HEADER OXIDOREDUCTASE 22-MAY-13 4KVK TITLE CRYSTAL STRUCTURE OF ORYZA SATIVA FATTY ACID ALPHA-DIOXYGENASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: FATTY ACID ALPHA-OXIDASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ORYZA SATIVA; SOURCE 3 ORGANISM_COMMON: RED RICE; SOURCE 4 ORGANISM_TAXID: 4530; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PIOX, COX-LIKE PROTEIN, FATTY ACID ALPHA-DIOXYGENASE, HEME BINDING, KEYWDS 2 CALCIUM BINDING, MONOTOPIC MEMBRANE PROTEIN, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR G.ZHU,M.KOSZELAK-ROSENBLUM,M.G.MALKOWSKI REVDAT 5 28-FEB-24 4KVK 1 REMARK SEQADV LINK REVDAT 4 15-NOV-17 4KVK 1 REMARK REVDAT 3 16-OCT-13 4KVK 1 JRNL REVDAT 2 28-AUG-13 4KVK 1 JRNL REVDAT 1 21-AUG-13 4KVK 0 JRNL AUTH G.ZHU,M.KOSZELAK-ROSENBLUM,M.G.MALKOWSKI JRNL TITL CRYSTAL STRUCTURES OF ALPHA-DIOXYGENASE FROM ORYZA SATIVA: JRNL TITL 2 INSIGHTS INTO SUBSTRATE BINDING AND ACTIVATION BY HYDROGEN JRNL TITL 3 PEROXIDE. JRNL REF PROTEIN SCI. V. 22 1432 2013 JRNL REFN ISSN 0961-8368 JRNL PMID 23934749 JRNL DOI 10.1002/PRO.2327 REMARK 2 REMARK 2 RESOLUTION. 1.98 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 1.98 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 106.27 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 58757 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) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.192 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3133 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) : 1.98 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.03 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4294 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.96 REMARK 3 BIN R VALUE (WORKING SET) : 0.2290 REMARK 3 BIN FREE R VALUE SET COUNT : 242 REMARK 3 BIN FREE R VALUE : 0.2610 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4913 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 176 REMARK 3 SOLVENT ATOMS : 470 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.44 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.24000 REMARK 3 B22 (A**2) : 0.36000 REMARK 3 B33 (A**2) : -0.60000 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): 0.133 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.120 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.084 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.526 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.959 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5340 ; 0.008 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7214 ; 1.050 ; 1.996 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 642 ; 5.383 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 254 ;33.073 ;23.976 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 913 ;13.743 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 36 ;16.258 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 755 ; 0.075 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4030 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 