HEADER OXIDOREDUCTASE 13-DEC-19 6TPO TITLE CONFORMATION OF CD1 NITRITE REDUCTASE NIRS WITHOUT BOUND HEME D1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NITRITE REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CYTOCHROME CD1,CYTOCHROME OXIDASE,HYDROXYLAMINE REDUCTASE; COMPND 5 EC: 1.7.2.1,1.7.99.1 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA (STRAIN ATCC 15692 / DSM SOURCE 3 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1); SOURCE 4 ORGANISM_TAXID: 208964 KEYWDS CD1 NITRITE REDUCTASE, NIRS, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR T.KLUENEMANN,W.BLANKENFELDT REVDAT 3 06-NOV-24 6TPO 1 REMARK REVDAT 2 24-JAN-24 6TPO 1 REMARK REVDAT 1 18-NOV-20 6TPO 0 JRNL AUTH T.KLUNEMANN,W.BLANKENFELDT JRNL TITL STRUCTURE OF HEME D 1 -FREE CD 1 NITRITE REDUCTASE NIRS. JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 76 250 2020 JRNL REFN ESSN 2053-230X JRNL PMID 32510465 JRNL DOI 10.1107/S2053230X20006676 REMARK 2 REMARK 2 RESOLUTION. 1.86 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV-3714 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.86 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 54.36 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 54747 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 2726 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 54.3640 - 4.9634 1.00 3058 149 0.1891 0.2106 REMARK 3 2 4.9634 - 3.9399 1.00 2840 150 0.1313 0.1556 REMARK 3 3 3.9399 - 3.4420 1.00 2807 157 0.1477 0.1756 REMARK 3 4 3.4420 - 3.1273 1.00 2787 136 0.1610 0.1813 REMARK 3 5 3.1273 - 2.9032 1.00 2743 132 0.1722 0.1817 REMARK 3 6 2.9032 - 2.7320 1.00 2754 147 0.1674 0.1923 REMARK 3 7 2.7320 - 2.5952 1.00 2716 137 0.1650 0.2080 REMARK 3 8 2.5952 - 2.4822 1.00 2725 147 0.1717 0.2075 REMARK 3 9 2.4822 - 2.3867 1.00 2694 142 0.1677 0.2246 REMARK 3 10 2.3867 - 2.3043 1.00 2725 150 0.1703 0.2049 REMARK 3 11 2.3043 - 2.2323 1.00 2689 152 0.1679 0.2061 REMARK 3 12 2.2323 - 2.1685 1.00 2650 146 0.1745 0.2208 REMARK 3 13 2.1685 - 2.1114 1.00 2718 155 0.1771 0.1716 REMARK 3 14 2.1114 - 2.0599 1.00 2685 153 0.1868 0.2419 REMARK 3 15 2.0599 - 2.0130 1.00 2687 142 0.1868 0.1978 REMARK 3 16 2.0130 - 1.9702 1.00 2668 139 0.1814 0.2111 REMARK 3 17 1.9702 - 1.9308 1.00 2690 134 0.1820 0.2056 REMARK 3 18 1.9308 - 1.8943 1.00 2738 113 0.2039 0.2561 REMARK 3 19 1.8943 - 1.8610 1.00 2647 145 0.2209 0.2469 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.840 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.49 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 21 THROUGH 64 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.9829 1.6149 -15.7525 REMARK 3 T