HEADER OXIDOREDUCTASE 10-MAY-13 4KNT TITLE COPPER NITRITE REDUCTASE FROM NITROSOMONAS EUROPAEA PH 8.5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MULTICOPPER OXIDASE TYPE 1; COMPND 3 CHAIN: A, B, C SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NITROSOMONAS EUROPAEA; SOURCE 3 ORGANISM_TAXID: 228410; SOURCE 4 STRAIN: ATCC 19718 / NBRC 14298 KEYWDS NITRITE REDUCTASE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR A.C.ROSENZWEIG,T.L.LAWTON,L.A.SAYAVEDRA-SOTO,D.J.ARP REVDAT 4 28-FEB-24 4KNT 1 REMARK LINK REVDAT 3 18-SEP-13 4KNT 1 JRNL REVDAT 2 14-AUG-13 4KNT 1 JRNL REVDAT 1 24-JUL-13 4KNT 0 JRNL AUTH T.J.LAWTON,K.E.BOWEN,L.A.SAYAVEDRA-SOTO,D.J.ARP, JRNL AUTH 2 A.C.ROSENZWEIG JRNL TITL CHARACTERIZATION OF A NITRITE REDUCTASE INVOLVED IN JRNL TITL 2 NITRIFIER DENITRIFICATION. JRNL REF J.BIOL.CHEM. V. 288 25575 2013 JRNL REFN ISSN 0021-9258 JRNL PMID 23857587 JRNL DOI 10.1074/JBC.M113.484543 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.11 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 78099 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4130 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5477 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.45 REMARK 3 BIN R VALUE (WORKING SET) : 0.2720 REMARK 3 BIN FREE R VALUE SET COUNT : 296 REMARK 3 BIN FREE R VALUE : 0.3020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6663 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 78 REMARK 3 SOLVENT ATOMS : 842 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.97000 REMARK 3 B22 (A**2) : -0.73000 REMARK 3 B33 (A**2) : 0.05000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.14000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.133 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.122 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.075 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.521 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.941 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7032 ; 0.006 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9585 ; 1.027 ; 1.940 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 894 ; 6.120 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 342 ;36.155 ;24.649 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1092 ;11.288 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 33 ;17.821 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1029 ; 0.070 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5490 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 4329 ; 0.310 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 7020 ; 0.609 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2703 ; 0.978 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2547 ; 1.707 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 4KNT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-MAY-13. REMARK 100 THE DEPOSITION ID IS D_1000079570. