HEADER OXIDOREDUCTASE 19-NOV-17 5YTL TITLE CRYSTAL STRUCTURE OF GEOBACILLUS THERMODENITRIFICANS COPPER-CONTAINING TITLE 2 NITRITE REDUCTASE DETERMINED WITH AN ANAEROBICALLY MANIPULATED TITLE 3 CRYSTAL 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; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS COPPER, NITRITE REDUCTASE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.FUKUDA,T.MATSUSAKI,K.M.TSE,E.MIZOHATA,M.E.P.MURPHY,T.INOUE REVDAT 2 27-MAR-24 5YTL 1 LINK REVDAT 1 22-AUG-18 5YTL 0 JRNL AUTH Y.FUKUDA,T.MATSUSAKI,K.M.TSE,E.MIZOHATA,M.E.P.MURPHY,T.INOUE JRNL TITL CRYSTALLOGRAPHIC STUDY OF DIOXYGEN CHEMISTRY IN A JRNL TITL 2 COPPER-CONTAINING NITRITE REDUCTASE FROM GEOBACILLUS JRNL TITL 3 THERMODENITRIFICANS. JRNL REF ACTA CRYSTALLOGR D STRUCT V. 74 769 2018 JRNL REF 2 BIOL JRNL REFN ISSN 2059-7983 JRNL PMID 30082512 JRNL DOI 10.1107/S2059798318010082 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.32 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.980 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 81973 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.115 REMARK 3 R VALUE (WORKING SET) : 0.113 REMARK 3 FREE R VALUE : 0.140 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.940 REMARK 3 FREE R VALUE TEST SET COUNT : 4050 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 26.3254 - 4.2979 0.95 2576 147 0.1257 0.1482 REMARK 3 2 4.2979 - 3.4137 0.98 2614 161 0.1072 0.1190 REMARK 3 3 3.4137 - 2.9829 0.98 2668 111 0.1138 0.1369 REMARK 3 4 2.9829 - 2.7104 0.99 2680 161 0.1244 0.1686 REMARK 3 5 2.7104 - 2.5163 0.99 2662 132 0.1270 0.1483 REMARK 3 6 2.5163 - 2.3681 0.99 2701 141 0.1154 0.1407 REMARK 3 7 2.3681 - 2.2495 0.99 2699 117 0.1086 0.1292 REMARK 3 8 2.2495 - 2.1517 0.99 2672 150 0.1018 0.1427 REMARK 3 9 2.1517 - 2.0689 1.00 2653 142 0.0955 0.1205 REMARK 3 10 2.0689 - 1.9975 1.00 2725 123 0.0946 0.1098 REMARK 3 11 1.9975 - 1.9351 1.00 2716 131 0.0924 0.1059 REMARK 3 12 1.9351 - 1.8798 1.00 2692 129 0.0875 0.1155 REMARK 3 13 1.8798 - 1.8303 1.00 2734 116 0.0883 0.1191 REMARK 3 14 1.8303 - 1.7857 1.00 2684 146 0.0895 0.1180 REMARK 3 15 1.7857 - 1.7451 1.00 2683 126 0.0883 0.1300 REMARK 3 16 1.7451 - 1.7079 1.00 2734 145 0.0913 0.1345 REMARK 3 17 1.7079 - 1.6738 1.00 2679 139 0.0931 0.1188 REMARK 3 18 1.6738 - 1.6422 1.00 2690 151 0.1012 0.1306 REMARK 3 19 1.6422 - 1.6129 1.00 2696 160 0.1058 0.1609 REMARK 3 20 1.6129 - 1.5855 1.00 2700 145 0.1133 0.1577 REMARK 3 21 1.5855 - 1.5600 1.00 2667 143 0.1153 0.1552 REMARK 3 22 1.5600 - 1.5360 1.00 2697 141 0.1288 0.1479 REMARK 3 23 1.5360 - 1.5134 1.00 2695 168 0.1383 0.1837 REMARK 3 24 1.5134 - 1.4921 1.00 2743 122 0.1421 0.1650 REMARK 3 25 1.4921 - 1.4719 1.00 2668 139 0.1497 0.1574 REMARK 3 26 1.4719 - 1.4528 1.00 2679 140 0.1622 0.1946 REMARK 3 27 1.4528 - 1.4346 1.00 2733 140 0.1776 0.1967 REMARK 3 28 1.4346 - 1.4173 1.00 2697 127 0.1891 0.2447 REMARK 3 29 1.4173 - 1.4009 0.99 2686 157 0.1962 0.2196 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) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 11.780 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.50 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 : 0.005 2521 REMARK 3 ANGLE : 0.884 3458 REMARK 3 CHIRALITY : 0.088 377 REMARK 3 PLANARITY : 0.006 460 REMARK 3 DIHEDRAL : 18.152 936 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 5YTL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-NOV-17. REMARK 100 THE DEPOSITION ID IS D_1300005894. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-OCT-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL32XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9790 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 81993 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 2.900 REMARK 200 R MERGE (I) : NULL 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) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.500 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 (%): 59.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M ACETATE BUFFER PH 4.5, 6.0 % PEG REMARK 280 4000, 75MM CUSO4, VAPOR DIFFUSION, HANGING DROP, 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 57.65700 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 33.28828 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 28.17800 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 57.65700 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 33.28828 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 28.17800 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 57.65700 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 33.28828 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 28.17800 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 66.57657 