TENSOR REMARK 3 T11: 0.3667 T22: 0.2480 REMARK 3 T33: 0.3570 T12: -0.0378 REMARK 3 T13: -0.0690 T23: 0.0485 REMARK 3 L TENSOR REMARK 3 L11: 0.3089 L22: 0.2215 REMARK 3 L33: 0.5791 L12: 0.1667 REMARK 3 L13: 0.0718 L23: 0.1893 REMARK 3 S TENSOR REMARK 3 S11: 0.2427 S12: -0.1873 S13: -0.2827 REMARK 3 S21: 0.4745 S22: 0.0954 S23: -0.0425 REMARK 3 S31: 0.2519 S32: -0.2047 S33: 0.0223 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 65 THROUGH 206 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.4178 17.6769 -26.0022 REMARK 3 T TENSOR REMARK 3 T11: 0.1550 T22: 0.2157 REMARK 3 T33: 0.2266 T12: 0.0128 REMARK 3 T13: 0.0200 T23: -0.0055 REMARK 3 L TENSOR REMARK 3 L11: 0.4437 L22: 0.4082 REMARK 3 L33: 1.1350 L12: -0.2577 REMARK 3 L13: 0.3237 L23: -0.0145 REMARK 3 S TENSOR REMARK 3 S11: 0.0336 S12: 0.0789 S13: -0.0996 REMARK 3 S21: -0.0025 S22: -0.0278 S23: 0.0135 REMARK 3 S31: 0.1175 S32: 0.0785 S33: -0.0000 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 207 THROUGH 328 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.6963 29.4759 -12.0290 REMARK 3 T TENSOR REMARK 3 T11: 0.2221 T22: 0.2054 REMARK 3 T33: 0.1931 T12: 0.0019 REMARK 3 T13: -0.0006 T23: 0.0029 REMARK 3 L TENSOR REMARK 3 L11: 0.2477 L22: 0.1880 REMARK 3 L33: 1.2244 L12: -0.1410 REMARK 3 L13: -0.2432 L23: -0.0291 REMARK 3 S TENSOR REMARK 3 S11: 0.0064 S12: 0.0203 S13: -0.0339 REMARK 3 S21: -0.0043 S22: -0.0395 S23: -0.0293 REMARK 3 S31: -0.0401 S32: 0.0158 S33: -0.0000 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 329 THROUGH 444 ) REMARK 3 ORIGIN FOR THE GROUP (A): -14.9251 36.6786 -24.3409 REMARK 3 T TENSOR REMARK 3 T11: 0.2180 T22: 0.1706 REMARK 3 T33: 0.2015 T12: 0.0336 REMARK 3 T13: -0.0070 T23: 0.0111 REMARK 3 L TENSOR REMARK 3 L11: 0.6329 L22: 0.3751 REMARK 3 L33: 0.4869 L12: 0.0698 REMARK 3 L13: 0.1360 L23: 0.2917 REMARK 3 S TENSOR REMARK 3 S11: -0.0224 S12: -0.0492 S13: -0.0564 REMARK 3 S21: 0.0814 S22: 0.0089 S23: 0.0279 REMARK 3 S31: -0.0311 S32: -0.1016 S33: 0.0000 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 445 THROUGH 472 ) REMARK 3 ORIGIN FOR THE GROUP (A): -15.3223 32.6482 -43.1005 REMARK 3 T TENSOR REMARK 3 T11: 0.2173 T22: 0.2274 REMARK 3 T33: 0.2550 T12: 0.0405 REMARK 3 T13: -0.0195 T23: -0.0140 REMARK 3 L TENSOR REMARK 3 L11: 0.1325 L22: 0.0771 REMARK 3 L33: 0.2109 L12: 0.1084 REMARK 3 L13: 0.0219 L23: 0.0349 REMARK 3 S TENSOR REMARK 3 S11: -0.0932 S12: 0.2489 S13: 0.0047 REMARK 3 S21: -0.0729 S22: -0.0041 S23: 0.2158 REMARK 3 S31: -0.0000 S32: -0.1360 S33: -0.0010 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 473 THROUGH 543 ) REMARK 3 ORIGIN FOR THE GROUP (A): -0.6790 30.2831 -40.4065 