55 -1 O PHE A 54 N VAL A 46 SHEET 1 C 2 VAL A 84 VAL A 87 0 SHEET 2 C 2 GLN A 226 LEU A 229 -1 O SER A 228 N LEU A 85 SHEET 1 D 7 ALA A 104 ALA A 107 0 SHEET 2 D 7 ARG A 97 VAL A 101 -1 N LEU A 99 O HIS A 106 SHEET 3 D 7 GLY A 332 LEU A 334 1 O LEU A 334 N TYR A 100 SHEET 4 D 7 VAL A 343 VAL A 347 -1 O ILE A 346 N HIS A 333 SHEET 5 D 7 LEU A 363 LEU A 369 -1 O MET A 368 N GLY A 345 SHEET 6 D 7 ALA A 311 TYR A 321 -1 N VAL A 317 O VAL A 367 SHEET 7 D 7 HIS A 409 PRO A 420 -1 O HIS A 415 N VAL A 314 SHEET 1 E 3 GLY A 259 LEU A 262 0 SHEET 2 E 3 TRP A 268 SER A 271 -1 O SER A 271 N GLY A 259 SHEET 3 E 3 SER A 276 ALA A 279 -1 O LEU A 277 N VAL A 270 CISPEP 1 PRO A 120 PRO A 121 0 0.78 CISPEP 2 SER A 359 PRO A 360 0 -0.14 SITE 1 AC1 17 ARG A 97 ARG A 168 GLY A 169 VAL A 170 SITE 2 AC1 17 ALA A 172 PHE A 331 GLY A 332 HIS A 333 SITE 3 AC1 17 LEU A 334 LEU A 344 GLY A 345 VAL A 347 SITE 4 AC1 17 MET A 368 ILE A 419 FAD A 479 HOH A 530 SITE 5 AC1 17 HOH A 536 SITE 1 AC2 37 GLY A 9 GLY A 11 ILE A 12 SER A 13 SITE 2 AC2 37 VAL A 33 GLU A 34 SER A 35 GLY A 41 SITE 3 AC2 37 TRP A 42 LEU A 56 GLY A 57 PRO A 58 SITE 4 AC2 37 ARG A 59 GLY A 60 PRO A 256 VAL A 257 SITE 5 AC2 37 ALA A 285 ILE A 286 VAL A 316 GLY A 448 SITE 6 AC2 37 ALA A 449 VAL A 454 ALA A 455 VAL A 456 SITE 7 AC2 37 CYS A 459 ACJ A 478 HOH A 480 HOH A 481 SITE 8 AC2 37 HOH A 484 HOH A 497 HOH A 510 HOH A 531 SITE 9 AC2 37 HOH A 533 HOH A 535 HOH A 541 HOH A 615 SITE 10 AC2 37 HOH A 625 SITE 1 AC3 5 GLY A 425 GLN A 428 LYS A 429 SER A 432 SITE 2 AC3 5 HOH A 729 SITE 1 AC4 6 ALA A 214 TRP A 427 ARG A 434 GLU A 452 SITE 2 AC4 6 HOH A 492 HOH A 548 CRYST1 136.702 136.702 158.877 90.00 90.00 120.00 H 3 2 18 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 0.007315 0.004223 0.000000 0.00000 SCALE2 0.000000 0.008447 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006294 0.00000