HEADER OXIDOREDUCTASE 05-DEC-24 9KVL TITLE NEUTRON AND X-RAY JOINT REFINED STRUCTURE OF A COPPER-CONTAINING TITLE 2 NITRITE REDUCTASE (C135A MUTANT) IN COMPLEX WITH NITRITE COMPND MOL_ID: 1; COMPND 2 MOLECULE: COPPER-CONTAINING NITRITE REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.7.2.1; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACILLUS THERMODENITRIFICANS NG80-2; SOURCE 3 ORGANISM_TAXID: 420246; SOURCE 4 GENE: NIRK, GTNG_0650; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS COPPER, DENITRIFICATION, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION; NEUTRON DIFFRACTION AUTHOR Y.FUKUDA,M.LINTULUOTO,Y.HIRANO,K.KUSAKA,T.INOUE,T.TAMADA REVDAT 2 02-JUL-25 9KVL 1 JRNL REVDAT 1 11-JUN-25 9KVL 0 JRNL AUTH Y.FUKUDA,M.LINTULUOTO,Y.HIRANO,K.KUSAKA,T.INOUE,T.TAMADA JRNL TITL STRUCTURAL BASIS OF CUPROENZYME NITRITE REDUCTION AT THE JRNL TITL 2 LEVEL OF A SINGLE HYDROGEN ATOM. JRNL REF J.BIOL.CHEM. V. 301 10290 2025 JRNL REFN ESSN 1083-351X JRNL PMID 40436316 JRNL DOI 10.1016/J.JBC.2025.110290 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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 NEUTRON DATA. REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 13.20 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 3 NUMBER OF REFLECTIONS : 43442 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.156 REMARK 3 R VALUE (WORKING SET) : 0.156 REMARK 3 FREE R VALUE : 0.172 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.610 REMARK 3 FREE R VALUE TEST SET COUNT : 2003 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 13.2000 - 4.0600 0.95 2979 150 0.1472 0.1482 REMARK 3 2 4.0600 - 3.2400 1.00 3098 148 0.1587 0.1583 REMARK 3 3 3.2400 - 2.8300 1.00 3139 149 0.1596 0.1810 REMARK 3 4 2.8300 - 2.5800 1.00 3101 151 0.1506 0.1759 REMARK 3 5 2.5800 - 2.3900 1.00 3139 149 0.1369 0.1423 REMARK 3 6 2.3900 - 2.2500 1.00 3088 148 0.1334 0.1565 REMARK 3 7 2.2500 - 2.1400 0.99 3141 156 0.1378 0.1569 REMARK 3 8 2.1400 - 2.0500 0.96 2979 148 0.1480 0.1713 REMARK 3 9 2.0500 - 1.9700 0.93 2885 138 0.1518 0.1667 REMARK 3 10 1.9700 - 1.9000 0.91 2824 139 0.1547 0.1783 REMARK 3 11 1.9000 - 1.8400 0.90 2830 138 0.1705 0.1833 REMARK 3 12 1.8400 - 1.7900 0.89 2778 132 0.1747 0.1947 REMARK 3 13 1.7900 - 1.7400 0.88 2733 129 0.1835 0.2193 REMARK 3 14 1.7400 - 1.7000 0.86 2725 128 0.1943 0.2267 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) : 0.110 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.330 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 : 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 : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 3 X-RAY DATA. REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.16 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 102513 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.114 REMARK 3 FREE R VALUE : 0.132 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 28.1600 - 3.9900 1.00 3357 164 0.1323 0.1397 