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-JUL-11 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.3776 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 78099 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 34.110 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 49.93400 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 61.54500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 49.93400 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 61.54500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 8040 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28720 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -45.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 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 LEU A 92 -157.22 -139.89 REMARK 500 SER A 239 17.25 57.70 REMARK 500 SER A 278 99.19 -68.26 REMARK 500 SER A 278 99.15 -68.20 REMARK 500 LEU B 92 -159.43 -139.47 REMARK 500 SER B 239 16.25 58.22 REMARK 500 SER B 278 99.82 -69.34 REMARK 500 ASP B 295 31.46 -99.70 REMARK 500 LEU C 92 -157.04 -140.45 REMARK 500 SER C 239 17.29 58.59 REMARK 500 SER C 278 96.95 -68.70 REMARK 500 SER C 278 96.92 -68.72 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 408 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 83 ND1 REMARK 620 2 CYS A 123 SG 132.8 REMARK 620 3 HIS A 131 ND1 100.7 107.2 REMARK 620 4 MET A 136 SD 85.1 113.1 117.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 407 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 88 NE2 REMARK 620 2 HIS A 122 NE2 122.1 REMARK 620 3 HOH A 658 O 93.2 99.2 REMARK 620 4 HIS B 277 NE2 113.4 114.4 110.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU C 405 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 277 NE2 REMARK 620 2 HIS C 88 NE2 112.0 REMARK 620 3 HIS C 122 NE2 114.3 124.7 REMARK 620 4 HOH C 723 O 109.6 93.8 97.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU B 404 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 83 ND1 REMARK 620 2 CYS B 123 SG 133.2 REMARK 620 3 HIS B 131 ND1 103.1 105.9 REMARK 620 4 MET B 136 SD 84.3 112.6 117.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU B 403 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 88 NE2 REMARK 620 2 HIS B 122 NE2 120.2 REMARK 620 3 HOH B 665 O 100.1 96.4 REMARK 620 4 HIS C 277 NE2 114.7 113.0 109.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU C 406 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS C 83 ND1 REMARK 620 2 CYS C 123 SG 132.4 REMARK 620 3 HIS C 131 ND1 101.2 109.2 REMARK 620 4 MET C 136 SD 83.3 113.1 116.0 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 GOL A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU B 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL C 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL C 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL C 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL C 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU C 