REMARK 3 T TENSOR REMARK 3 T11: 0.1935 T22: 0.1868 REMARK 3 T33: 0.2047 T12: 0.0223 REMARK 3 T13: 0.0056 T23: -0.0150 REMARK 3 L TENSOR REMARK 3 L11: 0.8673 L22: 0.3361 REMARK 3 L33: 1.0209 L12: -0.1468 REMARK 3 L13: -0.0706 L23: -0.4465 REMARK 3 S TENSOR REMARK 3 S11: 0.0275 S12: 0.1324 S13: -0.0772 REMARK 3 S21: -0.1076 S22: -0.0360 S23: 0.0489 REMARK 3 S31: 0.0500 S32: -0.0118 S33: 0.0000 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 6TPO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-DEC-19. REMARK 100 THE DEPOSITION ID IS D_1292105852. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-SEP-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.033217 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.1 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54867 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.860 REMARK 200 RESOLUTION RANGE LOW (A) : 69.280 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 24.00 REMARK 200 R MERGE (I) : 0.15700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.86 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.96 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 18.70 REMARK 200 R MERGE FOR SHELL (I) : 1.40600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: PHASER REMARK 200 STARTING MODEL: 1HZU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M PHOSPHATE/CITRATE PH4.2 40% (V/V) REMARK 280 PEG300, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z+1/2 REMARK 290 7555 Y,X,-Z+1/4 REMARK 290 8555 -Y,-X,-Z+3/4 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 138.55200 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 207.82800 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 69.27600 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 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 138.55200 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 69.27600 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 207.82800 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 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 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -69.27600 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 A1060 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1105 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 LYS A 1 REMARK 465 ASP A 2 REMARK 465 ASP A 3 REMARK 465 MET A 4 REMARK 465 LYS A 5 REMARK 465 ALA A 6 REMARK 465 ALA A 7 REMARK 465 GLU A 8 REMARK 465 GLN A 9 REMARK 465 TYR A 10 REMARK 465 GLN A 11 REMARK 465 GLY A 12 REMARK 465 ALA A 13 REMARK 465 ALA A 14 REMARK 465 SER A 15 REMARK 465 ALA A 16 REMARK 465 VAL A 17 REMARK 465 ASP A 18 REMARK 465 