REMARK 3 2 3.9900 - 3.1700 1.00 3375 160 0.1372 0.1440 REMARK 3 3 3.1700 - 2.7700 1.00 3391 162 0.1236 0.1460 REMARK 3 4 2.7700 - 2.5200 1.00 3361 165 0.1178 0.1267 REMARK 3 5 2.5200 - 2.3400 1.00 3369 157 0.1131 0.1390 REMARK 3 6 2.3400 - 2.2000 1.00 3375 164 0.1145 0.1166 REMARK 3 7 2.2000 - 2.0900 1.00 3393 168 0.1202 0.1271 REMARK 3 8 2.0900 - 2.0000 1.00 3384 157 0.1279 0.1484 REMARK 3 9 2.0000 - 1.9200 1.00 3350 164 0.1336 0.1565 REMARK 3 10 1.9200 - 1.8500 1.00 3340 159 0.1193 0.1247 REMARK 3 11 1.8500 - 1.8000 1.00 3412 155 0.1127 0.1364 REMARK 3 12 1.8000 - 1.7400 1.00 3357 152 0.1115 0.1178 REMARK 3 13 1.7400 - 1.7000 1.00 3399 154 0.1051 0.1252 REMARK 3 14 1.7000 - 1.6600 1.00 3435 119 0.1038 0.1142 REMARK 3 15 1.6600 - 1.6200 1.00 3372 119 0.1007 0.1183 REMARK 3 16 1.6200 - 1.5900 1.00 3430 124 0.1004 0.1329 REMARK 3 17 1.5800 - 1.5500 1.00 3417 117 0.1019 0.1194 REMARK 3 18 1.5500 - 1.5200 1.00 3434 121 0.0992 0.1233 REMARK 3 19 1.5200 - 1.5000 1.00 3418 118 0.0962 0.1097 REMARK 3 20 1.5000 - 1.4700 1.00 3387 121 0.0947 0.1182 REMARK 3 21 1.4700 - 1.4500 1.00 3472 122 0.0939 0.1063 REMARK 3 22 1.4500 - 1.4300 1.00 3388 119 0.0922 0.1024 REMARK 3 23 1.4300 - 1.4000 1.00 3390 118 0.0907 0.1202 REMARK 3 24 1.4000 - 1.3800 1.00 3418 119 0.0888 0.1219 REMARK 3 25 1.3800 - 1.3700 1.00 3426 123 0.0903 0.1154 REMARK 3 26 1.3700 - 1.3500 1.00 3435 118 0.0929 0.1373 REMARK 3 27 1.3500 - 1.3300 1.00 3426 120 0.0947 0.1175 REMARK 3 28 1.3300 - 1.3200 1.00 3405 118 0.1003 0.1154 REMARK 3 29 1.3200 - 1.3000 1.00 3400 120 0.1063 0.1429 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) : 0.110 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.330 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 : 0.020 5837 REMARK 3 ANGLE : 1.134 9808 REMARK 3 CHIRALITY : 0.088 401 REMARK 3 PLANARITY : 0.007 927 REMARK 3 DIHEDRAL : 16.335 1508 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 9KVL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-DEC-24. REMARK 100 THE DEPOSITION ID IS D_1300054424. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-FEB-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 225316 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.000 REMARK 200 RESOLUTION RANGE LOW (A) : 42.920 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.10 REMARK 200 R MERGE FOR SHELL (I) : 0.33000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 4YSO REMARK 200 REMARK 200 REMARK: NULL REMARK 230 REMARK 230 EXPERIMENTAL DETAILS REMARK 230 EXPERIMENT TYPE : NEUTRON DIFFRACTION REMARK 230 DATE OF DATA COLLECTION : 28-JAN-20 REMARK 230 TEMPERATURE (KELVIN) : 100.0 REMARK 230 PH : 4.50 REMARK 230 NUMBER OF CRYSTALS USED : NULL REMARK 230 REMARK 230 NEUTRON SOURCE : SPALLATION SOURCE REMARK 230 BEAMLINE : BL-03 REMARK 230 WAVELENGTH OR RANGE (A) : 2.15-4.89 REMARK 230 MONOCHROMATOR : NULL REMARK 230 OPTICS : NULL REMARK 230 REMARK 230 DETECTOR TYPE : DIFFRACTOMETER REMARK 230 