3113 ; 0.980 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5031 ; 1.744 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2227 ; 2.839 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2170 ; 4.394 ; 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 8 A 701 REMARK 3 ORIGIN FOR THE GROUP (A): 24.3982 41.4209 67.9962 REMARK 3 T TENSOR REMARK 3 T11: 0.0689 T22: 0.0771 REMARK 3 T33: 0.0608 T12: -0.0088 REMARK 3 T13: 0.0014 T23: -0.0348 REMARK 3 L TENSOR REMARK 3 L11: 0.2307 L22: 0.2268 REMARK 3 L33: 0.4241 L12: 0.0329 REMARK 3 L13: 0.0918 L23: 0.2049 REMARK 3 S TENSOR REMARK 3 S11: 0.0540 S12: 0.0068 S13: 0.0114 REMARK 3 S21: 0.0371 S22: -0.0931 S23: -0.0164 REMARK 3 S31: 0.1013 S32: -0.0836 S33: 0.0391 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 4KVK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-JUN-13. REMARK 100 THE DEPOSITION ID IS D_1000079848. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JUL-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.1 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID 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 : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AUTOPROC, SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 61897 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.980 REMARK 200 RESOLUTION RANGE LOW (A) : 106.270 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.98 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.08 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : 0.51600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 45% PEG 400, 0.2M LITHIUM CHLORIDE, REMARK 280 0.1M SODIUM CITRATE, PH 6.1, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 300K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 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+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 0.00000 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 0.00000 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 36.23000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 64.29150 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 94.37000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 36.23000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 64.29150 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 94.37000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 36.23000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 64.29150 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 94.37000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 36.23000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 64.29150 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 94.37000 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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 A1251 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 MET A -2 REMARK 465 ARG A -1 REMARK 465 GLY A 0 REMARK 465 SER A 1 REMARK 465 HIS A 2 REMARK 465 HIS A 3 REMARK 