HEADER OXIDOREDUCTASE 16-OCT-19 6L46 TITLE HIGH-RESOLUTION NEUTRON AND X-RAY JOINT REFINED STRUCTURE OF COPPER- TITLE 2 CONTAINING NITRITE REDUCTASE FROM GEOBACILLUS THERMODENITRIFICANS 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 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACILLUS THERMODENITRIFICANS; SOURCE 3 ORGANISM_TAXID: 33940; SOURCE 4 GENE: NIRK, GTHT12_00198; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS COPPER, NITRITE REDUCTASE, NEUTRON, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION; NEUTRON DIFFRACTION AUTHOR Y.FUKUDA,Y.HIRANO,K.KUSAKA,T.INOUE,T.TAMADA REVDAT 5 03-APR-24 6L46 1 REMARK REVDAT 4 27-MAR-24 6L46 1 LINK REVDAT 3 11-MAR-20 6L46 1 JRNL REVDAT 2 26-FEB-20 6L46 1 JRNL REVDAT 1 12-FEB-20 6L46 0 JRNL AUTH Y.FUKUDA,Y.HIRANO,K.KUSAKA,T.INOUE,T.TAMADA JRNL TITL HIGH-RESOLUTION NEUTRON CRYSTALLOGRAPHY VISUALIZES AN JRNL TITL 2 OH-BOUND RESTING STATE OF A COPPER-CONTAINING NITRITE JRNL TITL 3 REDUCTASE. JRNL REF PROC.NATL.ACAD.SCI.USA V. 117 4071 2020 JRNL REFN ESSN 1091-6490 JRNL PMID 32041886 JRNL DOI 10.1073/PNAS.1918125117 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15_3448 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 X-RAY DATA. REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.13 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 100127 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.098 REMARK 3 R VALUE (WORKING SET) : 0.097 REMARK 3 FREE R VALUE : 0.112 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.510 REMARK 3 FREE R VALUE TEST SET COUNT : 2516 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 34.1000 - 3.4100 1.00 5395 167 0.1113 0.1208 REMARK 3 2 3.4100 - 2.7000 1.00 5388 171 0.0999 0.1086 REMARK 3 3 2.7000 - 2.3600 1.00 5406 176 0.0960 0.1100 REMARK 3 4 2.3600 - 2.1500 1.00 5381 176 0.0920 0.0988 REMARK 3 5 2.1500 - 1.9900 1.00 5374 172 0.1006 0.1152 REMARK 3 6 1.9900 - 1.8700 1.00 5400 169 0.1048 0.1342 REMARK 3 7 1.8700 - 1.7800 1.00 5407 174 0.0974 0.1202 REMARK 3 8 1.7800 - 1.7000 1.00 5357 168 0.0912 0.0893 REMARK 3 9 1.7000 - 1.6400 1.00 5431 174 0.0896 0.1007 REMARK 3 10 1.6400 - 1.5800 1.00 5381 169 0.0868 0.1069 REMARK 3 11 1.5800 - 1.5300 1.00 5423 175 0.0881 0.1068 REMARK 3 12 1.5300 - 1.4900 1.00 5365 140 0.0878 0.1142 REMARK 3 13 1.4900 - 1.4500 1.00 5519 82 0.0903 0.1011 REMARK 3 14 1.4500 - 1.4100 1.00 5464 79 0.0926 0.1021 REMARK 3 15 1.4100 - 1.3800 1.00 5493 82 0.0921 0.1366 REMARK 3 16 1.3800 - 1.3500 1.00 5462 81 0.0947 0.0990 REMARK 3 17 1.3500 - 1.3200 1.00 5485 80 0.0946 0.1241 REMARK 3 18 1.3200 - 1.3000 1.00 5480 81 0.0971 0.1377 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) : 0.062 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 10.382 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 6.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.48 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 5648 REMARK 3 ANGLE : 1.054 9476 REMARK 3 CHIRALITY : 0.090 383 REMARK 3 PLANARITY : 0.008 898 REMARK 3 DIHEDRAL : 21.039 1444 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 NEUTRON DATA. REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 17.07 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 64964 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.142 REMARK 3 R VALUE (WORKING SET) : 0.142 REMARK 3 FREE R VALUE : 0.159 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.090 REMARK 3 FREE R VALUE TEST SET COUNT : 2006 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 17.0700 - 3.6046 0.97 4391 138 0.1584 0.1445 REMARK 3 2 3.6046 - 2.8655 1.00 4505 144 0.1331 0.1415 REMARK 3 3 2.8655 - 2.5046 1.00 4522 145 0.1270 0.1476 REMARK 3 4 2.5046 - 2.2762 1.00 4494 144 0.1102 0.1339 REMARK 3 5 2.2762 - 2.1133 1.00 4494 148 0.1104 0.1220 