HEADER OXIDOREDUCTASE 10-MAR-15 4YNR TITLE DOSS GAFA DOMAIN REDUCED CO BOUND CRYSTAL STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: REDOX SENSOR HISTIDINE KINASE RESPONSE REGULATOR DEVS; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 63-210; COMPND 5 EC: 2.7.13.3; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS (STRAIN CDC 1551 / SOURCE 3 OSHKOSH); SOURCE 4 ORGANISM_TAXID: 83331; SOURCE 5 STRAIN: CDC 1551 / OSHKOSH; SOURCE 6 ATCC: 25618; SOURCE 7 GENE: DEVS, DOSS, MT3218; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PET22B KEYWDS DOSS, TUBERCULOSIS, HEME, GAS SENSOR, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.MADRONA REVDAT 4 28-FEB-24 4YNR 1 LINK REVDAT 3 11-DEC-19 4YNR 1 JRNL REVDAT 2 20-SEP-17 4YNR 1 REMARK REVDAT 1 24-FEB-16 4YNR 0 JRNL AUTH D.BASUDHAR,Y.MADRONA,S.KANDEL,J.N.LAMPE,C.R.NISHIDA, JRNL AUTH 2 P.R.DE MONTELLANO JRNL TITL ANALYSIS OF CYTOCHROME P450 CYP119 LIGAND-DEPENDENT JRNL TITL 2 CONFORMATIONAL DYNAMICS BY TWO-DIMENSIONAL NMR AND X-RAY JRNL TITL 3 CRYSTALLOGRAPHY. JRNL REF J.BIOL.CHEM. V. 290 10000 2015 JRNL REFN ESSN 1083-351X JRNL PMID 25670859 JRNL DOI 10.1074/JBC.M114.627935 REMARK 2 REMARK 2 RESOLUTION. 1.92 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.9_1692) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.92 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.01 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 22479 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.150 REMARK 3 FREE R VALUE TEST SET COUNT : 1157 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 19.0056 - 3.8233 0.95 2778 157 0.1650 0.1941 REMARK 3 2 3.8233 - 3.0387 1.00 2755 150 0.1789 0.2240 REMARK 3 3 3.0387 - 2.6557 1.00 2754 156 0.1983 0.2792 REMARK 3 4 2.6557 - 2.4135 1.00 2710 145 0.2015 0.2447 REMARK 3 5 2.4135 - 2.2408 1.00 2702 148 0.2077 0.2553 REMARK 3 6 2.2408 - 2.1088 1.00 2694 148 0.2080 0.2932 REMARK 3 7 2.1088 - 2.0033 1.00 2721 123 0.2295 0.2631 REMARK 3 8 2.0033 - 1.9162 0.82 2208 130 0.2852 0.3338 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.380 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.33 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 2337 REMARK 3 ANGLE : 1.295 3199 REMARK 3 CHIRALITY : 0.052 352 REMARK 3 PLANARITY : 0.006 418 REMARK 3 DIHEDRAL : 14.897 839 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ( CHAIN A AND RESID 61:90 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.2521 79.6676 -1.2442 REMARK 3 T TENSOR REMARK 3 T11: 0.3260 T22: 0.2392 REMARK 3 T33: 0.2802 T12: 0.0485 REMARK 3 T13: -0.0811 T23: -0.0068 REMARK 3 L TENSOR REMARK 3 L11: 6.8115 L22: 4.2060 REMARK 3 L33: 3.8831 L12: 0.9173 REMARK 3 L13: -0.3240 L23: -0.1006 REMARK 3 S TENSOR REMARK 3 S11: 0.1119 S12: 0.5991 S13: -0.1669 REMARK 3 S21: -0.4600 S22: 0.0516 S23: 0.8149 REMARK 3 S31: -0.3000 S32: -0.3196 S33: -0.2253 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN A AND RESID 91:101 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.3356 90.9774 -2.1948 REMARK 3 T TENSOR REMARK 3 T11: 0.7647 T22: 0.2939 REMARK 3 T33: 0.5446 T12: 0.1091 REMARK 3 T13: -0.0905 T23: 0.1426 REMARK 3 L TENSOR REMARK 3 L11: 4.9747 L22: 7.0917 REMARK 3 L33: 7.9441 L12: 2.0191 REMARK 3 L13: -1.1547 L23: -7.3948 REMARK 3 S TENSOR REMARK 3 S11: -0.0138 S12: 0.4950 S13: 1.2139 REMARK 3 S21: -1.1117 S22: 0.0320 S23: 0.4418 REMARK 3 S31: -0.7248 S32: -0.5755 S33: -0.2410 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: ( CHAIN A AND RESID 102:173 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.1238 86.9754 6.6692 REMARK 3 T TENSOR REMARK 3 T11: 0.2205 T22: 0.2169 REMARK 3 T33: 0.2318 T12: -0.0305 REMARK 3 T13: -0.0385 T23: 0.0634 REMARK 3 L TENSOR REMARK 3 L11: 3.7652 L22: 3.0570 REMARK 3 L33: 2.3212 L12: -0.8678 REMARK 3 L13: -0.3931 L23: 0.7536 REMARK 3 S TENSOR REMARK 3 S11: -0.0628 S12: 0.0951 S13: 0.3327 REMARK 3 S21: -0.2470 S22: 0.0044 S23: -0.0604 REMARK 3 S31: -0.2514 S32: 0.0619 S33: 0.0383 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: ( CHAIN A AND RESID 174:203 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.0313 76.4016 -1.6461 REMARK 3 T TENSOR REMARK 3 T11: 0.3908 T22: 0.2298 REMARK 3 T33: 0.2344 T12: 0.0149 REMARK 3 T13: -0.0150 T23: -0.0392 REMARK 3 L TENSOR REMARK 3 L11: 4.3214 L22: 4.5105 REMARK 3 L33: 3.3237 L12: -1.6156 REMARK 3 L13: 3.0218 L23: -2.2283 REMARK 3 S TENSOR REMARK 3 S11: 0.1785 S12: 0.5697 S13: -0.1302 REMARK 3 S21: -0.9326 S22: -0.2488 S23: -0.2875 REMARK 3 S31: 0.4315 S32: 0.7087 S33: 0.0604 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: ( CHAIN B AND RESID 61:92 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.0533 70.8106 -20.9609 REMARK 3 T TENSOR REMARK 3 T11: 0.3047 T22: 0.2438 REMARK 3 T33: 0.1910 T12: -0.0320 REMARK 3 T13: 0.0053 T23: 0.0585 REMARK 3 L TENSOR REMARK 3 L11: 7.4164 L22: 6.5132 REMARK 3 L33: 4.6278 L12: 0.4980 REMARK 3 L13: 0.3073 L23: 0.0477 REMARK 3 S TENSOR REMARK 3 S11: -0.1502 S12: 0.4325 S13: 0.4440 REMARK 3 S21: -0.2535 S22: 0.1040 S23: 0.1006 REMARK 3 S31: -0.5605 S32: -0.1894 S33: 0.0770 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: ( CHAIN B AND RESID 93:153 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.7658 59.3686 -25.0567 REMARK 3 T TENSOR REMARK 3 T11: 0.2361 T22: 0.2196 REMARK 3 T33: 0.2275 T12: -0.0421 REMARK 3 T13: -0.0657 T23: -0.0026 REMARK 3 L TENSOR REMARK 3 L11: 1.9886 L22: 4.8336 REMARK 3 L33: 7.2707 L12: 0.4900 REMARK 3 L13: -1.2902 L23: -3.5351 REMARK 3 S TENSOR REMARK 3 S11: -0.0728 S12: 0.2360 S13: -0.0011 REMARK 3 S21: -0.4463 S22: 0.1437 S23: 0.2503 REMARK 3 S31: 0.3919 S32: -0.1819 S33: -0.0459 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: ( CHAIN B AND RESID 154:163 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.4544 66.6006 -14.4058 REMARK 3 T TENSOR REMARK 3 T11: 0.2331 T22: 0.3979 REMARK 3 T33: 0.3459 T12: -0.0398 REMARK 3 T13: 0.0099 T23: -0.0224 REMARK 3 L TENSOR REMARK 3 L11: 2.6210 L22: 2.8103 REMARK 3 L33: 7.0386 L12: 1.4006 REMARK 3 L13: -2.2796 L23: 1.9376 