DETECTOR MANUFACTURER : IBIX REMARK 230 INTENSITY-INTEGRATION SOFTWARE : STARGAZER, AUTOXDS REMARK 230 DATA SCALING SOFTWARE : SCALA REMARK 230 REMARK 230 NUMBER OF UNIQUE REFLECTIONS : 43445 REMARK 230 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 230 RESOLUTION RANGE LOW (A) : 20.000 REMARK 230 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 230 REMARK 230 OVERALL. REMARK 230 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 230 DATA REDUNDANCY : 7.300 REMARK 230 R MERGE (I) : 0.24700 REMARK 230 R SYM (I) : NULL REMARK 230 FOR THE DATA SET : 8.8000 REMARK 230 REMARK 230 IN THE HIGHEST RESOLUTION SHELL. REMARK 230 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 230 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.79 REMARK 230 COMPLETENESS FOR SHELL (%) : 87.1 REMARK 230 DATA REDUNDANCY IN SHELL : 5.80 REMARK 230 R MERGE FOR SHELL (I) : 0.56500 REMARK 230 R SYM FOR SHELL (I) : NULL REMARK 230 FOR SHELL : 3.000 REMARK 230 REMARK 230 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 230 SOFTWARE USED : MOLREP REMARK 230 STARTING MODEL: 4YSO REMARK 230 REMARK 230 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M ACETATE BUFFER PH 4.5, 5.5% REMARK 280 (W/V) PEG 4000, AND 75 MM CUSO4, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 57.53000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 33.21496 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 28.16100 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 57.53000 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 33.21496 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 28.16100 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 57.53000 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 33.21496 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 28.16100 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 66.42992 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 56.32200 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 66.42992 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 56.32200 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 66.42992 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 56.32200 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 12540 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -119.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 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 O DOD A 903 LIES ON A SPECIAL POSITION. 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 OE1 GLU A 44 D1 DOD A 603 1.49 REMARK 500 OE2 GLU A 169 DH TYR A 231 1.57 REMARK 500 DE2 HIS A 39 O DOD A 609 1.58 REMARK 500 O DOD A 834 O DOD A 849 2.10 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 DE2 GLU A 34 OD2 ASP A 51 6445 1.50 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 242 78.37 -112.33 REMARK 500 ASP A 256 12.51 57.27 REMARK 500 SER A 274 2.68 80.45 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 VAL A 292 THR A 293 145.55 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 CU A 506 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 42 NE2 REMARK 620 2 GLU A 53 OE1 36.1 REMARK 620 3 GLU A 53 OE2 38.2 2.3 REMARK 620 4 HIS A 83 ND1 95.0 75.5 75.