REMARK 3 6 2.1133 - 1.9889 1.00 4528 144 0.1124 0.1330 REMARK 3 7 1.9889 - 1.8895 1.00 4494 142 0.1285 0.1654 REMARK 3 8 1.8895 - 1.8073 1.00 4563 145 0.1375 0.1528 REMARK 3 9 1.8073 - 1.7378 1.00 4485 143 0.1458 0.1873 REMARK 3 10 1.7378 - 1.6779 1.00 4500 141 0.1469 0.1796 REMARK 3 11 1.6779 - 1.6255 1.00 4480 143 0.1560 0.1715 REMARK 3 12 1.6255 - 1.5790 1.00 4522 144 0.1689 0.1758 REMARK 3 13 1.5790 - 1.5375 1.00 4491 145 0.1760 0.1969 REMARK 3 14 1.5400 - 1.5000 0.99 4484 140 0.1908 0.2240 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) : 0.062 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 10.382 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 : 0.008 5648 REMARK 3 ANGLE : 1.054 9476 REMARK 3 CHIRALITY : 0.090 383 REMARK 3 PLANARITY : 0.008 898 REMARK 3 DIHEDRAL : 21.039 1444 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 6L46 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-OCT-19. REMARK 100 THE DEPOSITION ID IS D_1300014147. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-DEC-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 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-NE3A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 201251 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.030 REMARK 200 RESOLUTION RANGE LOW (A) : 42.580 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 9.600 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.03 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : 7.10 REMARK 200 R MERGE FOR SHELL (I) : 0.64100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.500 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 : 26-NOV-18 REMARK 230 TEMPERATURE (KELVIN) : 100.0 REMARK 230 PH : 4.60 REMARK 230 NUMBER OF CRYSTALS USED : 1 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 REMARK 230 DATA SCALING SOFTWARE : SCALA REMARK 230 REMARK 230 NUMBER OF UNIQUE REFLECTIONS : 64997 REMARK 230 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 230 RESOLUTION RANGE LOW (A) : 17.380 REMARK 230 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 230 REMARK 230 OVERALL. REMARK 230 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 230 DATA REDUNDANCY : 6.600 REMARK 230 R MERGE (I) : 0.23000 REMARK 230 R SYM (I) : NULL REMARK 230 FOR THE DATA SET : 9.5000 REMARK 230 REMARK 230 IN THE HIGHEST RESOLUTION SHELL. REMARK 230 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 230 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.59 REMARK 230 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 230 DATA REDUNDANCY IN SHELL : 5.30 REMARK 230 R MERGE FOR SHELL (I) : 0.60800 REMARK 230 R SYM FOR SHELL (I) : NULL REMARK 230 FOR SHELL : 2.200 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 (%): 58.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M ACETATE BUFFER PH 4.6, 5.5% REMARK 280 (W/V) PEG 4000, AND 50 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 57.10600 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 32.97016 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 27.89600 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 57.10600 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 32.97016 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 27.89600 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 57.10600 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 32.97016 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 27.89600 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 65.94033 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 55.79200 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 65.94033 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 55.79200 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 65.94033 