REMARK 3 S TENSOR REMARK 3 S11: 0.0026 S12: -0.2987 S13: -0.0165 REMARK 3 S21: 0.4672 S22: -0.1076 S23: 1.1881 REMARK 3 S31: -0.2579 S32: -0.6399 S33: 0.2414 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: ( CHAIN B AND RESID 164:203 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.5485 67.0699 -13.2254 REMARK 3 T TENSOR REMARK 3 T11: 0.2723 T22: 0.2475 REMARK 3 T33: 0.2047 T12: -0.0019 REMARK 3 T13: -0.0215 T23: -0.0164 REMARK 3 L TENSOR REMARK 3 L11: 3.0646 L22: 5.9584 REMARK 3 L33: 5.8376 L12: 0.0028 REMARK 3 L13: -0.1908 L23: 0.0490 REMARK 3 S TENSOR REMARK 3 S11: 0.0271 S12: -0.1771 S13: 0.0718 REMARK 3 S21: 0.1800 S22: -0.0812 S23: 0.2864 REMARK 3 S31: -0.2836 S32: -0.2467 S33: 0.0726 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4YNR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-MAR-15. REMARK 100 THE DEPOSITION ID IS D_1000207632. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-NOV-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.115867 REMARK 200 MONOCHROMATOR : DOUBLE FLAT CRYSTAL, SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22480 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.916 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.7700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.92 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.74900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.700 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 (%): 44.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS-HCL, 15-18% PEG 4000, 0.2M REMARK 280 CALCIUM ACETATE, PH 7.0, VAPOR DIFFUSION, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 16.75250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.72550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.62350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.72550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.75250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.62350 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13240 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -65.0 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 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 GLY A 57 REMARK 465 ALA A 58 REMARK 465 MET A 59 REMARK 465 SER A 60 REMARK 465 ARG A 163 REMARK 465 ASP A 164 REMARK 465 GLU A 165 REMARK 465 ARG A 204 REMARK 465 LEU A 205 REMARK 465 TYR A 206 REMARK 465 GLN A 207 REMARK 465 GLN A 208 REMARK 465 ALA A 209 REMARK 465 LYS A 210 REMARK 465 GLY B 57 REMARK 465 ALA B 58 REMARK 465 MET B 59 REMARK 465 SER B 60 REMARK 465 ARG B 204 REMARK 465 LEU B 205 REMARK 465 TYR B 206 REMARK 465 GLN B 207 REMARK 465 GLN B 208 REMARK 465 ALA B 209 REMARK 465 LYS B 210 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 OD1 ASP A 63 NH1 ARG B 163 2.07 REMARK 500 O HOH A 403 O HOH A 418 2.12 REMARK 500 O HOH A 416 O HOH A 466 2.14 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 82 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP A 63 -73.20 -50.65 REMARK 500 TYR A 148 -8.48 75.52 REMARK 500 ARG A 153 -75.96 -113.41 REMARK 500 TYR B 148 -7.56 74.57 REMARK 500 ARG B 153 -74.90 -115.32 REMARK 500 VAL B 162 -35.44 -135.48 REMARK 500 ARG B 163 -95.34 -173.01 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 301 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 149 NE2 REMARK 620 2 HEM A 301 NA 95.5 REMARK 620 3 HEM A 301 NB 88.5 91.7 REMARK 620 4 HEM A 301 NC 86.4 177.9 89.2 REMARK 620 5 HEM A 301 ND 89.9 87.7 178.2 91.5 REMARK 620 6 CMO A 302 C 175.5 84.6 87.0 93.6 94.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM B 301 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 149 NE2 REMARK 620 2 HEM B 301 NA 89.4 REMARK 620 3 HEM B 301 NB 88.2 90.1 REMARK 620 4 HEM B 301 NC 87.7 177.1 90.2 REMARK 620 5 HEM B 301 ND 89.1 87.8 176.6 91.9 REMARK 620 6 CMO B 302 C 177.1 87.9 90.7 95.0 91.9 REMARK 620 N 1 2 3 4 5 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 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CMO A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HEM B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CMO B 302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2W3D RELATED DB: PDB REMARK 900 2W3D CONTAINS THE SAME PROTEIN OXIDIZED AND WITHOUT A CO LIGAND. REMARK 900 RELATED ID: 2W3F RELATED DB: PDB REMARK 900 2W3F CONTAINS THE SAME PROTEIN WITHOUT THE CO LIGAND DBREF 4YNR A 63 210 UNP P9WGK2 DEVS_MYCTO 63 210 DBREF 4YNR B 63 210 UNP P9WGK2 DEVS_MYCTO 63 210 SEQADV 4YNR GLY A 57 UNP P9WGK2 EXPRESSION TAG SEQADV 4YNR ALA A 58 UNP P9WGK2 EXPRESSION TAG SEQADV 4YNR MET A 59 UNP P9WGK2 EXPRESSION TAG SEQADV 4YNR SER A 60 UNP P9WGK2 EXPRESSION TAG SEQADV 4YNR ASP A 61 UNP P9WGK2 EXPRESSION TAG SEQADV 4YNR PRO A 62 UNP P9WGK2 EXPRESSION TAG SEQADV 4YNR GLY B 57 UNP P9WGK2 EXPRESSION TAG SEQADV 4YNR ALA B 58 UNP P9WGK2 EXPRESSION TAG SEQADV 4YNR MET B 59 UNP P9WGK2 EXPRESSION TAG SEQADV 4YNR SER B 60 UNP P9WGK2 EXPRESSION TAG SEQADV 4YNR ASP B 61 UNP P9WGK2 EXPRESSION TAG SEQADV 4YNR PRO B 62 UNP P9WGK2 EXPRESSION TAG SEQRES 1 A 154 GLY ALA MET SER ASP PRO ASP LEU GLU ALA THR LEU ARG SEQRES 2 A 154 ALA ILE VAL HIS SER ALA THR SER LEU VAL ASP ALA ARG SEQRES 3 A 154 TYR GLY ALA MET GLU VAL HIS ASP ARG GLN HIS ARG VAL SEQRES 4 A 154 LEU HIS PHE VAL TYR GLU GLY ILE ASP GLU GLU THR VAL SEQRES 5 A 154 ARG ARG ILE GLY HIS LEU PRO LYS GLY LEU GLY VAL ILE SEQRES 6 A 154 GLY LEU LEU ILE GLU ASP PRO LYS PRO LEU ARG LEU ASP SEQRES 7 A 154 ASP VAL SER ALA HIS PRO ALA SER ILE GLY PHE PRO PRO SEQRES 8 A 154 TYR HIS PRO PRO MET ARG THR PHE LEU GLY VAL PRO VAL SEQRES 9 A 154 ARG VAL ARG ASP GLU SER PHE GLY THR LEU TYR LEU THR SEQRES 10 A 154 ASP LYS THR ASN GLY GLN PRO PHE SER ASP ASP ASP GLU SEQRES 11 A 154 VAL LEU VAL GLN ALA LEU ALA ALA ALA ALA GLY ILE ALA SEQRES 12 A 154 VAL ALA ASN ALA ARG LEU TYR GLN GLN ALA LYS SEQRES 1 B 154 GLY ALA MET SER ASP PRO ASP LEU GLU ALA THR LEU ARG SEQRES 2 B 154 ALA ILE VAL HIS SER ALA THR SER LEU VAL ASP ALA ARG SEQRES 3 B 154 TYR GLY ALA MET GLU VAL HIS ASP ARG