HEADER OXIDOREDUCTASE 21-AUG-12 4GPH TITLE STRUCTURE OF HMUO, HEME OXYGENASE FROM CORYNEBACTERIUM DIPHTHERIAE, IN TITLE 2 COMPLEX WITH THE PUTATIVE REACTION INTERMEDIATES BETWEEN FE3+- TITLE 3 BILIVERDIN AND BILIVERDIN (DATA SET IV) COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEME OXYGENASE; COMPND 3 CHAIN: A, B, C; COMPND 4 EC: 1.14.99.3; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CORYNEBACTERIUM DIPHTHERIAE; SOURCE 3 ORGANISM_TAXID: 1717; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HELIX, HEME DEGRADATION, HEME, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR M.UNNO,M.IKEDA-SAITO REVDAT 3 20-MAR-24 4GPH 1 HETSYN REVDAT 2 29-JUL-20 4GPH 1 REMARK SITE REVDAT 1 21-AUG-13 4GPH 0 JRNL AUTH M.UNNO,A.ARDEVOL,C.ROVIRA,M.IKEDA-SAITO JRNL TITL CRYSTAL STRUCTURES OF THE SUBSTRATE-FREE AND THE JRNL TITL 2 PRODUCT-BOUND FORMS OF HMUO, A HEME OXYGENASE FROM JRNL TITL 3 CORYNEBACTERIUM DIPHTHERIAE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 69486 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) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 7805 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4899 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.59 REMARK 3 BIN R VALUE (WORKING SET) : 0.2770 REMARK 3 BIN FREE R VALUE SET COUNT : 538 REMARK 3 BIN FREE R VALUE : 0.3260 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4961 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 183 REMARK 3 SOLVENT ATOMS : 473 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.93 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.38000 REMARK 3 B22 (A**2) : 0.73000 REMARK 3 B33 (A**2) : -0.22000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.37000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.103 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.104 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.060 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.953 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.955 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5361 ; 0.028 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7281 ; 2.336 ; 2.096 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 627 ; 5.352 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 271 ;33.476 ;23.764 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 848 ;14.250 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 44 ;18.332 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 753 ; 0.171 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4186 ; 0.027 ; 0.022 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): 3122 ; 1.388 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4949 ; 2.258 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2239 ; 3.591 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2332 ; 5.553 ; 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 : 6 