HEADER OXIDOREDUCTASE 19-NOV-17 5YTM TITLE C135A MUTANT OF COPPER-CONTAINING NITRITE REDUCTASE FROM GEOBACILLUS TITLE 2 THERMODENITRIFICANS DETERMINED BY IN-OUSE SOURCE 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; 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 5YTM 1 LINK REVDAT 1 22-AUG-18 5YTM 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. 1.50 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 17.51 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.020 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 65562 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.119 REMARK 3 R VALUE (WORKING SET) : 0.117 REMARK 3 FREE R VALUE : 0.153 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.890 REMARK 3 FREE R VALUE TEST SET COUNT : 3206 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 17.5081 - 4.2461 0.97 2656 139 0.1301 0.1552 REMARK 3 2 4.2461 - 3.3782 0.96 2663 120 0.1127 0.1549 REMARK 3 3 3.3782 - 2.9535 0.95 2615 134 0.1233 0.1566 REMARK 3 4 2.9535 - 2.6845 0.97 2667 135 0.1253 0.1530 REMARK 3 5 2.6845 - 2.4927 0.97 2659 133 0.1221 0.1404 REMARK 3 6 2.4927 - 2.3461 0.98 2699 126 0.1182 0.1485 REMARK 3 7 2.3461 - 2.2288 0.98 2692 136 0.1107 0.1609 REMARK 3 8 2.2288 - 2.1320 0.98 2710 131 0.1056 0.1413 REMARK 3 9 2.1320 - 2.0500 0.98 2663 157 0.1045 0.1446 REMARK 3 10 2.0500 - 1.9794 0.99 2754 121 0.1056 0.1624 REMARK 3 11 1.9794 - 1.9176 0.99 2711 163 0.0999 0.1305 REMARK 3 12 1.9176 - 1.8628 0.99 2722 159 0.0943 0.1329 REMARK 3 13 1.8628 - 1.8138 1.00 2704 152 0.0958 0.1401 REMARK 3 14 1.8138 - 1.7696 1.00 2747 152 0.1001 0.1459 REMARK 3 15 1.7696 - 1.7294 1.00 2748 148 0.1067 0.1421 REMARK 3 16 1.7294 - 1.6927 1.00 2743 122 0.1150 0.1743 REMARK 3 17 1.6927 - 1.6588 1.00 2757 153 0.1244 0.1851 REMARK 3 18 1.6588 - 1.6276 1.00 2753 122 0.1234 0.1477 REMARK 3 19 1.6276 - 1.5985 1.00 2745 134 0.1211 0.1642 REMARK 3 20 1.5985 - 1.5714 1.00 2736 158 0.1251 0.1754 REMARK 3 21 1.5714 - 1.5461 1.00 2760 119 0.1381 0.1842 REMARK 3 22 1.5461 - 1.5223 1.00 2740 141 0.1553 0.1883 REMARK 3 23 1.5223 - 1.4999 1.00 2712 151 0.1912 0.2192 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 12.230 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.10 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 2476 REMARK 3 ANGLE : 0.851 3380 REMARK 3 CHIRALITY : 0.088 366 REMARK 3 PLANARITY : 0.005 448 REMARK 3 DIHEDRAL : 14.817 904 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 5YTM 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_1300005895. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-FEB-17 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS VII REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 65738 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 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 (%) : 98.7 REMARK 200 DATA REDUNDANCY : 1.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M ACETATE BUFFER PH 4.5, 5.0% PEG REMARK 280 4000, 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 57.53900 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 33.22016 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 28.01433 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 57.53900 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 33.22016 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 28.01433 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 57.53900 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 33.22016 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 28.01433 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 66.44031 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 56.02867 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 66.44031 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 56.02867 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 66.44031 