HEADER OXIDOREDUCTASE/ELECTRON TRANSPORT 04-DEC-15 5B1J TITLE CRYSTAL STRUCTURE OF THE ELECTRON-TRANSFER COMPLEX OF COPPER NITRITE TITLE 2 REDUCTASE WITH A CUPREDOXIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: COPPER-CONTAINING NITRITE REDUCTASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 25-360; COMPND 5 SYNONYM: DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE,NITRITE COMPND 6 REDUCTASE (NIR); COMPND 7 EC: 1.7.2.1; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: BLUE COPPER PROTEIN; COMPND 10 CHAIN: C; COMPND 11 SYNONYM: PSEUDOAZURIN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ALCALIGENES XYLOSOXYDANS XYLOSOXYDANS; SOURCE 3 ORGANISM_COMMON: ACHROMOBACTER XYLOSOXIDANS; SOURCE 4 ORGANISM_TAXID: 85698; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: HYPHOMICROBIUM DENITRIFICANS; SOURCE 7 ORGANISM_TAXID: 53399 KEYWDS COMPLEX, COPPER NITRITE REDUCTASE, ELECTRON TRANSFER, OXIDOREDUCTASE- KEYWDS 2 ELECTRON TRANSPORT COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.NOJIRI,H.KOTEISHI,R.YONEDA,D.HIRA REVDAT 3 08-NOV-23 5B1J 1 LINK REVDAT 2 26-FEB-20 5B1J 1 REMARK REVDAT 1 23-NOV-16 5B1J 0 JRNL AUTH M.NOJIRI JRNL TITL STRUCTURE AND FUNCTION OF COPPER NITRITE REDUCTASE JRNL REF METALLOENZYMES IN 91 2016 JRNL REF 2 DENITRIFICATION: JRNL REF 3 APPLICATIONS AND JRNL REF 4 ENVIRONMENTAL IMPACTS JRNL PUBL RSC PUBLISHING JRNL REFN JRNL DOI 10.1039/9781782623762-00091 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 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) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.10 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 22698 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) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1217 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) : 3.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.08 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1690 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.16 REMARK 3 BIN R VALUE (WORKING SET) : 0.2670 REMARK 3 BIN FREE R VALUE SET COUNT : 82 REMARK 3 BIN FREE R VALUE : 0.3700 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6050 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 53.35 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.369 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.280 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 15.431 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.908 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6210 ; 0.011 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 5889 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8446 ; 1.569 ; 1.951 REMARK 3 BOND ANGLES OTHERS (DEGREES): 13596 ; 0.817 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 789 ; 7.892 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 259 ;36.607 ;24.672 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 988 ;17.870 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;22.273 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 929 ; 0.082 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7047 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1364 ; 0.001 ; 0.020 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): 3165 ; 3.283 ; 5.206 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3164 ; 3.281 ; 5.205 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3951 ; 5.182 ; 7.802 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3952 ; 5.183 ; 7.803 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3045 ; 3.209 ; 5.460 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3045 ; 3.209 ; 5.460 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4495 ; 5.111 ; 8.069 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 6715 ; 7.241 ;41.161 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 6716 ; 7.241 ;41.165 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 5B1J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-DEC-15. REMARK 100 THE DEPOSITION ID IS D_1300000362. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JAN-10 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 : BL44XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23931 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 19.