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 5 A 213 REMARK 3 ORIGIN FOR THE GROUP (A): 23.8680 0.7260 0.0260 REMARK 3 T TENSOR REMARK 3 T11: 0.0533 T22: 0.0559 REMARK 3 T33: 0.0297 T12: 0.0166 REMARK 3 T13: 0.0028 T23: -0.0203 REMARK 3 L TENSOR REMARK 3 L11: 1.5182 L22: 2.3841 REMARK 3 L33: 1.6940 L12: 0.2232 REMARK 3 L13: 0.6378 L23: 0.2842 REMARK 3 S TENSOR REMARK 3 S11: 0.1646 S12: 0.0381 S13: -0.0992 REMARK 3 S21: -0.0414 S22: -0.1684 S23: 0.0112 REMARK 3 S31: 0.0009 S32: 0.0459 S33: 0.0039 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 307 B 514 REMARK 3 ORIGIN FOR THE GROUP (A): 7.8410 16.0670 27.6770 REMARK 3 T TENSOR REMARK 3 T11: 0.0352 T22: 0.0899 REMARK 3 T33: 0.0147 T12: 0.0044 REMARK 3 T13: 0.0176 T23: 0.0122 REMARK 3 L TENSOR REMARK 3 L11: 1.3977 L22: 0.9028 REMARK 3 L33: 0.8966 L12: 0.4740 REMARK 3 L13: -0.1153 L23: 0.0452 REMARK 3 S TENSOR REMARK 3 S11: -0.0479 S12: 0.1461 S13: -0.0511 REMARK 3 S21: -0.1219 S22: 0.0834 S23: -0.0246 REMARK 3 S31: -0.0720 S32: -0.0487 S33: -0.0354 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 603 C 813 REMARK 3 ORIGIN FOR THE GROUP (A): 29.7480 5.8280 51.4260 REMARK 3 T TENSOR REMARK 3 T11: 0.0242 T22: 0.0971 REMARK 3 T33: 0.0376 T12: 0.0034 REMARK 3 T13: 0.0054 T23: 0.0303 REMARK 3 L TENSOR REMARK 3 L11: 1.1786 L22: 0.5187 REMARK 3 L33: 0.6586 L12: -0.2222 REMARK 3 L13: -0.2025 L23: -0.2988 REMARK 3 S TENSOR REMARK 3 S11: -0.0765 S12: -0.1377 S13: -0.0219 REMARK 3 S21: 0.0793 S22: -0.0266 S23: -0.0736 REMARK 3 S31: -0.0134 S32: 0.0893 S33: 0.1032 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 3002 A 3002 REMARK 3 ORIGIN FOR THE GROUP (A): 24.7880 -9.4730 0.8460 REMARK 3 T TENSOR REMARK 3 T11: 0.3114 T22: 0.1173 REMARK 3 T33: 0.3817 T12: 0.0286 REMARK 3 T13: -0.1300 T23: -0.1687 REMARK 3 L TENSOR REMARK 3 L11: 71.2262 L22: 22.5269 REMARK 3 L33: 49.7770 L12: -0.1442 REMARK 3 L13: 15.3723 L23: 2.8799 REMARK 3 S TENSOR REMARK 3 S11: 2.1074 S12: 2.5101 S13: -4.3620 REMARK 3 S21: -0.5150 S22: -0.4962 S23: -0.0113 REMARK 3 S31: 2.8875 S32: -0.2240 S33: -1.6113 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 601 B 601 REMARK 3 ORIGIN FOR THE GROUP (A): 5.7510 19.0070 17.5160 REMARK 3 T TENSOR REMARK 3 T11: 1.2145 T22: 3.0561 REMARK 3 T33: 1.4544 T12: -0.9605 REMARK 3 T13: -0.5663 T23: 0.8268 REMARK 3 L TENSOR REMARK 3 L11: 50.9326 L22: 31.2219 REMARK 3 L33: 2.9628 L12: 39.8138 REMARK 3 L13: -2.5222 L23: -2.1348 REMARK 3 S TENSOR REMARK 3 S11: -2.0966 S12: 2.3320 S13: 1.5641 REMARK 3 S21: -1.5349 S22: 1.1936 S23: 1.1431 REMARK 3 S31: -1.2809 S32: 2.4751 S33: 0.9030 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 902 C 902 REMARK 3 ORIGIN FOR THE GROUP (A): 31.5460 0.9470 59.8980 REMARK 3 T TENSOR REMARK 3 T11: 0.2221 T22: 0.2167 REMARK 3 T33: 0.2079 T12: -0.1199 REMARK 3 T13: 0.1806 T23: -0.0352 REMARK 3 L TENSOR REMARK 3 L11: 15.9363 L22: 5.0825 REMARK 3 L33: 13.7479 L12: 1.5936 REMARK 3 L13: 0.5845 L23: -8.1298 REMARK 3 S TENSOR REMARK 3 S11: -0.0379 S12: -0.3434 S13: 0.4204 REMARK 3 S21: -0.1782 S22: -0.0241 S23: 0.0921 REMARK 3 S31: 0.4412 S32: -0.1141 S33: 0.0619 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 4GPH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-AUG-12. REMARK 100 THE DEPOSITION ID IS D_1000074474. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-APR-05 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 : SPRING-8 REMARK 200 BEAMLINE : BL38B1 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 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU JUPITER 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 77319 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 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 (%) : 98.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL 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 (%) : 95.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, MES, PH 6.1, VAPOR REMARK 280 DIFFUSION, TEMPERATURE 303K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 31.48300 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 350 REMARK 350 BIOMOLECULE: 2 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: 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: 3 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: C 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 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 THR A 2 REMARK 465 THR A 3 REMARK 465 ALA A 4 REMARK 465 GLY A 214 REMARK 465 LEU A 215 REMARK 465 MET B 301 REMARK 465 THR B 302 REMARK 465 THR B 303 REMARK 465 ALA B 304 REMARK 465 THR B 305 REMARK 465 ALA B 306 REMARK 465 MET C 601 REMARK 465 THR C 602 REMARK 465 LEU C 815 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 THR A 5 OG1 CG2 REMARK 470 LYS A 22 CG CD CE NZ REMARK 470 GLU A 81 CG CD OE1 OE2 REMARK 470 LYS A 170 CG CD CE NZ REMARK 470 GLU B 321 CG CD OE1 OE2 REMARK 470 LYS B 322 CG CD CE NZ REMARK 470 GLU B 456 CG CD OE1 OE2 REMARK 470 GLU B 478 CG CD OE1 OE2 REMARK 470 THR C 603 OG1 CG2 REMARK 470 LYS C 622 CG CD CE NZ REMARK 470 GLU C 756 CG CD OE1 OE2 REMARK 470 GLU C 764 CG CD OE1 OE2 REMARK 470 LYS C 813 CG CD CE NZ 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 OD2 ASP A 118 NH2 ARG B 445 1.95 REMARK 500 O HOH C 1104 O HOH C 1146 2.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NE2 GLN A 141 O HOH B 881 2645 1.88 REMARK 500 REMARK 500 REMARK: NULL 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 GLU B 381 CG GLU B 381 CD 0.091 REMARK 500 GLU B 381 CD GLU B 381 OE1 0.095 REMARK 500 GLU B 395 CB GLU B 395 CG 0.122 REMARK 500 TYR B 409 CD1 TYR B 409 CE1 0.125 REMARK 500 ARG B 432 CZ ARG B 432 NH2 0.114 REMARK 500 GLU C 681 CG GLU C 681 CD 0.111 REMARK 500 GLU C 681 CD GLU C 681 OE1 0.120 REMARK 500 GLU C 791 CG GLU C 791 CD 0.109 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 