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 504 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 95 ND1 REMARK 620 2 HIS A 143 ND1 104.8 REMARK 620 3 MET A 148 SD 100.0 155.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 505 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 100 NE2 REMARK 620 2 HIS A 134 NE2 109.5 REMARK 620 3 HIS A 294 NE2 69.3 101.0 REMARK 620 4 NO2 A 503 N 135.4 108.6 124.0 REMARK 620 5 NO2 A 503 O1 165.9 81.9 117.8 30.5 REMARK 620 6 NO2 A 503 O2 108.4 120.9 134.4 29.3 57.6 REMARK 620 N 1 2 3 4 5 DBREF 9KVL A 16 315 UNP A4IL26 A4IL26_GEOTN 45 344 SEQADV 9KVL ALA A 135 UNP A4IL26 CYS 164 ENGINEERED MUTATION SEQRES 1 A 300 ASN VAL ILE ALA ALA HIS LYS GLY VAL ASN GLN ALA PRO SEQRES 2 A 300 VAL PRO LEU LYS MET GLU ARG VAL GLY PRO HIS ASP VAL SEQRES 3 A 300 HIS ILE GLU MET THR ALA GLN ILE THR ASP ILE GLU ILE SEQRES 4 A 300 ASP LYS GLY LYS ILE TYR LYS ALA TRP THR PHE ASN GLY SEQRES 5 A 300 GLN ALA PRO GLY PRO LEU VAL VAL VAL ASN GLU GLY ASP SEQRES 6 A 300 THR ILE HIS PHE THR LEU LYS ASN MET ASP PRO VAL VAL SEQRES 7 A 300 PRO HIS SER MET ASP PHE HIS ALA VAL HIS ALA SER PRO SEQRES 8 A 300 SER LYS ASP PHE ILE ASP VAL MET PRO ASN LYS SER GLY SEQRES 9 A 300 THR PHE THR TYR PRO ALA ASN LYS PRO GLY VAL PHE MET SEQRES 10 A 300 TYR HIS ALA GLY THR LYS PRO VAL LEU GLN HIS ILE ALA SEQRES 11 A 300 ASN GLY MET HIS GLY VAL ILE ILE VAL LYS PRO LYS ASN SEQRES 12 A 300 GLY TYR PRO THR ASP LYS GLU VAL ASP ARG GLU TYR VAL SEQRES 13 A 300 LEU ILE GLN ASN GLU TRP TYR LYS TYR ASN ASP MET ASN SEQRES 14 A 300 ASP PHE GLN ASN GLY VAL PRO SER TYR VAL VAL PHE SER SEQRES 15 A 300 SER LYS ALA LEU LYS PRO GLY ASP PRO ASN THR ASN GLY SEQRES 16 A 300 ASP THR PHE THR LEU LYS GLU LYS PRO LEU LEU ALA LYS SEQRES 17 A 300 VAL GLY GLU LYS ILE ARG LEU TYR ILE ASN ASN VAL GLY SEQRES 18 A 300 PRO ASN GLU VAL SER SER PHE HIS VAL VAL GLY THR VAL SEQRES 19 A 300 PHE ASP ASP VAL TYR LEU ASP GLY ASN PRO ASN ASN HIS SEQRES 20 A 300 LEU GLN GLY MET GLN THR VAL MET LEU PRO ALA SER GLY SEQRES 21 A 300 GLY ALA VAL VAL GLU PHE THR VAL THR ARG PRO GLY THR SEQRES 22 A 300 TYR PRO ILE VAL THR HIS GLN PHE ASN HIS ALA GLN LYS SEQRES 23 A 300 GLY ALA VAL ALA MET LEU LYS VAL THR GLU THR GLY GLU SEQRES 24 A 300 ASP HET MPD A 501 22 HET MRD A 502 22 HET NO2 A 503 3 HET CU A 504 1 HET CU A 505 1 HET CU A 506 1 HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM MRD (4R)-2-METHYLPENTANE-2,4-DIOL HETNAM NO2 NITRITE ION HETNAM CU COPPER (II) ION FORMUL 2 MPD C6 H14 O2 FORMUL 3 MRD C6 H14 O2 FORMUL 4 NO2 N O2 1- FORMUL 5 CU 3(CU 2+) FORMUL 8 DOD *336(D2 O) HELIX 1 AA1 ILE A 18 LYS A 22 5 5 HELIX 2 AA2 SER A 105 PHE A 110 1 6 HELIX 3 AA3 PRO A 139 ASN A 146 1 8 HELIX 4 AA4 THR