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.09300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 0.57000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.000 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: 1OE1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, POTASSIUM CHLORIDE, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 5555 Z,X,Y REMARK 290 6555 Z+1/2,-X+1/2,-Y REMARK 290 7555 -Z+1/2,-X,Y+1/2 REMARK 290 8555 -Z,X+1/2,-Y+1/2 REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z+1/2,-X+1/2 REMARK 290 11555 Y+1/2,-Z+1/2,-X REMARK 290 12555 -Y+1/2,-Z,X+1/2 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 76.61300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 76.61300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 76.61300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 76.61300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 76.61300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 76.61300 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 76.61300 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 76.61300 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 76.61300 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 76.61300 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 76.61300 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 76.61300 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 76.61300 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 76.61300 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 76.61300 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 76.61300 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 76.61300 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 76.61300 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 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 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 GLN A 1 REMARK 465 ARG A 336 REMARK 465 GLN B 1 REMARK 465 ARG B 336 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS C 10 CG CD CE NZ REMARK 470 LYS C 39 CE NZ REMARK 470 LYS C 58 NZ REMARK 470 LYS C 71 NZ REMARK 470 LYS C 106 CG CD CE NZ REMARK 470 LYS C 113 NZ REMARK 470 LYS C 121 NZ 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 GLN A 24 -93.32 -90.17 REMARK 500 LYS A 27 38.60 -99.94 REMARK 500 ASN A 59 17.40 57.42 REMARK 500 ASN A 81 79.72 -108.49 REMARK 500 ASN A 90 -156.16 -155.62 REMARK 500 ALA A 131 68.88 -151.68 REMARK 500 ALA A 220 -39.83 -33.68 REMARK 500 ALA A 265 -7.07 -59.48 REMARK 500 HIS B 22 147.89 -176.03 REMARK 500 GLN B 24 -95.44 -73.71 REMARK 500 SER B 28 153.23 -34.65 REMARK 500 ASN B 59 39.58 73.20 REMARK 500 PRO B 82 153.44 -44.81 REMARK 500 ASN B 90 -160.51 -178.55 REMARK 500 MET B 135 21.28 -149.89 REMARK 500 GLN B 160 34.26 -88.82 REMARK 500 ILE B 328 -77.89 -75.10 REMARK 500 PRO B 331 108.25 -44.41 REMARK 500 ALA C 13 38.13 -92.48 REMARK 500 MET C 17 77.98 52.25 REMARK 500 PRO C 36 50.57 -64.60 REMARK 500 SER C 40 -22.42 120.01 REMARK 500 ALA C 55 99.70 -29.60 REMARK 500 SER C 62 7.04 58.22 REMARK 500 VAL C 65 149.89 -174.68 REMARK 500 ALA C 69 75.03 -65.56 REMARK 500 GLU C 70 -88.88 -85.79 REMARK 500 PRO C 96 38.63 -85.08 REMARK 500 TYR C 105 120.45 -31.98 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 HIS A 300 ASN A 301 147.95 REMARK 500 HIS B 300 ASN B 301 147.43 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 500 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 89 ND1 REMARK 620 2 CYS A 130 SG 116.9 REMARK 620 3 HIS A 139 ND1 99.8 131.5 REMARK 620 4 MET A 144 SD 85.8 108.6 104.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 501 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 94 NE2 REMARK 620 2 HIS A 129 NE2 106.8 REMARK 620 3 HIS A 300 NE2 69.2 89.7 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU B 500 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 89 ND1 REMARK 620 2 CYS B 130 SG 125.5 REMARK 620 3 HIS B 139 ND1 97.6 125.1 REMARK 620 4 MET B 144 SD 83.1 106.3 111.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU B 501 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 94 NE2 REMARK 620 2 HIS B 129 NE2 109.4 REMARK 620 3 HIS B 300 NE2 72.0 94.