GLN HIS ARG VAL SEQRES 4 B 154 LEU HIS PHE VAL TYR GLU GLY ILE ASP GLU GLU THR VAL SEQRES 5 B 154 ARG ARG ILE GLY HIS LEU PRO LYS GLY LEU GLY VAL ILE SEQRES 6 B 154 GLY LEU LEU ILE GLU ASP PRO LYS PRO LEU ARG LEU ASP SEQRES 7 B 154 ASP VAL SER ALA HIS PRO ALA SER ILE GLY PHE PRO PRO SEQRES 8 B 154 TYR HIS PRO PRO MET ARG THR PHE LEU GLY VAL PRO VAL SEQRES 9 B 154 ARG VAL ARG ASP GLU SER PHE GLY THR LEU TYR LEU THR SEQRES 10 B 154 ASP LYS THR ASN GLY GLN PRO PHE SER ASP ASP ASP GLU SEQRES 11 B 154 VAL LEU VAL GLN ALA LEU ALA ALA ALA ALA GLY ILE ALA SEQRES 12 B 154 VAL ALA ASN ALA ARG LEU TYR GLN GLN ALA LYS HET HEM A 301 43 HET CMO A 302 2 HET HEM B 301 43 HET CMO B 302 2 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM CMO CARBON MONOXIDE HETSYN HEM HEME FORMUL 3 HEM 2(C34 H32 FE N4 O4) FORMUL 4 CMO 2(C O) FORMUL 7 HOH *130(H2 O) HELIX 1 AA1 ASP A 61 VAL A 79 1 19 HELIX 2 AA2 ASP A 104 GLY A 112 1 9 HELIX 3 AA3 LEU A 118 ASP A 127 1 10 HELIX 4 AA4 ASP A 135 HIS A 139 5 5 HELIX 5 AA5 SER A 182 ALA A 203 1 22 HELIX 6 AA6 PRO B 62 VAL B 79 1 18 HELIX 7 AA7 ASP B 104 GLY B 112 1 9 HELIX 8 AA8 LEU B 118 ASP B 127 1 10 HELIX 9 AA9 ASP B 135 HIS B 139 5 5 HELIX 10 AB1 SER B 182 ASN B 202 1 21 SHEET 1 AA1 5 VAL A 95 GLU A 101 0 SHEET 2 AA1 5 ALA A 81 HIS A 89 -1 N VAL A 88 O LEU A 96 SHEET 3 AA1 5 GLY A 168 LYS A 175 -1 O TYR A 171 N ALA A 85 SHEET 4 AA1 5 PHE A 155 VAL A 160 -1 N VAL A 160 O GLY A 168 SHEET 5 AA1 5 LEU A 131 LEU A 133 -1 N LEU A 131 O GLY A 157 SHEET 1 AA2 5 VAL B 95 GLU B 101 0 SHEET 2 AA2 5 ALA B 81 HIS B 89 -1 N VAL B 88 O LEU B 96 SHEET 3 AA2 5 SER B 166 LYS B 175 -1 O PHE B 167 N HIS B 89 SHEET 4 AA2 5 PHE B 155 ARG B 161 -1 N VAL B 158 O LEU B 170 SHEET 5 AA2 5 LEU B 131 LEU B 133 -1 N LEU B 131 O GLY B 157 LINK NE2 HIS A 149 FE HEM A 301 1555 1555 2.15 LINK FE HEM A 301 C CMO A 302 1555 1555 1.88 LINK NE2 HIS B 149 FE HEM B 301 1555 1555 2.10 LINK FE HEM B 301 C CMO B 302 1555 1555 1.83 SITE 1 AC1 23 GLY A 84 GLU A 101 ILE A 103 ILE A 111 SITE 2 AC1 23 HIS A 113 PRO A 115 LYS A 116 GLY A 117 SITE 3 AC1 23 LEU A 118 GLY A 119 VAL A 120 ILE A 121 SITE 4 AC1 23 SER A 142 ILE A 143 GLY A 144 PHE A 145 SITE 5 AC1 23 PRO A 146 HIS A 149 MET A 152 THR A 173 SITE 6 AC1 23 CMO A 302 HOH A 409 HOH A 445 SITE 1 AC2 5 PHE A 98 PRO A 115 ILE A 121 TYR A 171 SITE 2 AC2 5 HEM A 301 SITE 1 AC3 25 GLY B 84 ALA B 85 PHE B 98 GLU B 101 SITE 2 AC3 25 ILE B 103 VAL B 108 HIS B 113 LEU B 114 SITE 3 AC3 25 PRO B 115 LYS B 116 GLY B 117 LEU B 118 SITE 4 AC3 25 GLY B 119 VAL B 120 ILE B 121 SER B 142 SITE 5 AC3 25 ILE B 143 GLY B 144 PRO B 146 HIS B 149 SITE 6 AC3 25 MET B 152 PHE B 155 CMO B 302 HOH B 408 SITE 7 AC3 25 HOH B 409 SITE 1 AC4 5 PHE B 98 PRO B 115 ILE B 121 TYR B 171 SITE 2 AC4 5 HEM B 301 CRYST1 33.505 79.247 109.451 90.00 90.00 90.00 P 21 21 21 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 0.029846 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012619 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009137 0.00000