465 HIS A 4 REMARK 465 HIS A 5 REMARK 465 HIS A 6 REMARK 465 HIS A 7 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 O HOH A 850 O HOH A 1252 1.95 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 SER A 72 32.40 -78.83 REMARK 500 HIS A 73 105.50 -55.64 REMARK 500 ALA A 75 101.81 -26.15 REMARK 500 ASN A 92 -61.41 -91.26 REMARK 500 ARG A 135 -103.33 -103.82 REMARK 500 ARG A 135 -105.23 -102.07 REMARK 500 TRP A 213 82.21 -67.99 REMARK 500 ASN A 221 -80.24 -50.67 REMARK 500 ASN A 222 146.27 175.28 REMARK 500 ASN A 222 -154.86 -124.83 REMARK 500 GLU A 224 -32.29 174.22 REMARK 500 ASP A 314 -68.33 -126.25 REMARK 500 LEU A 320 79.17 -114.52 REMARK 500 ASP A 399 -167.79 -78.78 REMARK 500 ASN A 448 23.71 -143.31 REMARK 500 ASN A 455 56.90 -141.95 REMARK 500 THR A 567 -95.50 -129.32 REMARK 500 THR A 576 157.26 74.10 REMARK 500 ASP A 617 36.27 -86.63 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 HEM A 701 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 157 NE2 REMARK 620 2 HEM A 701 NA 90.6 REMARK 620 3 HEM A 701 NB 95.3 90.3 REMARK 620 4 HEM A 701 NC 88.4 178.4 88.5 REMARK 620 5 HEM A 701 ND 85.4 89.4 179.3 91.8 REMARK 620 6 HIS A 382 NE2 173.6 95.3 87.3 85.8 92.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 712 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 210 OG1 REMARK 620 2 TRP A 212 O 95.0 REMARK 620 3 ASP A 214 OD1 77.6 80.3 REMARK 620 4 SER A 216 OG 93.2 157.7 81.3 REMARK 620 5 HOH A 874 O 166.2 79.7 88.9 87.5 REMARK 620 6 HOH A1085 O 86.8 126.1 150.7 75.0 106.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 717 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 505 O REMARK 620 2 1PE A 705 OH3 76.2 REMARK 620 3 HOH A 980 O 87.8 142.4 REMARK 620 4 HOH A 981 O 137.8 77.9 131.4 REMARK 620 5 HOH A1117 O 124.8 99.7 62.0 92.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 718 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 608 OG REMARK 620 2 PG4 A 707 O4 61.8 REMARK 620 3 PG4 A 707 O2 84.4 104.6 REMARK 620 4 HOH A1228 O 67.5 121.5 97.3 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMU A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PG4 A 703 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 704 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 1PE A 705 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGE A 706 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PG4 A 707 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 708 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PG4 A 709 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 710 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 711 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 712 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 713 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 714 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 715 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 716 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 717 