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU C 406 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4KNU RELATED DB: PDB REMARK 900 RELATED ID: 4KNS RELATED DB: PDB REMARK 900 SAME PROTEIN REDUCED AND AT PH 6.5 DBREF 4KNT A 25 309 UNP Q82VX5 Q82VX5_NITEU 25 309 DBREF 4KNT B 25 309 UNP Q82VX5 Q82VX5_NITEU 25 309 DBREF 4KNT C 25 309 UNP Q82VX5 Q82VX5_NITEU 25 309 SEQRES 1 A 285 LYS THR VAL GLN VAL THR LEU HIS ALA VAL GLU THR ASP SEQRES 2 A 285 VAL ALA TYR ASP ASN LYS GLY SER THR TYR ARG ALA TRP SEQRES 3 A 285 THR PHE ASP GLY LYS VAL PRO GLY PRO VAL VAL ARG VAL SEQRES 4 A 285 THR GLU GLY ASP THR VAL GLU PHE THR LEU ILE ASN ASP SEQRES 5 A 285 LYS ASN SER LYS ASN SER HIS SER MET ASP PHE HIS ALA SEQRES 6 A 285 ALA ARG LEU ASP VAL VAL GLU ASP PHE GLU SER ILE LYS SEQRES 7 A 285 PRO GLY GLU THR LYS LYS TYR THR PHE THR ALA ASP ASN SEQRES 8 A 285 PRO GLY VAL PHE PHE TYR HIS CYS GLY SER ASP PRO MET SEQRES 9 A 285 ILE GLN HIS ILE ALA ARG GLY MET TYR GLY VAL ILE ILE SEQRES 10 A 285 VAL ASP PRO LYS ASP ALA ASN ALA LEU PRO LYS ALA ASP SEQRES 11 A 285 ARG GLU TYR VAL LEU ILE GLN ALA GLU HIS TYR GLU ASN SEQRES 12 A 285 PRO ASP ASP LYS THR ALA MET MET GLN ASN LYS TRP SER SEQRES 13 A 285 ASN VAL VAL PHE ASN GLY GLY VAL PHE LYS TYR ASP PRO SEQRES 14 A 285 VAL HIS ASP SER GLU ALA THR SER TRP LEU GLN ALA LYS SEQRES 15 A 285 PRO GLY GLU ARG VAL ARG ILE TYR PHE VAL ASN ALA GLY SEQRES 16 A 285 PRO ASN GLU LEU SER SER LEU HIS PRO ILE ALA GLY ILE SEQRES 17 A 285 TRP ASP ARG VAL TYR PRO SER GLY ASN PRO LYS ASN VAL SEQRES 18 A 285 GLN TYR ALA LEU GLN SER TYR LEU ILE GLY ALA GLY ASP SEQRES 19 A 285 ALA ALA THR LEU ASP LEU ILE SER PRO VAL GLU GLY ALA SEQRES 20 A 285 ASN ALA ILE VAL ASP HIS SER MET ARG HIS ALA HIS SER SEQRES 21 A 285 GLY ALA ILE ALA VAL ILE MET PHE THR ASN ASP ALA ASP SEQRES 22 A 285 PRO GLU ALA GLY ARG GLY GLU ASN ILE LEU ILE ARG SEQRES 1 B 285 LYS THR VAL GLN VAL THR LEU HIS ALA VAL GLU THR ASP SEQRES 2 B 285 VAL ALA TYR ASP ASN LYS GLY SER THR TYR ARG ALA TRP SEQRES 3 B 285 THR PHE ASP GLY LYS VAL PRO GLY PRO VAL VAL ARG VAL SEQRES 4 B 285 THR GLU GLY ASP THR VAL GLU PHE THR LEU ILE ASN ASP SEQRES 5 B 285 LYS ASN SER LYS ASN SER HIS SER MET ASP PHE HIS ALA SEQRES 6 B 285 ALA ARG LEU ASP VAL VAL GLU ASP PHE GLU SER ILE LYS SEQRES 7 B 285 PRO GLY GLU THR LYS LYS TYR THR PHE THR ALA ASP ASN SEQRES 8 B 285 PRO GLY VAL PHE PHE TYR HIS CYS GLY SER ASP PRO MET SEQRES 9 B 285 ILE GLN HIS ILE ALA ARG GLY MET TYR GLY VAL ILE ILE SEQRES 10 B 285 VAL ASP PRO LYS ASP ALA ASN ALA LEU PRO LYS ALA ASP SEQRES 11 B 285 ARG GLU TYR VAL LEU ILE GLN ALA GLU HIS TYR GLU ASN SEQRES 12 B 285 PRO ASP ASP LYS THR ALA MET MET GLN ASN LYS TRP SER SEQRES 13 B 285 ASN VAL VAL PHE ASN GLY GLY VAL PHE LYS TYR ASP PRO SEQRES 14 B 285 VAL HIS ASP SER GLU ALA THR SER TRP LEU GLN ALA LYS SEQRES 15 B 285 PRO GLY GLU ARG VAL ARG ILE TYR PHE VAL ASN ALA GLY SEQRES 16 B 285 PRO ASN GLU LEU SER SER LEU HIS PRO ILE ALA GLY ILE SEQRES 17 B 285 TRP ASP