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 55.79200 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: 11550 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -227.0 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 947 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 GLU A 2 REMARK 465 SER A 3 REMARK 465 LYS A 4 REMARK 465 ASN A 5 REMARK 465 LYS A 6 REMARK 465 THR A 7 REMARK 465 ALA A 8 REMARK 465 ALA A 9 REMARK 465 THR A 10 REMARK 465 GLN A 11 REMARK 465 GLN A 12 REMARK 465 SER A 13 REMARK 465 GLU A 14 REMARK 465 PRO A 15 REMARK 465 ASN A 16 REMARK 465 VAL A 17 REMARK 465 ASP A 316 REMARK 465 GLY A 317 REMARK 465 THR A 318 REMARK 465 GLU A 319 REMARK 465 THR A 320 REMARK 465 SER A 321 REMARK 465 GLY A 322 REMARK 465 HIS A 323 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 D1 DOD A 929 O DOD A 940 1.46 REMARK 500 D2 DOD A 711 O DOD A 829 1.54 REMARK 500 D1 DOD A 729 O DOD A 890 1.57 REMARK 500 O DOD A 626 D2 DOD A 723 1.58 REMARK 500 OG SER A 198 D2 DOD A 508 1.59 REMARK 500 D2 DOD A 711 O DOD A 937 1.60 REMARK 500 OD2 ASP A 315 O DOD A 501 1.78 REMARK 500 O DOD A 830 O DOD A 837 1.82 REMARK 500 O DOD A 950 O DOD A 954 1.89 REMARK 500 O DOD A 502 O DOD A 519 1.92 REMARK 500 O DOD A 548 O DOD A 803 2.01 REMARK 500 O DOD A 590 O DOD A 641 2.03 REMARK 500 O DOD A 739 O DOD A 794 2.04 REMARK 500 O DOD A 513 O DOD A 776 2.08 REMARK 500 O DOD A 812 O DOD A 850 2.09 REMARK 500 O DOD A 711 O DOD A 937 2.12 REMARK 500 O DOD A 790 O DOD A 841 2.14 REMARK 500 OD2 ASP A 167 O DOD A 502 2.14 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 6555 1.58 REMARK 500 NE2 HIS A 244 CU CU A 404 3555 1.68 REMARK 500 O DOD A 957 O DOD A 957 2555 1.95 REMARK 500 O DOD A 824 O DOD A 931 2555 2.04 REMARK 500 O DOD A 789 O DOD A 949 8544 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 GLU A 34 CD GLU A 34 OE1 -0.066 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 78.97 -112.78 REMARK 500 ASP A 256 12.87 58.07 REMARK 500 SER A 274 1.30 81.45 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 293 144.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 DOD A 957 DISTANCE = 6.04 ANGSTROMS REMARK 525 DOD A 958 DISTANCE = 6.06 ANGSTROMS 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 403 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 42 NE2 REMARK 620 2 GLU A 53 OE1 37.0 REMARK 620 3 GLU A 53 OE2 39.2 2.3 REMARK 620 4 HIS A 83 ND1 94.7 76.1 75.8 REMARK 620 5 DOD A 584 O 174.2 147.7 145.4 90.5 REMARK 620 6 DOD A 771 O 94.3 69.1 67.1 105.0 86.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 401 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 95 ND1 REMARK 620 2 CYS A 135 SG 138.4 REMARK 620 3 HIS A 143 ND1 101.8 102.4 REMARK 620 4 MET A 148 SD 82.3 111.8 122.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 405 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 98 OD2 REMARK 620 2 DOD A 520 O 73.3 REMARK 620 3 DOD A 526 O 66.8 140.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 402 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 100 NE2 REMARK 620 2 HIS A 134 NE2 106.8 REMARK 620 3 HIS A 294 NE2 65.8 100.2 REMARK 620 4 CL A 406 CL 150.6 101.4 117.4 REMARK 620 5 DOD A 520 O 88.5 104.3 148.8 76.4 REMARK 620 6 DOD A 781 O 154.6 95.0 123.6 7.8 73.3 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 CU A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CU A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CU A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CU A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MPD A 407 DBREF1 6L46 A 2 323 UNP A0A1W6VP04_GEOTD DBREF2 6L46 A A0A1W6VP04 31 352 SEQADV 6L46 MET A 1 UNP A0A1W6VP0 EXPRESSION TAG SEQRES 1 A 323 MET GLU SER LYS ASN LYS THR ALA ALA THR GLN GLN SER SEQRES 2 A 323 GLU PRO ASN VAL