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 718 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4KVJ RELATED DB: PDB REMARK 900 RELATED ID: 4KVL RELATED DB: PDB DBREF 4KVK A 10 618 UNP Q9M5J1 Q9M5J1_ORYSA 10 618 SEQADV 4KVK MET A -2 UNP Q9M5J1 EXPRESSION TAG SEQADV 4KVK ARG A -1 UNP Q9M5J1 EXPRESSION TAG SEQADV 4KVK GLY A 0 UNP Q9M5J1 EXPRESSION TAG SEQADV 4KVK SER A 1 UNP Q9M5J1 EXPRESSION TAG SEQADV 4KVK HIS A 2 UNP Q9M5J1 EXPRESSION TAG SEQADV 4KVK HIS A 3 UNP Q9M5J1 EXPRESSION TAG SEQADV 4KVK HIS A 4 UNP Q9M5J1 EXPRESSION TAG SEQADV 4KVK HIS A 5 UNP Q9M5J1 EXPRESSION TAG SEQADV 4KVK HIS A 6 UNP Q9M5J1 EXPRESSION TAG SEQADV 4KVK HIS A 7 UNP Q9M5J1 EXPRESSION TAG SEQADV 4KVK GLY A 8 UNP Q9M5J1 EXPRESSION TAG SEQADV 4KVK SER A 9 UNP Q9M5J1 EXPRESSION TAG SEQRES 1 A 621 MET ARG GLY SER HIS HIS HIS HIS HIS HIS GLY SER VAL SEQRES 2 A 621 HIS PRO ASP LEU ARG ASP VAL PHE SER LYS MET SER PHE SEQRES 3 A 621 PHE ASP LYS ILE GLY PHE LEU PHE ILE HIS ALA PHE ASP SEQRES 4 A 621 LYS ARG ASN LEU TRP HIS LYS VAL PRO VAL PRO ILE GLY SEQRES 5 A 621 LEU LEU TYR LEU ASN THR ARG ARG THR LEU LEU GLU LYS SEQRES 6 A 621 TYR ASN LEU LEU ALA VAL GLY ARG SER SER HIS GLY ALA SEQRES 7 A 621 LEU PHE ASP PRO LYS GLU PHE LEU TYR ARG THR GLU ASP SEQRES 8 A 621 GLY LYS TYR ASN ASP PRO HIS ASN ALA GLU ALA GLY SER SEQRES 9 A 621 GLN ASN THR PHE PHE GLY ARG ASN MET GLU PRO VAL ASP SEQRES 10 A 621 GLN GLN ASP GLU LEU MET SER PRO ASP PRO PHE VAL VAL SEQRES 11 A 621 ALA THR LYS LEU LEU ALA ARG ARG GLU TYR LYS ASP THR SEQRES 12 A 621 GLY LYS GLN PHE ASN ILE LEU ALA ALA ALA TRP ILE GLN SEQRES 13 A 621 PHE MET VAL HIS ASP TRP MET ASP HIS MET GLU ASP THR SEQRES 14 A 621 GLY GLN ILE GLY ILE THR ALA PRO LYS GLU VAL ALA ASN SEQRES 15 A 621 GLU CYS PRO LEU LYS SER PHE LYS PHE HIS PRO THR LYS SEQRES 16 A 621 GLU LEU PRO THR ASN SER ASP GLY ILE LYS ILE GLY HIS SEQRES 17 A 621 TYR ASN ILE ARG THR ALA TRP TRP ASP GLY SER ALA VAL SEQRES 18 A 621 TYR GLY ASN ASN GLU GLU ARG ALA GLU LYS LEU ARG THR SEQRES 19 A 621 TYR VAL ASP GLY LYS LEU VAL ILE GLY ASP ASP GLY LEU SEQRES 20 A 621 LEU LEU HIS LYS GLU ASN GLY VAL ALA LEU SER GLY ASP SEQRES 21 A 621 ILE ARG ASN SER TRP ALA GLY VAL SER ILE LEU GLN ALA SEQRES 22 A 621 LEU PHE VAL LYS GLU HIS ASN ALA VAL CYS ASP ALA ILE SEQRES 23 A 621 LYS GLU GLU HIS PRO ASN LEU SER ASP GLU GLU LEU TYR SEQRES 24 A 621 ARG TYR ALA LYS LEU VAL THR SER ALA VAL ILE ALA LYS SEQRES 25 A 621 VAL HIS THR ILE ASP TRP THR VAL GLU LEU LEU LYS THR SEQRES 26 A 621 LYS THR MET ARG ALA ALA MET ARG ALA ASN TRP TYR GLY SEQRES 27 A 621 LEU LEU GLY LYS LYS ILE LYS ASP THR PHE GLY HIS ILE SEQRES 28 A 621 GLY GLY PRO ILE LEU GLY GLY LEU VAL GLY LEU LYS LYS SEQRES 29 A 621 PRO ASN ASN HIS GLY VAL PRO TYR SER LEU THR GLU GLU SEQRES 30 A 621 PHE THR SER VAL TYR ARG MET HIS SER LEU ILE PRO SER SEQRES 31 A 621 THR LEU LYS LEU ARG ASP PRO THR GLY GLN PRO ASP ALA SEQRES 32 A 621 ASN ASN SER PRO PRO CYS LEU GLU ASP ILE ASP ILE GLY SEQRES 33 A 621 GLU MET ILE GLY LEU LYS GLY GLU GLU GLN LEU SER