ARG VAL TYR PRO SER GLY ASN PRO LYS ASN VAL SEQRES 18 B 285 GLN TYR ALA LEU GLN SER TYR LEU ILE GLY ALA GLY ASP SEQRES 19 B 285 ALA ALA THR LEU ASP LEU ILE SER PRO VAL GLU GLY ALA SEQRES 20 B 285 ASN ALA ILE VAL ASP HIS SER MET ARG HIS ALA HIS SER SEQRES 21 B 285 GLY ALA ILE ALA VAL ILE MET PHE THR ASN ASP ALA ASP SEQRES 22 B 285 PRO GLU ALA GLY ARG GLY GLU ASN ILE LEU ILE ARG SEQRES 1 C 285 LYS THR VAL GLN VAL THR LEU HIS ALA VAL GLU THR ASP SEQRES 2 C 285 VAL ALA TYR ASP ASN LYS GLY SER THR TYR ARG ALA TRP SEQRES 3 C 285 THR PHE ASP GLY LYS VAL PRO GLY PRO VAL VAL ARG VAL SEQRES 4 C 285 THR GLU GLY ASP THR VAL GLU PHE THR LEU ILE ASN ASP SEQRES 5 C 285 LYS ASN SER LYS ASN SER HIS SER MET ASP PHE HIS ALA SEQRES 6 C 285 ALA ARG LEU ASP VAL VAL GLU ASP PHE GLU SER ILE LYS SEQRES 7 C 285 PRO GLY GLU THR LYS LYS TYR THR PHE THR ALA ASP ASN SEQRES 8 C 285 PRO GLY VAL PHE PHE TYR HIS CYS GLY SER ASP PRO MET SEQRES 9 C 285 ILE GLN HIS ILE ALA ARG GLY MET TYR GLY VAL ILE ILE SEQRES 10 C 285 VAL ASP PRO LYS ASP ALA ASN ALA LEU PRO LYS ALA ASP SEQRES 11 C 285 ARG GLU TYR VAL LEU ILE GLN ALA GLU HIS TYR GLU ASN SEQRES 12 C 285 PRO ASP ASP LYS THR ALA MET MET GLN ASN LYS TRP SER SEQRES 13 C 285 ASN VAL VAL PHE ASN GLY GLY VAL PHE LYS TYR ASP PRO SEQRES 14 C 285 VAL HIS ASP SER GLU ALA THR SER TRP LEU GLN ALA LYS SEQRES 15 C 285 PRO GLY GLU ARG VAL ARG ILE TYR PHE VAL ASN ALA GLY SEQRES 16 C 285 PRO ASN GLU LEU SER SER LEU HIS PRO ILE ALA GLY ILE SEQRES 17 C 285 TRP ASP ARG VAL TYR PRO SER GLY ASN PRO LYS ASN VAL SEQRES 18 C 285 GLN TYR ALA LEU GLN SER TYR LEU ILE GLY ALA GLY ASP SEQRES 19 C 285 ALA ALA THR LEU ASP LEU ILE SER PRO VAL GLU GLY ALA SEQRES 20 C 285 ASN ALA ILE VAL ASP HIS SER MET ARG HIS ALA HIS SER SEQRES 21 C 285 GLY ALA ILE ALA VAL ILE MET PHE THR ASN ASP ALA ASP SEQRES 22 C 285 PRO GLU ALA GLY ARG GLY GLU ASN ILE LEU ILE ARG HET GOL A 401 6 HET GOL A 402 6 HET GOL A 403 6 HET GOL A 404 6 HET GOL A 405 6 HET GOL A 406 6 HET CU A 407 1 HET CU A 408 1 HET GOL B 401 6 HET GOL B 402 6 HET CU B 403 1 HET CU B 404 1 HET GOL C 401 6 HET GOL C 402 6 HET GOL C 403 6 HET GOL C 404 6 HET CU C 405 1 HET CU C 406 1 HETNAM GOL GLYCEROL HETNAM CU COPPER (II) ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 4 GOL 12(C3 H8 O3) FORMUL 10 CU 6(CU 2+) FORMUL 22 HOH *842(H2 O) HELIX 1 1 PRO A 127 ARG A 134 1 8 HELIX 2 2 ASP A 170 GLN A 176 1 7 HELIX 3 3 GLY A 240 VAL A 245 5 6 HELIX 4 4 SER A 278 SER A 284 1 7 HELIX 5 5 ARG A 302 ILE A 306 5 5 HELIX 6 6 PRO B 127 ARG B 134 1 8 HELIX 7 7 ASP B 170 GLN B 176 1 7 HELIX 8 8 GLY B 240 VAL B 245 5 6 HELIX 9 9 SER B 278 HIS B 283 1 6 HELIX 10 10 PRO C 127 ARG C 134 1 8 HELIX 11 11 ASP C 170 GLN C 176 1 7 HELIX 12 12 GLY C 240 VAL C 245 5 6 HELIX 13 13 SER C 278 SER C 284 1 7 HELIX 14 14 ARG C 302 ILE C 306 5 5 SHEET 1 A 4 THR A 46 PHE A 52 0 SHEET 2 A 4 THR A 26 ALA A 39 -1 N VAL A 34 O THR A 51 SHEET 3 A 4 THR A 68 ASN A 75 1 O GLU A 70 N VAL A 27 SHEET 4 A 4 THR