44 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 97 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 TYR A 109 CB - CG - CD2 ANGL. DEV. = -4.2 DEGREES REMARK 500 ARG A 112 NE - CZ - NH1 ANGL. DEV. = -6.8 DEGREES REMARK 500 ARG A 112 NE - CZ - NH2 ANGL. DEV. = 5.3 DEGREES REMARK 500 ASP B 408 CB - CG - OD1 ANGL. DEV. = -5.8 DEGREES REMARK 500 TYR B 409 CB - CG - CD2 ANGL. DEV. = -4.0 DEGREES REMARK 500 ASP B 421 CB - CG - OD2 ANGL. DEV. = -6.8 DEGREES REMARK 500 ASP B 436 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG B 445 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG B 445 NE - CZ - NH2 ANGL. DEV. = -4.3 DEGREES REMARK 500 ASP B 454 CB - CG - OD1 ANGL. DEV. = 7.7 DEGREES REMARK 500 ARG B 490 CG - CD - NE ANGL. DEV. = -17.0 DEGREES REMARK 500 ARG B 490 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG B 490 NE - CZ - NH2 ANGL. DEV. = -4.6 DEGREES REMARK 500 ASP B 510 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 MET C 629 CG - SD - CE ANGL. DEV. = -13.1 DEGREES REMARK 500 ARG C 644 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 PHE C 652 CB - CG - CD2 ANGL. DEV. = -5.0 DEGREES REMARK 500 ARG C 699 NE - CZ - NH1 ANGL. DEV. = -5.5 DEGREES REMARK 500 ASP C 708 CB - CG - OD1 ANGL. DEV. = 6.4 DEGREES REMARK 500 ASP C 708 CB - CG - OD2 ANGL. DEV. = -6.7 DEGREES REMARK 500 ARG C 717 NE - CZ - NH1 ANGL. DEV. = -3.2 DEGREES REMARK 500 ASP C 721 CB - CG - OD2 ANGL. DEV. = -7.1 DEGREES REMARK 500 ARG C 777 NE - CZ - NH2 ANGL. DEV. = -4.1 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 LEU A 37 -136.05 -107.00 REMARK 500 ALA A 167 -76.25 -89.05 REMARK 500 LEU B 337 -125.65 -103.10 REMARK 500 ALA C 606 147.17 83.42 REMARK 500 LEU C 637 -128.61 -104.99 REMARK 500 LYS C 768 78.83 -112.64 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 FE A3001 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 BLA A3002 NA REMARK 620 2 BLA A3002 NB 105.7 REMARK 620 3 BLA A3002 NC 171.0 82.9 REMARK 620 4 BLA A3002 ND 92.5 150.5 80.7 REMARK 620 5 HOH A3161 O 103.9 103.8 70.9 93.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE C 901 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 BLA C 902 NA REMARK 620 2 BLA C 902 NB 89.3 REMARK 620 3 BLA C 902 NC 151.1 99.1 REMARK 620 4 BLA C 902 ND 94.3 168.6 82.9 REMARK 620 5 ASC C 903 O3 84.3 103.4 66.9 87.7 REMARK 620 N 1 2 3 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1IW0 RELATED DB: PDB REMARK 900 RELATED ID: 1IW1 RELATED DB: PDB REMARK 900 RELATED ID: 4GOH RELATED DB: PDB REMARK 900 RELATED ID: 4GPC RELATED DB: PDB REMARK 900 RELATED ID: 4GPF RELATED DB: PDB DBREF 4GPH A 1 215 UNP Q54AI1 Q54AI1_CORDP 1 215 DBREF 4GPH B 301 515 UNP Q54AI1 Q54AI1_CORDP 1 215 DBREF 4GPH C 601 815 UNP Q54AI1 Q54AI1_CORDP 1 215 SEQRES 1 A 215 MET THR THR ALA THR ALA GLY LEU ALA VAL GLU LEU LYS SEQRES 2 A 215 GLN SER THR ALA GLN ALA HIS GLU LYS ALA GLU