A 162 VAL A 166 5 5 HELIX 5 AA5 ASP A 182 GLY A 189 1 8 HELIX 6 AA6 PHE A 213 LYS A 218 1 6 HELIX 7 AA7 GLN A 295 LYS A 301 1 7 SHEET 1 AA1 3 LYS A 32 GLY A 37 0 SHEET 2 AA1 3 ASP A 40 ASP A 55 -1 O HIS A 42 N GLU A 34 SHEET 3 AA1 3 LYS A 58 PHE A 65 -1 O TYR A 60 N ILE A 52 SHEET 1 AA2 4 LYS A 32 GLY A 37 0 SHEET 2 AA2 4 ASP A 40 ASP A 55 -1 O HIS A 42 N GLU A 34 SHEET 3 AA2 4 ASP A 80 ASN A 88 1 O THR A 85 N ILE A 43 SHEET 4 AA2 4 SER A 118 ALA A 125 -1 O PHE A 121 N PHE A 84 SHEET 1 AA3 4 VAL A 74 ASN A 77 0 SHEET 2 AA3 4 HIS A 149 LYS A 155 1 O ILE A 153 N VAL A 74 SHEET 3 AA3 4 GLY A 129 HIS A 134 -1 N GLY A 129 O VAL A 154 SHEET 4 AA3 4 ASP A 98 PHE A 99 -1 N ASP A 98 O HIS A 134 SHEET 1 AA4 6 TYR A 193 LYS A 199 0 SHEET 2 AA4 6 ARG A 168 TRP A 177 -1 N ASN A 175 O VAL A 195 SHEET 3 AA4 6 LYS A 227 GLY A 236 1 O ARG A 229 N ARG A 168 SHEET 4 AA4 6 GLY A 276 THR A 282 -1 O PHE A 281 N ILE A 228 SHEET 5 AA4 6 PHE A 250 LEU A 255 -1 N TYR A 254 O VAL A 278 SHEET 6 AA4 6 HIS A 262 MET A 266 -1 O MET A 266 N PHE A 250 SHEET 1 AA5 5 LEU A 220 LYS A 223 0 SHEET 2 AA5 5 VAL A 304 THR A 310 1 O LYS A 308 N LEU A 220 SHEET 3 AA5 5 GLY A 287 THR A 293 -1 N GLY A 287 O VAL A 309 SHEET 4 AA5 5 SER A 241 VAL A 245 -1 N HIS A 244 O VAL A 292 SHEET 5 AA5 5 VAL A 269 LEU A 271 -1 O LEU A 271 N SER A 241 LINK NE2 HIS A 42 CU CU A 506 1555 1555 2.01 LINK OE1 GLU A 53 CU CU A 506 1555 8444 2.62 LINK OE2 GLU A 53 CU CU A 506 1555 8444 1.99 LINK ND1 HIS A 83 CU CU A 506 1555 1555 2.01 LINK ND1 HIS A 95 CU CU A 504 1555 1555 2.08 LINK NE2 HIS A 100 CU CU A 505 1555 1555 2.02 LINK NE2 HIS A 134 CU CU A 505 1555 1555 2.02 LINK ND1 HIS A 143 CU CU A 504 1555 1555 1.97 LINK SD MET A 148 CU CU A 504 1555 1555 2.17 LINK NE2 HIS A 294 CU CU A 505 1555 3555 2.01 LINK N ANO2 A 503 CU CU A 505 1555 1555 2.68 LINK O1 ANO2 A 503 CU CU A 505 1555 1555 2.67 LINK O2 ANO2 A 503 CU CU A 505 1555 1555 1.77 CISPEP 1 ALA A 69 PRO A 70 0 -9.64 CISPEP 2 LYS A 138 PRO A 139 0 -7.24 CISPEP 3 LYS A 138 PRO A 139 0 -3.38 CISPEP 4 GLY A 236 PRO A 237 0 19.63 CRYST1 115.060 115.060 84.483 90.00 90.00 120.00 H 3 9 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 0.008691 0.005018 0.000000 0.00000 SCALE2 0.000000 0.010036 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011837 0.00000 CONECT 426 5159 CONECT 1208 5159 CONECT 1437 5157 CONECT 1519 5158 CONECT 2106 5158 CONECT 2252 5157 CONECT 2321 5157 CONECT 5110 5111 CONECT 5111 5110 5112 5113 5114 CONECT 5112 5111 CONECT 5113 5111 CONECT 5114 5111 5115 CONECT 5115 5114 5116 5117 CONECT 5116 5115 CONECT 5117 5115 CONECT 5132 5133 CONECT 5133 5132 5134 5135 5136 CONECT 5134 5133 CONECT 5135 5133 CONECT 5136 5133 5137 CONECT 5137 5136 5138 5139 CONECT 5138 5137 CONECT 5139 5137 CONECT 5154 5155 5156 5158 CONECT 5155 5154 5158 CONECT 5156 5154 5158 CONECT 5157 1437 2252 2321 CONECT 5158 1519 2106 5154 5155 CONECT 5158 5156 CONECT 5159 426 1208 MASTER 473 0 6 7 22 0 0 6 2686 1 30 24 END