PRO A 19 REMARK 465 ALA A 20 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 HIS A 21 CG ND1 CD2 CE1 NE2 REMARK 470 ARG A 24 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 233 CG CD CE NZ REMARK 470 ASN A 343 CG OD1 ND2 REMARK 470 ASN A 344 CG OD1 ND2 REMARK 470 LYS A 403 CG CD CE NZ REMARK 470 GLU A 476 CG CD OE1 OE2 REMARK 470 ASP A 503 CG OD1 OD2 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 OG SER A 32 H GLU A 35 1.41 REMARK 500 O HOH A 1070 O HOH A 1232 1.89 REMARK 500 O HOH A 1216 O HOH A 1220 2.00 REMARK 500 OE1 GLN A 262 O HOH A 1001 2.09 REMARK 500 OG SER A 229 O HOH A 1002 2.16 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 TYR A 82 CE2 TYR A 82 CD2 -0.094 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 ALA A 58 -100.06 -149.58 REMARK 500 TRP A 119 88.37 -155.04 REMARK 500 THR A 177 -71.87 -118.16 REMARK 500 HIS A 182 -76.63 -121.68 REMARK 500 ALA A 284 149.23 -172.22 REMARK 500 ALA A 322 -94.61 -121.63 REMARK 500 HIS A 327 -138.83 -111.55 REMARK 500 THR A 439 45.05 -150.72 REMARK 500 ASN A 458 76.77 -151.80 REMARK 500 GLN A 483 85.55 66.02 REMARK 500 THR A 530 -99.35 -121.20 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 HEC A 903 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 51 NE2 REMARK 620 2 HEC A 903 NA 91.2 REMARK 620 3 HEC A 903 NB 88.9 90.1 REMARK 620 4 HEC A 903 NC 88.7 179.8 89.8 REMARK 620 5 HEC A 903 ND 89.6 89.1 178.2 91.0 REMARK 620 6 MET A 88 SD 173.3 94.1 87.1 85.9 94.5 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 1PE A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BU3 A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HEC A 903 DBREF 6TPO A 1 543 UNP P24474 NIRS_PSEAE 26 568 SEQRES 1 A 543 LYS ASP ASP MET LYS ALA ALA GLU GLN TYR GLN GLY ALA SEQRES 2 A 543 ALA SER ALA VAL ASP PRO ALA HIS VAL VAL ARG THR ASN SEQRES 3 A 543 GLY ALA PRO ASP MET SER GLU SER GLU PHE ASN GLU ALA SEQRES 4 A 543 LYS GLN ILE TYR PHE GLN ARG CYS ALA GLY CYS HIS GLY SEQRES 5 A 543 VAL LEU ARG LYS GLY ALA THR GLY LYS PRO LEU THR PRO SEQRES 6 A 543 ASP ILE THR GLN GLN ARG GLY GLN GLN TYR LEU GLU ALA SEQRES 7 A 543 LEU ILE THR TYR GLY THR PRO LEU GLY MET PRO ASN TRP SEQRES 8 A 543 GLY SER SER GLY GLU LEU SER LYS GLU GLN ILE THR LEU SEQRES 9 A 543 MET ALA LYS TYR ILE GLN HIS THR PRO PRO GLN PRO PRO SEQRES 10 A 543 GLU TRP GLY MET PRO GLU MET ARG GLU SER TRP LYS VAL SEQRES 11 A 543 LEU VAL LYS PRO GLU ASP ARG PRO LYS LYS GLN LEU ASN SEQRES 12 A 543 ASP LEU ASP LEU PRO ASN LEU PHE SER VAL THR LEU ARG SEQRES 13 A 543 ASP ALA GLY GLN ILE ALA LEU VAL ASP GLY ASP SER LYS SEQRES 14 A 543 LYS ILE VAL LYS VAL ILE ASP THR GLY TYR ALA VAL HIS SEQRES 15 