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 56.02867 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: 11790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -211.0 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 S SO4 A 408 LIES ON A SPECIAL POSITION. REMARK 375 O2 SO4 A 408 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 NE2 HIS A 39 O HOH A 501 2.08 REMARK 500 O HOH A 506 O HOH A 753 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP A 256 12.91 56.56 REMARK 500 SER A 274 -1.63 80.80 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 293 147.15 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 403 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 42 NE2 REMARK 620 2 GLU A 53 OE2 44.7 REMARK 620 3 HIS A 83 ND1 108.6 81.8 REMARK 620 4 HOH A 535 O 170.5 142.9 80.2 REMARK 620 5 HOH A 749 O 103.2 72.5 98.4 78.4 REMARK 620 N 1 2 3 4 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 HIS A 143 ND1 93.7 REMARK 620 3 MET A 148 SD 105.4 153.2 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 111.5 REMARK 620 3 HIS A 294 NE2 71.5 103.8 REMARK 620 4 HOH A 506 O 86.3 105.1 148.5 REMARK 620 5 HOH A 753 O 135.6 102.7 126.8 57.4 REMARK 620 N 1 2 3 4 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 ASP A 167 OD2 REMARK 620 2 HOH A 505 O 95.5 REMARK 620 3 HOH A 619 O 99.1 77.5 REMARK 620 N 1 2 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 ACY A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACY A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MRD A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 409 DBREF1 5YTM A 2 323 UNP A0A1W6VP04_GEOTD DBREF2 5YTM A A0A1W6VP04 31 352 SEQADV 5YTM MET A 1 UNP A0A1W6VP0 EXPRESSION TAG SEQADV 5YTM ALA A 135 UNP A0A1W6VP0 CYS 164 ENGINEERED MUTATION 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 ALA 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 ACY A 405 4 HET ACY A 406 8 HET MRD A 407 8 HET SO4 A 408 5 HET SO4 A 409 5 HETNAM CU COPPER (II) ION HETNAM ACY ACETIC ACID HETNAM MRD (4R)-2-METHYLPENTANE-2,4-DIOL HETNAM SO4 SULFATE ION FORMUL 2 CU 4(CU 2+) FORMUL 6 ACY 2(C2 H4 O2) FORMUL 8 MRD C6 H14 O2 FORMUL 9 SO4 2(O4 S 2-) FORMUL 11 HOH *356(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 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 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 TYR A 289 O LEU A 307 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 2.06 LINK OE2 GLU A 53 CU CU A 403 1555 6555 1.99 LINK ND1 HIS A 83 CU CU A 403 1555 1555 1.98 LINK ND1 HIS A 95 CU CU A 401 1555 1555 1.99 LINK NE2 HIS A 100 CU CU A 402 1555 1555 2.01 LINK NE2 HIS A 134 CU CU A 402 1555 1555 2.06 LINK ND1 HIS A 143 CU CU A 401 1555 1555 2.13 LINK SD MET A 148 CU CU A 401 1555 1555 2.07 LINK OD2 ASP A 167 CU CU A 404 1555 1555 2.05 LINK NE2 HIS A 294 CU CU A 402 1555 2555 2.03 LINK CU CU A 402 O HOH A 506 1555 1555 2.19 LINK CU CU A 402 O HOH A 753 1555 1555 2.26 LINK CU CU A 403 O HOH A 535 1555 8544 2.34 LINK CU CU A 403 O HOH A 749 1555 1555 2.39 LINK CU CU A 404 O HOH A 505 1555 1555 2.25 LINK CU CU A 404 O HOH A 619 1555 1555 2.51 CISPEP 1 ALA A 69 PRO A 70 0 -6.67 CISPEP 2 LYS A 138 PRO A 139 0 -3.12 CISPEP 3 GLY A 236 PRO A 237 0 12.62 SITE 1 AC1 4 HIS A 95 ALA A 135 HIS A 143 MET A 148 SITE 1 AC2 5 HIS A 100 HIS A 134 HIS A 294 HOH A 506 SITE 2 AC2 5 HOH A 753 SITE 1 AC3 5 HIS A 42 GLU A 53 HIS A 83 HOH A 535 SITE 2 AC3 5 HOH A 749 SITE 1 AC4 4 ASP A 167 HOH A 505 HOH A 619 HOH A 705 SITE 1 AC5 2 TYR A 180 ASN A 181 SITE 1 AC6 4 HIS A 103 ASN A 126 ASP A 251 HOH A 503 SITE 1 AC7 5 ASP A 163 VAL A 166 ASP A 167 GLU A 169 SITE 2 AC7 5 HOH A 649 SITE 1 AC8 4 ASP A 55 THR A 212 GLN A 300 LYS A 301 CRYST1 115.078 115.078 84.043 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 0.008690 0.005017 0.000000 0.00000 SCALE2 0.000000 0.010034 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011899 0.00000