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 56.35600 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 66.57657 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 56.35600 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 66.57657 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 56.35600 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: 11230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28210 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -122.0 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 CU CU A 404 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 788 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 801 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 THR A 312 REMARK 465 GLY A 313 REMARK 465 GLU A 314 REMARK 465 ASP A 315 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 O HOH A 613 O HOH A 675 2.03 REMARK 500 O HOH A 503 O HOH A 730 2.09 REMARK 500 O HOH A 691 O HOH A 798 2.14 REMARK 500 NE2 HIS A 39 O HOH A 501 2.14 REMARK 500 OE2 GLU A 44 O HOH A 502 2.18 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 NZ LYS A 108 O HOH A 765 3555 2.16 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 VAL A 92 -23.95 -142.00 REMARK 500 ASP A 256 13.64 56.42 REMARK 500 SER A 274 -3.06 82.19 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 293 146.95 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 HOH A 807 DISTANCE = 5.98 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 OE2 45.1 REMARK 620 3 HIS A 83 ND1 119.9 86.6 REMARK 620 N 1 2 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 134.2 REMARK 620 3 HIS A 143 ND1 103.3 107.1 REMARK 620 4 MET A 148 SD 83.1 112.4 115.5 REMARK 620 N 1 2 3 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 118.5 REMARK 620 3 HIS A 294 NE2 72.7 105.1 REMARK 620 4 HOH A 627 O 107.2 104.5 145.8 REMARK 620 5 HOH A 627 O 132.8 99.6 125.1 31.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 405 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 167 OD2 REMARK 620 2 HOH A 504 O 90.9 REMARK 620 3 HOH A 508 O 96.6 70.6 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 404 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 MET A 270 SD REMARK 620 2 MET A 270 SD 57.5 REMARK 620 3 MET A 270 SD 0.0 57.5 REMARK 620 4 MET A 270 SD 57.5 0.0 57.5 REMARK 620 N 1 2 3 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 CU A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MRD 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 5YTL A 2 323 UNP A0A1W6VP04_GEOTD DBREF2 5YTL A A0A1W6VP04 31 352 SEQADV 5YTL 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 CU A 405 1 HET MRD A 406 8 HET MPD A 407 8 HET ACY A 408 4 HETNAM CU COPPER (II) ION HETNAM MRD (4R)-2-METHYLPENTANE-2,4-DIOL HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM ACY ACETIC ACID FORMUL 2 CU 5(CU 2+) FORMUL 7 MRD C6 H14 O2 FORMUL 8 MPD C6 H14 O2 FORMUL 9 ACY C2 H4 O2 FORMUL 10 HOH *307(H2 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 HIS A 83 N VAL A 41 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 TYR A 231 N LEU A 172 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 LEU A 263 N VAL A 253 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 1.96 LINK OE2 GLU A 53 CU CU A 403 1555 6445 2.08 LINK ND1 HIS A 83 CU CU A 403 1555 1555 2.13 LINK ND1 HIS A 95 CU CU A 401 1555 1555 2.03 LINK NE2 HIS A 100 CU CU A 402 1555 1555 2.02 LINK NE2 HIS A 134 CU CU A 402 1555 1555 2.01 LINK SG CYS A 135 CU CU A 401 1555 1555 2.25 LINK ND1 HIS A 143 CU CU A 401 1555 1555 2.07 LINK SD MET A 148 CU CU A 401 1555 1555 2.61 LINK OD2 ASP A 167 CU CU A 405 1555 1555 2.01 LINK SD AMET A 270 CU CU A 404 1555 1555 2.44 LINK SD BMET A 270 CU CU A 404 1555 1555 2.46 LINK SD AMET A 270 CU CU A 404 1555 3555 2.37 LINK SD BMET A 270 CU CU A 404 1555 3555 2.40 LINK NE2 HIS A 294 CU CU A 402 1555 2555 2.04 LINK CU CU A 402 O AHOH A 627 1555 1555 2.22 LINK CU CU A 402 O BHOH A 627 1555 1555 2.44 LINK CU CU A 405 O HOH A 504 1555 1555 2.58 LINK CU CU A 405 O HOH A 508 1555 1555 2.27 CISPEP 1 ALA A 69 PRO A 70 0 -8.92 CISPEP 2 LYS A 138 PRO A 139 0 -4.40 CISPEP 3 LYS A 138 PRO A 139 0 -2.10 CISPEP 4 GLY A 236 PRO A 237 0 14.84 SITE 1 AC1 4 HIS A 95 CYS A 135 HIS A 143 MET A 148 SITE 1 AC2 4 HIS A 100 HIS A 134 HIS A 294 HOH A 627 SITE 1 AC3 5 HIS A 42 GLU A 53 HIS A 83 HOH A 503 SITE 2 AC3 5 HOH A 730 SITE 1 AC4 1 MET A 270 SITE 1 AC5 3 ASP A 167 HOH A 504 HOH A 508 SITE 1 AC6 4 ASP A 163 ASP A 167 ARG A 168 GLU A 169 SITE 1 AC7 4 LYS A 22 GLY A 23 ASP A 51 LYS A 61 CRYST1 115.314 115.314 84.534 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 0.008672 0.005007 0.000000 0.00000 SCALE2 0.000000 0.010014 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011830 0.00000