A 543 ILE SER ARG MET SER ALA SER GLY ARG TYR LEU LEU VAL SEQRES 16 A 543 ILE GLY ARG ASP ALA ARG ILE ASP MET ILE ASP LEU TRP SEQRES 17 A 543 ALA LYS GLU PRO THR LYS VAL ALA GLU ILE LYS ILE GLY SEQRES 18 A 543 ILE GLU ALA ARG SER VAL GLU SER SER LYS PHE LYS GLY SEQRES 19 A 543 TYR GLU ASP ARG TYR THR ILE ALA GLY ALA TYR TRP PRO SEQRES 20 A 543 PRO GLN PHE ALA ILE MET ASP GLY GLU THR LEU GLU PRO SEQRES 21 A 543 LYS GLN ILE VAL SER THR ARG GLY MET THR VAL ASP THR SEQRES 22 A 543 GLN THR TYR HIS PRO GLU PRO ARG VAL ALA ALA ILE ILE SEQRES 23 A 543 ALA SER HIS GLU HIS PRO GLU PHE ILE VAL ASN VAL LYS SEQRES 24 A 543 GLU THR GLY LYS VAL LEU LEU VAL ASN TYR LYS ASP ILE SEQRES 25 A 543 ASP ASN LEU THR VAL THR SER ILE GLY ALA ALA PRO PHE SEQRES 26 A 543 LEU HIS ASP GLY GLY TRP ASP SER SER HIS ARG TYR PHE SEQRES 27 A 543 MET THR ALA ALA ASN ASN SER ASN LYS VAL ALA VAL ILE SEQRES 28 A 543 ASP SER LYS ASP ARG ARG LEU SER ALA LEU VAL ASP VAL SEQRES 29 A 543 GLY LYS THR PRO HIS PRO GLY ARG GLY ALA ASN PHE VAL SEQRES 30 A 543 HIS PRO LYS TYR GLY PRO VAL TRP SER THR SER HIS LEU SEQRES 31 A 543 GLY ASP GLY SER ILE SER LEU ILE GLY THR ASP PRO LYS SEQRES 32 A 543 ASN HIS PRO GLN TYR ALA TRP LYS LYS VAL ALA GLU LEU SEQRES 33 A 543 GLN GLY GLN GLY GLY GLY SER LEU PHE ILE LYS THR HIS SEQRES 34 A 543 PRO LYS SER SER HIS LEU TYR VAL ASP THR THR PHE ASN SEQRES 35 A 543 PRO ASP ALA ARG ILE SER GLN SER VAL ALA VAL PHE ASP SEQRES 36 A 543 LEU LYS ASN LEU ASP ALA LYS TYR GLN VAL LEU PRO ILE SEQRES 37 A 543 ALA GLU TRP ALA ASP LEU GLY GLU GLY ALA LYS ARG VAL SEQRES 38 A 543 VAL GLN PRO GLU TYR ASN LYS ARG GLY ASP GLU VAL TRP SEQRES 39 A 543 PHE SER VAL TRP ASN GLY LYS ASN ASP SER SER ALA LEU SEQRES 40 A 543 VAL VAL VAL ASP ASP LYS THR LEU LYS LEU LYS ALA VAL SEQRES 41 A 543 VAL LYS ASP PRO ARG LEU ILE THR PRO THR GLY LYS PHE SEQRES 42 A 543 ASN VAL TYR ASN THR GLN HIS ASP VAL TYR HET 1PE A 901 38 HET BU3 A 902 16 HET HEC A 903 73 HETNAM 1PE PENTAETHYLENE GLYCOL HETNAM BU3 (R,R)-2,3-BUTANEDIOL HETNAM HEC HEME C HETSYN 1PE PEG400 FORMUL 2 1PE C10 H22 O6 FORMUL 3 BU3 C4 H10 O2 FORMUL 4 HEC C34 H34 FE N4 O4 FORMUL 5 HOH *255(H2 O) HELIX 1 AA1 GLU A 33 CYS A 47 1 15 HELIX 2 AA2 CYS A 47 GLY A 52 1 6 HELIX 3 AA3 THR A 64 GLY A 72 1 9 HELIX 4 AA4 GLY A 72 GLY A 83 1 12 HELIX 5 AA5 SER A 98 ILE A 109 1 12 HELIX 6 AA6 GLY A 120 TRP A 128 1 9 HELIX 7 AA7 LYS A 133 ARG A 137 5 5 HELIX 8 AA8 ASP A 146 PRO A 148 5 3 HELIX 9 AA9 ASP A 444 GLN A 449 1 6 HELIX 10 AB1 PRO A 467 ASP A 473 1 7 HELIX 11 AB2 VAL A 535 HIS A 540 1 6 SHEET 1 AA1 2 VAL A 22 VAL A 23 0 SHEET 2 AA1 2 MET A 31 SER A 32 -1 O MET A 31 N VAL A 23 SHEET 1 AA2 5 LYS A 129 VAL A 130 