ILE ALA ALA HIS LYS GLY VAL ASN GLN SEQRES 3 A 323 ALA PRO VAL PRO LEU LYS MET GLU ARG VAL GLY PRO HIS SEQRES 4 A 323 ASP VAL HIS ILE GLU MET THR ALA GLN ILE THR ASP ILE SEQRES 5 A 323 GLU ILE ASP LYS GLY LYS ILE TYR LYS ALA TRP THR PHE SEQRES 6 A 323 ASN GLY GLN ALA PRO GLY PRO LEU VAL VAL VAL ASN GLU SEQRES 7 A 323 GLY ASP THR ILE HIS PHE THR LEU LYS ASN MET ASP PRO SEQRES 8 A 323 VAL VAL PRO HIS SER MET ASP PHE HIS ALA VAL HIS ALA SEQRES 9 A 323 SER PRO SER LYS ASP PHE ILE ASP VAL MET PRO ASN LYS SEQRES 10 A 323 SER GLY THR PHE THR TYR PRO ALA ASN LYS PRO GLY VAL SEQRES 11 A 323 PHE MET TYR HIS CYS GLY THR LYS PRO VAL LEU GLN HIS SEQRES 12 A 323 ILE ALA ASN GLY MET HIS GLY VAL ILE ILE VAL LYS PRO SEQRES 13 A 323 LYS ASN GLY TYR PRO THR ASP LYS GLU VAL ASP ARG GLU SEQRES 14 A 323 TYR VAL LEU ILE GLN ASN GLU TRP TYR LYS TYR ASN ASP SEQRES 15 A 323 MET ASN ASP PHE GLN ASN GLY VAL PRO SER TYR VAL VAL SEQRES 16 A 323 PHE SER SER LYS ALA LEU LYS PRO GLY ASP PRO ASN THR SEQRES 17 A 323 ASN GLY ASP THR PHE THR LEU LYS GLU LYS PRO LEU LEU SEQRES 18 A 323 ALA LYS VAL GLY GLU LYS ILE ARG LEU TYR ILE ASN ASN SEQRES 19 A 323 VAL GLY PRO ASN GLU VAL SER SER PHE HIS VAL VAL GLY SEQRES 20 A 323 THR VAL PHE ASP ASP VAL TYR LEU ASP GLY ASN PRO ASN SEQRES 21 A 323 ASN HIS LEU GLN GLY MET GLN THR VAL MET LEU PRO ALA SEQRES 22 A 323 SER GLY GLY ALA VAL VAL GLU PHE THR VAL THR ARG PRO SEQRES 23 A 323 GLY THR TYR PRO ILE VAL THR HIS GLN PHE ASN HIS ALA SEQRES 24 A 323 GLN LYS GLY ALA VAL ALA MET LEU LYS VAL THR GLU THR SEQRES 25 A 323 GLY GLU ASP ASP GLY THR GLU THR SER GLY HIS HET CU A 401 1 HET CU A 402 1 HET CU A 403 1 HET CU A 404 1 HET NA A 405 1 HET CL A 406 1 HET MPD A 407 22 HETNAM CU COPPER (II) ION HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL FORMUL 2 CU 4(CU 2+) FORMUL 6 NA NA 1+ FORMUL 7 CL CL 1- FORMUL 8 MPD C6 H14 O2 FORMUL 9 DOD *458(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 SER A 198 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 403 1555 1555 1.98 LINK OE1 GLU A 53 CU CU A 403 1555 8544 2.61 LINK OE2 GLU A 53 CU CU A 403 1555 8544 1.96 LINK ND1 HIS A 83 CU CU A 403 1555 1555 1.99 LINK ND1 HIS A 95 CU CU A 401 1555 1555 1.97 LINK OD2 ASP A 98 NA B NA A 405 1555 1555 2.08 LINK NE2 HIS A 100 CU CU A 402 1555 1555 2.01 LINK NE2 HIS A 134 CU CU A 402 1555 1555 2.07 LINK SG CYS A 135 CU CU A 401 1555 1555 2.17 LINK ND1 HIS A 143 CU CU A 401 1555 1555 1.95 LINK SD MET A 148 CU CU A 401 1555 1555 2.57 LINK NE2 HIS A 294 CU CU A 402 1555 3555 1.96 LINK CU CU A 402 CL B CL A 406 1555 1555 2.18 LINK CU CU A 402 O DOD A 520 1555 1555 2.03 LINK CU CU A 402 O ADOD A 781 1555 1555 2.21 LINK CU CU A 403 O DOD A 584 1555 6555 2.01 LINK CU CU A 403 O DOD A 771 1555 1555 2.23 LINK CU B CU A 404 O DOD A 520 1555 1555 2.05 LINK NA B NA A 405 O DOD A 520 1555 1555 2.14 LINK NA B NA A 405 O DOD A 526 1555 1555 2.50 CISPEP 1 ALA A 69 PRO A 70 0 -10.74 CISPEP 2 LYS A 138 PRO A 139 0 -6.66 CISPEP 3 LYS A 138 PRO A 139 0 -4.92 CISPEP 4 GLY A 236 PRO A 237 0 19.65 SITE 1 AC1 4 HIS A 95 CYS A 135 HIS A 143 MET A 148 SITE 1 AC2 7 HIS A 100 HIS A 134 CU A 404 NA A 405 SITE 2 AC2 7 CL A 406 DOD A 520 DOD A 781 SITE 1 AC3 3 HIS A 42 HIS A 83 DOD A 771 SITE 1 AC4 5 ASP A 98 HIS A 100 CU A 402 DOD A 520 SITE 2 AC4 5 DOD A 640 SITE 1 AC5 8 ASP A 98 HIS A 134 CU A 402 CL A 406 SITE 2 AC5 8 DOD A 520 DOD A 526 DOD A 781 DOD A 807 SITE 1 AC6 5 HIS A 134 CU A 402 NA A 405 DOD A 520 SITE 2 AC6 5 DOD A 807 SITE 1 AC7 7 ASP A 163 ASP A 167 ARG A 168 GLU A 169 SITE 2 AC7 7 ARG A 229 DOD A 521 DOD A 612 CRYST1 114.212 114.212 83.688 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 0.008756 0.005055 0.000000 0.00000 SCALE2 0.000000 0.010110 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011949 0.00000