LYS SEQRES 34 A 621 ILE GLY PHE GLU LYS GLN ALA LEU SER MET GLY TYR GLN SEQRES 35 A 621 ALA CYS GLY ALA LEU GLU LEU TRP ASN TYR PRO SER PHE SEQRES 36 A 621 PHE ARG ASN LEU ILE PRO GLN ASN LEU ASP GLY THR ASN SEQRES 37 A 621 ARG SER ASP ARG ILE ASP LEU ALA ALA LEU GLU VAL TYR SEQRES 38 A 621 ARG ASP ARG GLU ARG SER VAL PRO ARG TYR ASN GLU PHE SEQRES 39 A 621 ARG ARG ARG LEU PHE LEU ILE PRO ILE LYS SER TRP GLU SEQRES 40 A 621 ASP LEU THR SER ASP LYS ASP ALA ILE GLU THR ILE ARG SEQRES 41 A 621 ALA ILE TYR GLY ASP ASP VAL GLU LYS LEU ASP LEU LEU SEQRES 42 A 621 VAL GLY LEU MET ALA GLU LYS LYS ILE LYS GLY PHE ALA SEQRES 43 A 621 ILE SER GLU THR ALA PHE ASN ILE PHE ILE LEU MET ALA SEQRES 44 A 621 SER ARG ARG LEU GLU ALA ASP ARG PHE PHE THR SER ASN SEQRES 45 A 621 PHE ASN GLU GLU THR TYR THR LYS LYS GLY MET GLN TRP SEQRES 46 A 621 VAL LYS THR THR GLU GLY LEU ARG ASP VAL ILE ASN ARG SEQRES 47 A 621 HIS TYR PRO GLU ILE THR ALA LYS TRP MET LYS SER SER SEQRES 48 A 621 SER ALA PHE SER VAL TRP ASP ALA ASP TYR HET HEM A 701 43 HET DMU A 702 33 HET PG4 A 703 13 HET PEG A 704 7 HET 1PE A 705 16 HET PGE A 706 10 HET PG4 A 707 13 HET PEG A 708 7 HET PG4 A 709 13 HET PEG A 710 7 HET PEG A 711 7 HET CA A 712 1 HET CL A 713 1 HET CL A 714 1 HET CL A 715 1 HET CL A 716 1 HET NA A 717 1 HET NA A 718 1 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM DMU DECYL-BETA-D-MALTOPYRANOSIDE HETNAM PG4 TETRAETHYLENE GLYCOL HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM 1PE PENTAETHYLENE GLYCOL HETNAM PGE TRIETHYLENE GLYCOL HETNAM CA CALCIUM ION HETNAM CL CHLORIDE ION HETNAM NA SODIUM ION HETSYN HEM HEME HETSYN DMU DECYLMALTOSIDE HETSYN 1PE PEG400 FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 DMU C22 H42 O11 FORMUL 4 PG4 3(C8 H18 O5) FORMUL 5 PEG 4(C4 H10 O3) FORMUL 6 1PE C10 H22 O6 FORMUL 7 PGE C6 H14 O4 FORMUL 13 CA CA 2+ FORMUL 14 CL 4(CL 1-) FORMUL 18 NA 2(NA 1+) FORMUL 20 HOH *470(H2 O) HELIX 1 1 HIS A 11 ASP A 13 5 3 HELIX 2 2 LEU A 14 MET A 21 1 8 HELIX 3 3 SER A 22 ARG A 38 1 17 HELIX 4 4 ASN A 39 VAL A 44 5 6 HELIX 5 5 PRO A 45 ASN A 64 1 20 HELIX 6 6 ASP A 78 PHE A 82 5 5 HELIX 7 7 ASP A 123 LEU A 132 1 10 HELIX 8 8 ASN A 145 MET A 160 1 16 HELIX 9 9 PRO A 174 ASN A 179 1 6 HELIX 10 10 GLY A 215 GLY A 220 1 6 HELIX 11 11 TRP A 262 HIS A 287 1 26 HELIX 12 12 SER A 291 ASP A 314 1 24 HELIX 13 13 ASP A 314 LEU A 320 1 7 HELIX 14 14 THR A 322 GLY A 335 1 14 HELIX 15 15 GLY A 338 GLY A 346 1 9 HELIX 16 16 THR A 372 TYR A 379 1 8 HELIX 17 17 ARG A 380 ILE A 385 5 6 HELIX 18 18 GLY A 413 MET A 415 5 3 HELIX 19 19 ILE A 416 GLY A 428 1 13 HELIX 20 20 GLY A 428 TYR A 438 1 11 HELIX 21 21 PRO A 450 LEU A 456 5 7 HELIX 22 22 ASP A 471 ARG A 483 1 13 HELIX 23 23 ARG A 487 LEU A 495 1 9 HELIX 24 24 SER A 502 LEU A 506 5 5 HELIX 25 25 ASP A 509 GLY A 521 1 13 HELIX 26 26 ASP A 528 GLU A 536 1 9 HELIX 27 27 SER A 545 ALA A 562 1 18 HELIX 28 28 ASP A 563 THR A 567 5 5 HELIX 29 29 ASN A 571 THR A 576 1 6 HELIX 30 30 THR A 576 THR A 585 1 10 HELIX 31 31 