A 106 THR A 112 -1 O PHE A 111 N VAL A 69 SHEET 1 B 4 VAL A 61 THR A 64 0 SHEET 2 B 4 TYR A 137 ASP A 143 1 O ILE A 141 N VAL A 61 SHEET 3 B 4 GLY A 117 HIS A 122 -1 N GLY A 117 O VAL A 142 SHEET 4 B 4 ASP A 86 PHE A 87 -1 N ASP A 86 O HIS A 122 SHEET 1 C 6 ASN A 181 PHE A 184 0 SHEET 2 C 6 ARG A 155 HIS A 164 -1 N HIS A 164 O ASN A 181 SHEET 3 C 6 VAL A 211 GLY A 219 1 O ARG A 212 N ARG A 155 SHEET 4 C 6 ASP A 258 LEU A 264 -1 O LEU A 262 N ILE A 213 SHEET 5 C 6 TRP A 233 PRO A 238 -1 N TYR A 237 O THR A 261 SHEET 6 C 6 GLN A 246 LEU A 249 -1 O LEU A 249 N TRP A 233 SHEET 1 D 5 LEU A 203 ALA A 205 0 SHEET 2 D 5 ILE A 287 PHE A 292 1 O MET A 291 N LEU A 203 SHEET 3 D 5 GLY A 270 ASP A 276 -1 N GLY A 270 O PHE A 292 SHEET 4 D 5 SER A 224 ILE A 229 -1 N HIS A 227 O VAL A 275 SHEET 5 D 5 TYR A 252 ILE A 254 -1 O ILE A 254 N SER A 224 SHEET 1 E 4 THR B 46 PHE B 52 0 SHEET 2 E 4 THR B 26 ALA B 39 -1 N VAL B 34 O THR B 51 SHEET 3 E 4 THR B 68 ASN B 75 1 O GLU B 70 N VAL B 27 SHEET 4 E 4 THR B 106 THR B 112 -1 O PHE B 111 N VAL B 69 SHEET 1 F 4 VAL B 61 THR B 64 0 SHEET 2 F 4 TYR B 137 ASP B 143 1 O ILE B 141 N VAL B 61 SHEET 3 F 4 GLY B 117 HIS B 122 -1 N GLY B 117 O VAL B 142 SHEET 4 F 4 ASP B 86 PHE B 87 -1 N ASP B 86 O HIS B 122 SHEET 1 G 6 ASN B 181 PHE B 184 0 SHEET 2 G 6 ARG B 155 HIS B 164 -1 N ALA B 162 O VAL B 183 SHEET 3 G 6 VAL B 211 GLY B 219 1 O TYR B 214 N TYR B 157 SHEET 4 G 6 ASP B 258 LEU B 264 -1 O LEU B 262 N ILE B 213 SHEET 5 G 6 TRP B 233 PRO B 238 -1 N TYR B 237 O THR B 261 SHEET 6 G 6 GLN B 246 LEU B 249 -1 O LEU B 249 N TRP B 233 SHEET 1 H 5 LEU B 203 ALA B 205 0 SHEET 2 H 5 ILE B 287 PHE B 292 1 O MET B 291 N LEU B 203 SHEET 3 H 5 GLY B 270 ASP B 276 -1 N GLY B 270 O PHE B 292 SHEET 4 H 5 SER B 224 ILE B 229 -1 N ILE B 229 O ALA B 273 SHEET 5 H 5 TYR B 252 ILE B 254 -1 O ILE B 254 N SER B 224 SHEET 1 I 4 THR C 46 PHE C 52 0 SHEET 2 I 4 THR C 26 ALA C 39 -1 N VAL C 34 O THR C 51 SHEET 3 I 4 THR C 68 ASN C 75 1 O GLU C 70 N VAL C 27 SHEET 4 I 4 THR C 106 THR C 112 -1 O PHE C 111 N VAL C 69 SHEET 1 J 4 VAL C 61 THR C 64 0 SHEET 2 J 4 TYR C 137 ASP C 143 1 O ILE C 141 N VAL C 61 SHEET 3 J 4 GLY C 117 HIS C 122 -1 N GLY C 117 O VAL C 142 SHEET 4 J 4 ASP C 86 PHE C 87 -1 N ASP C 86 O HIS C 122 SHEET 1 K 6 ASN C 181 PHE C 184 0 SHEET 2 K 6 ARG C 155 HIS C 164 -1 N HIS C 164 O ASN C 181 SHEET 3 K 6 VAL C 211 GLY C 219 1 O TYR C 214 N TYR C 157 SHEET 4 K 6 ASP C 258 LEU C 264 -1 O LEU C 262 N ILE C 213 SHEET 5 K 6 TRP C 233 PRO C 238 -1 N TYR C 237 O THR C 261 SHEET 6 K 6 GLN C 246 LEU C 249 -1 O LEU C 249 N TRP C 233 SHEET 1 L 5 LEU C 203 ALA C 205 0 SHEET 2 L 5 ILE C 287 PHE C 292 1 O MET C 291 N LEU C 203 SHEET 3 L 5 GLY C 270 ASP C 276 -1 N GLY C 270 O PHE C 292 SHEET 4 L 5 SER C 224 ILE C 229 -1 N ILE C 229 O ALA C 273 SHEET 5 L 5 TYR C 252 ILE C 254 -1 O ILE C 254 N SER C 224 LINK ND1 HIS A 83 CU CU A 408 1555 1555 2.14 LINK NE2 HIS A 88 CU CU A 407 1555 1555 2.02 LINK NE2 HIS A 