0 SHEET 2 AA2 5 THR A 213 LYS A 219 -1 O GLU A 217 N LYS A 129 SHEET 3 AA2 5 ARG A 201 ASP A 206 -1 N ILE A 202 O ILE A 218 SHEET 4 AA2 5 TYR A 192 GLY A 197 -1 N LEU A 193 O ILE A 205 SHEET 5 AA2 5 VAL A 181 MET A 186 -1 N ARG A 185 O LEU A 194 SHEET 1 AA3 4 ILE A 171 ASP A 176 0 SHEET 2 AA3 4 GLN A 160 ASP A 165 -1 N LEU A 163 O VAL A 172 SHEET 3 AA3 4 LEU A 150 LEU A 155 -1 N VAL A 153 O ALA A 162 SHEET 4 AA3 4 PRO A 529 ASN A 534 -1 O GLY A 531 N THR A 154 SHEET 1 AA4 4 GLU A 223 SER A 229 0 SHEET 2 AA4 4 TYR A 239 TRP A 246 -1 O TYR A 245 N GLU A 223 SHEET 3 AA4 4 GLN A 249 ASP A 254 -1 O MET A 253 N THR A 240 SHEET 4 AA4 4 PRO A 260 SER A 265 -1 O GLN A 262 N ILE A 252 SHEET 1 AA5 2 GLY A 268 MET A 269 0 SHEET 2 AA5 2 TYR A 276 HIS A 277 -1 O HIS A 277 N GLY A 268 SHEET 1 AA6 4 VAL A 282 ALA A 287 0 SHEET 2 AA6 4 GLU A 293 VAL A 298 -1 O ILE A 295 N ILE A 286 SHEET 3 AA6 4 LYS A 303 ASN A 308 -1 O LEU A 305 N VAL A 296 SHEET 4 AA6 4 THR A 316 GLY A 321 -1 O ILE A 320 N VAL A 304 SHEET 1 AA7 4 LEU A 326 TRP A 331 0 SHEET 2 AA7 4 TYR A 337 ALA A 342 -1 O MET A 339 N GLY A 330 SHEET 3 AA7 4 LYS A 347 ASP A 352 -1 O ALA A 349 N THR A 340 SHEET 4 AA7 4 ARG A 357 ASP A 363 -1 O SER A 359 N VAL A 350 SHEET 1 AA8 4 ALA A 374 HIS A 378 0 SHEET 2 AA8 4 GLY A 382 SER A 388 -1 O VAL A 384 N PHE A 376 SHEET 3 AA8 4 SER A 394 GLY A 399 -1 O ILE A 398 N TRP A 385 SHEET 4 AA8 4 LYS A 412 GLN A 417 -1 O LEU A 416 N ILE A 395 SHEET 1 AA9 4 ILE A 426 LYS A 427 0 SHEET 2 AA9 4 HIS A 434 VAL A 437 -1 O TYR A 436 N LYS A 427 SHEET 3 AA9 4 VAL A 451 ASP A 455 -1 O PHE A 454 N LEU A 435 SHEET 4 AA9 4 GLN A 464 LEU A 466 -1 O LEU A 466 N VAL A 451 SHEET 1 AB1 4 LYS A 479 TYR A 486 0 SHEET 2 AB1 4 GLU A 492 ASN A 499 -1 O TRP A 494 N GLU A 485 SHEET 3 AB1 4 SER A 505 ASP A 511 -1 O VAL A 510 N VAL A 493 SHEET 4 AB1 4 LYS A 516 VAL A 521 -1 O VAL A 521 N LEU A 507 LINK SG CYS A 47 CAB HEC A 903 1555 1555 1.90 LINK SG CYS A 50 CAC HEC A 903 1555 1555 1.93 LINK NE2 HIS A 51 FE HEC A 903 1555 1555 2.03 LINK SD MET A 88 FE HEC A 903 1555 1555 2.33 CISPEP 1 TRP A 246 PRO A 247 0 -10.50 SITE 1 AC1 5 ASN A 308 THR A 316 LYS A 354 ASP A 355 SITE 2 AC1 5 ARG A 356 SITE 1 AC2 2 HOH A1072 HOH A1082 SITE 1 AC3 16 ARG A 46 CYS A 47 CYS A 50 HIS A 51 SITE 2 AC3 16 GLY A 60 LYS A 61 LEU A 63 ARG A 71 SITE 3 AC3 16 TYR A 75 THR A 84 LEU A 86 GLY A 87 SITE 4 AC3 16 MET A 88 PRO A 89 TRP A 91 HOH A1074 CRYST1 67.245 67.245 277.104 90.00 90.00 90.00 P 43 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 0.014871 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014871 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003609 0.00000