GLY A 588 TYR A 597 1 10 HELIX 32 32 TYR A 597 MET A 605 1 9 SHEET 1 A 2 THR A 104 PHE A 105 0 SHEET 2 A 2 TYR A 206 ASN A 207 -1 O ASN A 207 N THR A 104 SHEET 1 B 2 ILE A 169 THR A 172 0 SHEET 2 B 2 SER A 185 PHE A 188 -1 O PHE A 188 N ILE A 169 SHEET 1 C 2 LEU A 194 PRO A 195 0 SHEET 2 C 2 ILE A 203 GLY A 204 -1 O GLY A 204 N LEU A 194 SHEET 1 D 2 THR A 388 ARG A 392 0 SHEET 2 D 2 CYS A 406 ASP A 411 -1 O LEU A 407 N LEU A 391 LINK NE2 HIS A 157 FE HEM A 701 1555 1555 2.11 LINK OG1 THR A 210 CA CA A 712 1555 1555 2.58 LINK O TRP A 212 CA CA A 712 1555 1555 2.90 LINK OD1 ASP A 214 CA CA A 712 1555 1555 2.36 LINK OG SER A 216 CA CA A 712 1555 1555 2.60 LINK NE2 HIS A 382 FE HEM A 701 1555 1555 2.07 LINK O ASP A 505 NA NA A 717 1555 1555 2.69 LINK OG ASER A 608 NA NA A 718 1555 1555 3.12 LINK OH3 1PE A 705 NA NA A 717 1555 1555 3.10 LINK O4 PG4 A 707 NA NA A 718 1555 1555 3.04 LINK O2 PG4 A 707 NA NA A 718 1555 1555 3.07 LINK CA CA A 712 O HOH A 874 1555 1555 2.53 LINK CA CA A 712 O HOH A1085 1555 1555 2.26 LINK NA NA A 717 O HOH A 980 1555 1555 2.43 LINK NA NA A 717 O HOH A 981 1555 1555 2.42 LINK NA NA A 717 O HOH A1117 1555 1555 2.64 LINK NA NA A 718 O HOH A1228 1555 1555 2.71 CISPEP 1 SER A 121 PRO A 122 0 -6.43 CISPEP 2 SER A 121 PRO A 122 0 -6.24 SITE 1 AC1 23 ALA A 149 ILE A 152 GLN A 153 VAL A 156 SITE 2 AC1 23 HIS A 157 ASP A 161 HIS A 162 ASN A 260 SITE 3 AC1 23 TRP A 262 THR A 376 TYR A 379 MET A 381 SITE 4 AC1 23 HIS A 382 ILE A 416 PHE A 453 LEU A 472 SITE 5 AC1 23 LEU A 475 ARG A 479 ARG A 483 HOH A 815 SITE 6 AC1 23 HOH A 843 HOH A 996 HOH A1180 SITE 1 AC2 13 SER A 19 LYS A 20 MET A 21 SER A 22 SITE 2 AC2 13 PHE A 23 LYS A 26 PHE A 31 ARG A 38 SITE 3 AC2 13 ILE A 348 PG4 A 709 HOH A 829 HOH A 928 SITE 4 AC2 13 HOH A1055 SITE 1 AC3 2 ASN A 54 ARG A 57 SITE 1 AC4 1 PHE A 24 SITE 1 AC5 13 ASN A 39 HIS A 42 LYS A 43 ARG A 492 SITE 2 AC5 13 ILE A 498 PRO A 499 ILE A 500 ASP A 505 SITE 3 AC5 13 GLU A 536 NA A 717 HOH A 832 HOH A1029 SITE 4 AC5 13 HOH A1117 SITE 1 AC6 4 GLU A 490 ARG A 493 ARG A 494 PHE A 496 SITE 1 AC7 5 ARG A 590 LYS A 606 SER A 608 TYR A 618 SITE 2 AC7 5 NA A 718 SITE 1 AC8 5 ILE A 239 GLY A 240 ASP A 241 GLY A 243 SITE 2 AC8 5 LYS A 274 SITE 1 AC9 5 ALA A 34 PHE A 35 ARG A 38 DMU A 702 SITE 2 AC9 5 HOH A1119 SITE 1 BC1 4 LYS A 323 ARG A 326 HOH A1023 HOH A1028 SITE 1 BC2 3 ARG A 517 ALA A 518 ILE A 519 SITE 1 BC3 6 THR A 210 TRP A 212 ASP A 214 SER A 216 SITE 2 BC3 6 HOH A 874 HOH A1085 SITE 1 BC4 3 LYS A 309 TRP A 333 HOH A1132 SITE 1 BC5 3 ARG A 330 LYS A 339 HOH A 954 SITE 1 BC6 4 GLY A 350 ILE A 352 LEU A 353 HOH A 922 SITE 1 BC7 2 HIS A 311 TYR A 379 SITE 1 BC8 5 ASP A 505 1PE A 705 HOH A 980 HOH A 981 SITE 2 BC8 5 HOH A1117 SITE 1 BC9 3 SER A 608 PG4 A 707 HOH A1228 CRYST1 72.460 128.583 188.740 90.00 90.00 90.00 I 2 2 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 0.013801 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007777 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005298 0.00000