122 CU CU A 407 1555 1555 2.05 LINK SG CYS A 123 CU CU A 408 1555 1555 2.22 LINK ND1 HIS A 131 CU CU A 408 1555 1555 2.15 LINK SD MET A 136 CU CU A 408 1555 1555 2.45 LINK NE2 HIS A 277 CU CU C 405 1555 1555 2.12 LINK CU CU A 407 O HOH A 658 1555 1555 2.24 LINK CU CU A 407 NE2 HIS B 277 1555 1555 2.10 LINK ND1 HIS B 83 CU CU B 404 1555 1555 2.14 LINK NE2 HIS B 88 CU CU B 403 1555 1555 2.05 LINK NE2 HIS B 122 CU CU B 403 1555 1555 2.07 LINK SG CYS B 123 CU CU B 404 1555 1555 2.29 LINK ND1 HIS B 131 CU CU B 404 1555 1555 2.15 LINK SD MET B 136 CU CU B 404 1555 1555 2.47 LINK CU CU B 403 O HOH B 665 1555 1555 2.33 LINK CU CU B 403 NE2 HIS C 277 1555 1555 2.13 LINK ND1 HIS C 83 CU CU C 406 1555 1555 2.15 LINK NE2 HIS C 88 CU CU C 405 1555 1555 2.01 LINK NE2 HIS C 122 CU CU C 405 1555 1555 2.09 LINK SG CYS C 123 CU CU C 406 1555 1555 2.27 LINK ND1 HIS C 131 CU CU C 406 1555 1555 2.11 LINK SD MET C 136 CU CU C 406 1555 1555 2.49 LINK CU CU C 405 O HOH C 723 1555 1555 2.37 CISPEP 1 VAL A 56 PRO A 57 0 -4.56 CISPEP 2 ASP A 126 PRO A 127 0 -5.80 CISPEP 3 GLY A 219 PRO A 220 0 9.49 CISPEP 4 VAL B 56 PRO B 57 0 -5.57 CISPEP 5 ASP B 126 PRO B 127 0 -7.17 CISPEP 6 GLY B 219 PRO B 220 0 8.10 CISPEP 7 VAL C 56 PRO C 57 0 -4.57 CISPEP 8 ASP C 126 PRO C 127 0 -5.56 CISPEP 9 GLY C 219 PRO C 220 0 8.39 SITE 1 AC1 9 ARG A 91 ASP A 114 ASN A 115 HOH A 513 SITE 2 AC1 9 HOH A 679 HOH A 688 ILE B 232 ASP B 234 SITE 3 AC1 9 HOH B 522 SITE 1 AC2 9 GLU A 99 GLU A 105 THR A 106 HOH A 747 SITE 2 AC2 9 GLU B 99 ILE B 101 GLU B 105 THR B 106 SITE 3 AC2 9 LYS B 107 SITE 1 AC3 9 ALA A 39 VAL A 56 ASN A 185 GLY A 186 SITE 2 AC3 9 GLY A 187 LYS A 190 HOH A 686 HOH A 689 SITE 3 AC3 9 HOH A 720 SITE 1 AC4 7 ILE A 232 ASP A 234 HOH A 509 HOH A 646 SITE 2 AC4 7 HOH A 693 ARG C 91 ASN C 115 SITE 1 AC5 5 THR A 200 SER A 201 TRP A 202 GLN A 204 SITE 2 AC5 5 HOH A 655 SITE 1 AC6 6 LYS A 178 TRP A 179 ARG A 280 HOH A 636 SITE 2 AC6 6 MET C 175 GLN C 176 SITE 1 AC7 4 HIS A 88 HIS A 122 HOH A 658 HIS B 277 SITE 1 AC8 4 HIS A 83 CYS A 123 HIS A 131 MET A 136 SITE 1 AC9 7 ARG B 91 ASN B 115 HOH B 598 HOH B 628 SITE 2 AC9 7 ILE C 232 ASP C 234 HOH C 634 SITE 1 BC1 7 MET A 175 GLN A 176 HOH A 756 LYS B 178 SITE 2 BC1 7 TRP B 179 ARG B 280 HOH B 546 SITE 1 BC2 4 HIS B 88 HIS B 122 HOH B 665 HIS C 277 SITE 1 BC3 4 HIS B 83 CYS B 123 HIS B 131 MET B 136 SITE 1 BC4 2 LYS C 206 ARG C 302 SITE 1 BC5 4 MET B 175 LYS C 178 TRP C 179 ARG C 280 SITE 1 BC6 8 ALA C 39 VAL C 56 ASN C 185 GLY C 186 SITE 2 BC6 8 GLY C 187 LYS C 190 HOH C 509 HOH C 661 SITE 1 BC7 5 VAL B 94 ASP C 192 VAL C 194 HIS C 195 SITE 2 BC7 5 VAL C 289 SITE 1 BC8 4 HIS A 277 HIS C 88 HIS C 122 HOH C 723 SITE 1 BC9 4 HIS C 83 CYS C 123 HIS C 131 MET C 136 CRYST1 99.868 123.090 88.431 90.00 97.23 90.00 C 1 2 1 12 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 0.010013 0.000000 0.001271 0.00000 SCALE2 0.000000 0.008124 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011399 0.00000