HIS SER SEQRES 3 A 215 THR PHE MET SER ASP LEU LEU LYS GLY ARG LEU GLY VAL SEQRES 4 A 215 ALA GLU PHE THR ARG LEU GLN GLU GLN ALA TRP LEU PHE SEQRES 5 A 215 TYR THR ALA LEU GLU GLN ALA VAL ASP ALA VAL ARG ALA SEQRES 6 A 215 SER GLY PHE ALA GLU SER LEU LEU ASP PRO ALA LEU ASN SEQRES 7 A 215 ARG ALA GLU VAL LEU ALA ARG ASP LEU ASP LYS LEU ASN SEQRES 8 A 215 GLY SER SER GLU TRP ARG SER ARG ILE THR ALA SER PRO SEQRES 9 A 215 ALA VAL ILE ASP TYR VAL ASN ARG LEU GLU GLU ILE ARG SEQRES 10 A 215 ASP ASN VAL ASP GLY PRO ALA LEU VAL ALA HIS HIS TYR SEQRES 11 A 215 VAL ARG TYR LEU GLY ASP LEU SER GLY GLY GLN VAL ILE SEQRES 12 A 215 ALA ARG MET MET GLN ARG HIS TYR GLY VAL ASP PRO GLU SEQRES 13 A 215 ALA LEU GLY PHE TYR HIS PHE GLU GLY ILE ALA LYS LEU SEQRES 14 A 215 LYS VAL TYR LYS ASP GLU TYR ARG GLU LYS LEU ASN ASN SEQRES 15 A 215 LEU GLU LEU SER ASP GLU GLN ARG GLU HIS LEU LEU LYS SEQRES 16 A 215 GLU ALA THR ASP ALA PHE VAL PHE ASN HIS GLN VAL PHE SEQRES 17 A 215 ALA ASP LEU GLY LYS GLY LEU SEQRES 1 B 215 MET THR THR ALA THR ALA GLY LEU ALA VAL GLU LEU LYS SEQRES 2 B 215 GLN SER THR ALA GLN ALA HIS GLU LYS ALA GLU HIS SER SEQRES 3 B 215 THR PHE MET SER ASP LEU LEU LYS GLY ARG LEU GLY VAL SEQRES 4 B 215 ALA GLU PHE THR ARG LEU GLN GLU GLN ALA TRP LEU PHE SEQRES 5 B 215 TYR THR ALA LEU GLU GLN ALA VAL ASP ALA VAL ARG ALA SEQRES 6 B 215 SER GLY PHE ALA GLU SER LEU LEU ASP PRO ALA LEU ASN SEQRES 7 B 215 ARG ALA GLU VAL LEU ALA ARG ASP LEU ASP LYS LEU ASN SEQRES 8 B 215 GLY SER SER GLU TRP ARG SER ARG ILE THR ALA SER PRO SEQRES 9 B 215 ALA VAL ILE ASP TYR VAL ASN ARG LEU GLU GLU ILE ARG SEQRES 10 B 215 ASP ASN VAL ASP GLY PRO ALA LEU VAL ALA HIS HIS TYR SEQRES 11 B 215 VAL ARG TYR LEU GLY ASP LEU SER GLY GLY GLN VAL ILE SEQRES 12 B 215 ALA ARG MET MET GLN ARG HIS TYR GLY VAL ASP PRO GLU SEQRES 13 B 215 ALA LEU GLY PHE TYR HIS PHE GLU GLY ILE ALA LYS LEU SEQRES 14 B 215 LYS VAL TYR LYS ASP GLU TYR ARG GLU LYS LEU ASN ASN SEQRES 15 B 215 LEU GLU LEU SER ASP GLU GLN ARG GLU HIS LEU LEU LYS SEQRES 16 B 215 GLU ALA THR ASP ALA PHE VAL PHE ASN HIS GLN VAL PHE SEQRES 17 B 215 ALA ASP LEU GLY LYS GLY LEU SEQRES 1 C 215 MET THR THR ALA THR ALA GLY LEU ALA VAL GLU LEU LYS SEQRES 2 C 215 GLN SER THR ALA GLN ALA HIS GLU LYS ALA GLU HIS SER SEQRES 3 C 215 THR PHE MET SER ASP LEU LEU LYS GLY ARG LEU GLY VAL SEQRES 4 C 215 ALA GLU PHE THR ARG LEU GLN GLU GLN ALA TRP LEU PHE SEQRES 5 C 215 TYR THR ALA LEU GLU GLN ALA VAL ASP ALA VAL ARG ALA SEQRES 6 C 215 SER GLY PHE ALA GLU SER LEU LEU ASP PRO ALA LEU ASN SEQRES 7 C 215 ARG ALA GLU VAL LEU ALA ARG ASP LEU ASP LYS LEU ASN SEQRES 8 C 215 GLY SER SER GLU TRP ARG SER ARG ILE THR ALA SER PRO SEQRES 9 C 215 ALA VAL ILE ASP TYR VAL ASN ARG LEU GLU GLU ILE ARG SEQRES 10 C 215 ASP ASN VAL ASP GLY PRO ALA LEU VAL ALA HIS HIS TYR SEQRES 11 C 215 VAL ARG TYR LEU GLY ASP LEU SER GLY GLY GLN VAL ILE SEQRES 12 C 215 ALA ARG MET MET GLN ARG HIS TYR GLY VAL ASP PRO GLU SEQRES 13 C 215 ALA LEU GLY PHE TYR HIS PHE GLU GLY ILE ALA LYS LEU SEQRES 14 C 215 LYS VAL TYR LYS ASP GLU TYR ARG GLU LYS LEU ASN ASN SEQRES 15 C 215 LEU GLU LEU SER ASP GLU GLN ARG GLU HIS LEU LEU LYS SEQRES 16 C 215 GLU ALA THR ASP ALA PHE VAL PHE ASN HIS GLN VAL PHE SEQRES 17 C 215 ALA ASP LEU GLY LYS GLY LEU HET FE A3001 1 HET BLA A3002 86 HET SO4 A3003 5 HET BLA B 601 43 HET SO4 B 602 5 HET SO4 B 603 5 HET SO4 B 604 5 HET SO4 B 605 5 HET SO4 B 606 5 HET FE C 901 1 HET BLA C 902 86 HET ASC C 903 12 HET SO4 C 904 5 HET SO4 C 905 5 HETNAM FE FE (III) ION HETNAM BLA BILIVERDINE IX ALPHA HETNAM SO4 SULFATE ION HETNAM ASC ASCORBIC ACID HETSYN ASC VITAMIN C FORMUL 4 FE 2(FE 3+) FORMUL 5 BLA 3(C33 H34 N4 O6) FORMUL 6 SO4 8(O4 S 2-) FORMUL 15 ASC C6 H8 O6 FORMUL 18 HOH *473(H2 O) HELIX 1 1 GLY A 7 THR A 16 1 10 HELIX 2 2 THR A 16 HIS A 25 1 10 HELIX 3 3 SER A 26 LYS A 34 1 9 HELIX 4 4 GLY A 38 SER A 66 1 29 HELIX 5 5 ASP A 74 ASN A 78 5 5 HELIX 6 6 ARG A 79 GLY A 92 1 14 HELIX 7 7 GLU A 95 ILE A 100 1 6 HELIX 8 8 SER A 103 VAL A 120 1 18 HELIX 9 9 ASP A 121 GLY A 139 1 19 HELIX 10 10 GLY A 139 GLY A 152 1 14 HELIX 11 11 ASP A 154 ALA A 157 5 4 HELIX 12 12 LEU A 158 PHE A 163 1 6 HELIX 13 13 LYS A 168 LEU A 183 1 16 HELIX 14 14 SER A 186 LYS A 213 1 28 HELIX 15 15 LEU B 308 THR B 316 1 9 HELIX 16 16 THR B 316 HIS B 325 1 10 HELIX 17 17 SER B 326 LYS B 334 1 9 HELIX 18 18 GLY B 338 SER B 366 1 29 HELIX 19 19 ASP B 374 ASN B 378 5 5 HELIX 20 20 ARG B 379 GLY B 392 1 14 HELIX 21 21 SER B 394 ARG B 399 5 6 HELIX 22 22 SER B 403 VAL B 420 1 18 HELIX 23 23 ASP B 421 GLY B 452 1 32 HELIX 24 24 ASP B 454 HIS B 462 5 9 HELIX 25 25 LYS B 468 LEU B 483 1 16 HELIX 26 26 SER B 486 GLY B 514 1 29 HELIX 27 27 GLY C 607 THR C 616 1 10 HELIX 28 28 THR C 616 HIS C 625 1 10 HELIX 29 29 SER C 626 LYS C 634 1 9 HELIX 30 30 GLY C 638 SER C 666 1 29 HELIX 31 31 ASP C 674 ASN C 678 5 5 HELIX 32 32 ARG C 679 GLY C 692 1 14 HELIX 33 33 SER C 694 ARG C 699 5 6 HELIX 34 34 SER C 703 VAL C 720 1 18 HELIX 35 35 ASP C 721 GLY C 752 1 32 HELIX 36 36 ASP C 754 HIS C 762 5 9 HELIX 37 37 LYS C 768 ASN C 782 1 15 HELIX 38 38 SER C 786 LYS C 813 1 28 LINK FE A FE A3001 NA ABLA A3002 1555 1555 1.60 LINK FE A FE A3001 NB ABLA A3002 1555 1555 1.95 LINK FE A FE A3001 NC ABLA A3002 1555 1555 2.34 LINK FE A FE A3001 ND ABLA A3002 1555 1555 2.25 LINK FE A FE A3001 O AHOH A3161 1555 1555 2.17 LINK FE A FE C 901 NA ABLA C 902 1555 1555 1.93 LINK FE A FE C 901 NB ABLA C 902 1555 1555 1.91 LINK FE A FE C 901 NC ABLA C 902 1555 1555 2.42 LINK FE A FE C 901 ND ABLA C 902 1555 1555 1.99 LINK FE A FE C 901 O3 ASC C 903 1555 1555 2.60 CRYST1 54.065 62.966 107.728 90.00 100.78 90.00 P 1 21 1 6 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 0.018496 0.000000 0.003522 0.00000 SCALE2 0.000000 0.015882 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009449 0.00000