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU C 401 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS C 41 ND1 REMARK 620 2 CYS C 79 SG 141.4 REMARK 620 3 HIS C 82 ND1 87.9 127.7 REMARK 620 4 MET C 87 SD 75.2 103.0 107.1 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 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CU A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CU B 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CU B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CU C 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5B1K RELATED DB: PDB DBREF 5B1J A 1 336 UNP O68601 O68601_ALCXX 25 360 DBREF 5B1J B 1 336 UNP O68601 O68601_ALCXX 25 360 DBREF 5B1J C 1 124 UNP A7VL37 A7VL37_9RHIZ 27 150 SEQRES 1 A 336 GLN ASP ALA ASP LYS LEU PRO HIS THR LYS VAL THR LEU SEQRES 2 A 336 VAL ALA PRO PRO GLN VAL HIS PRO HIS GLU GLN ALA THR SEQRES 3 A 336 LYS SER GLY PRO LYS VAL VAL GLU PHE THR MET THR ILE SEQRES 4 A 336 GLU GLU LYS LYS MET VAL ILE ASP ASP LYS GLY THR THR SEQRES 5 A 336 LEU GLN ALA MET THR PHE ASN GLY SER MET PRO GLY PRO SEQRES 6 A 336 THR LEU VAL VAL HIS GLU GLY ASP TYR VAL GLN LEU THR SEQRES 7 A 336 LEU VAL ASN PRO ALA THR ASN ALA MET PRO HIS ASN VAL SEQRES 8 A 336 ASP PHE HIS GLY ALA THR GLY ALA LEU GLY GLY ALA LYS SEQRES 9 A 336 LEU THR ASN VAL ASN PRO GLY GLU GLN ALA THR LEU ARG SEQRES 10 A 336 PHE LYS ALA ASP ARG SER GLY THR PHE VAL TYR HIS CYS SEQRES 11 A 336 ALA PRO GLU GLY MET VAL PRO TRP HIS VAL VAL SER GLY SEQRES 12 A 336 MET SER GLY THR LEU MET VAL LEU PRO ARG ASP GLY LEU SEQRES 13 A 336 LYS ASP PRO GLN GLY LYS PRO LEU HIS TYR ASP ARG ALA SEQRES 14 A 336 TYR THR ILE GLY GLU PHE ASP LEU TYR ILE PRO LYS GLY SEQRES 15 A 336 PRO ASP GLY LYS TYR LYS ASP TYR ALA THR LEU ALA GLU SEQRES 16 A 336 SER TYR GLY ASP THR VAL GLN VAL MET ARG THR LEU THR SEQRES 17 A 336 PRO SER HIS ILE VAL PHE ASN GLY LYS VAL GLY ALA LEU SEQRES 18 A 336 THR GLY ALA ASN ALA LEU THR ALA LYS VAL GLY GLU THR SEQRES 19 A 336 VAL LEU LEU ILE HIS SER GLN ALA ASN ARG ASP THR ARG SEQRES 20 A 336 PRO HIS LEU ILE GLY GLY HIS GLY ASP TRP VAL TRP GLU SEQRES 21 A 336 THR GLY LYS PHE ALA ASN PRO PRO GLN ARG ASP LEU GLU SEQRES 22 A 336 THR TRP PHE ILE ARG GLY GLY SER ALA GLY ALA ALA LEU SEQRES 23 A 336 TYR THR PHE LYS GLN PRO GLY VAL TYR ALA TYR LEU ASN SEQRES 24 A 336 HIS ASN LEU ILE GLU ALA PHE GLU LEU GLY ALA ALA GLY SEQRES 25 A 336 HIS ILE LYS VAL GLU GLY LYS TRP ASN ASP ASP LEU MET SEQRES 26 A 336 LYS GLN ILE LYS ALA PRO ALA PRO ILE PRO ARG SEQRES 1 B 336 GLN ASP ALA ASP LYS LEU PRO HIS THR LYS VAL THR LEU SEQRES 2 B 336 VAL ALA PRO PRO GLN VAL HIS PRO HIS GLU GLN ALA THR SEQRES 3 B 336 LYS SER GLY PRO LYS VAL VAL GLU PHE THR MET THR ILE SEQRES 4 B 336 GLU GLU LYS LYS MET VAL ILE ASP ASP LYS GLY THR THR SEQRES 5 B 336 LEU GLN ALA MET THR PHE ASN GLY SER MET PRO GLY PRO SEQRES 6 B 336 THR LEU VAL VAL HIS GLU GLY ASP TYR VAL GLN LEU THR SEQRES 7 B 336 LEU VAL ASN PRO ALA THR ASN ALA MET PRO HIS ASN VAL SEQRES 8 B 336 ASP PHE HIS GLY ALA THR GLY ALA LEU GLY GLY ALA LYS SEQRES 9 B 336 LEU THR ASN VAL ASN PRO GLY GLU GLN ALA THR LEU ARG SEQRES 10 B 336 PHE LYS ALA ASP ARG SER GLY THR PHE VAL TYR HIS CYS SEQRES 11 B 336 ALA PRO GLU GLY MET VAL PRO TRP HIS VAL VAL SER GLY SEQRES 12 B 336 MET SER GLY THR LEU MET VAL LEU PRO ARG ASP GLY LEU SEQRES 13 B 336 LYS ASP PRO GLN GLY LYS PRO LEU HIS TYR ASP ARG ALA SEQRES 14 B 336 TYR THR ILE GLY GLU PHE ASP LEU TYR ILE PRO LYS GLY SEQRES 15 B 336 PRO ASP GLY LYS TYR LYS ASP TYR ALA THR LEU ALA GLU SEQRES 16 B 336 SER TYR GLY ASP THR VAL GLN VAL MET ARG THR LEU THR SEQRES 17 B 336 PRO SER HIS ILE VAL PHE ASN GLY LYS VAL GLY ALA LEU SEQRES 18 B 336 THR GLY ALA ASN ALA LEU THR ALA LYS VAL GLY GLU THR SEQRES 19 B 336 VAL LEU LEU ILE HIS SER GLN ALA ASN ARG ASP THR ARG SEQRES 20 B 336 PRO HIS LEU ILE GLY GLY HIS GLY ASP TRP VAL TRP GLU SEQRES 21 B 336 THR GLY LYS PHE ALA ASN PRO PRO GLN ARG ASP LEU GLU SEQRES 22 B 336 THR TRP PHE ILE ARG GLY GLY SER ALA GLY ALA ALA LEU SEQRES 23 B 336 TYR THR PHE LYS GLN PRO GLY VAL TYR ALA TYR LEU ASN SEQRES 24 B 336 HIS ASN LEU ILE GLU ALA PHE GLU LEU GLY ALA ALA GLY SEQRES 25 B 336 HIS ILE LYS VAL GLU GLY LYS TRP ASN ASP ASP LEU MET SEQRES 26 B 336 LYS GLN ILE LYS ALA PRO ALA PRO ILE PRO ARG SEQRES 1 C 124 ALA GLU HIS ILE VAL GLU MET ARG ASN LYS ASP ASP ALA SEQRES 2 C 124 GLY ASN THR MET VAL PHE GLN PRO GLY PHE VAL LYS VAL SEQRES 3 C 124 GLU ALA GLY ASP THR VAL LYS PHE VAL PRO THR ASP LYS SEQRES 4 C 124 SER HIS ASN ALA GLU SER VAL ARG GLU VAL TRP PRO GLU SEQRES 5 C 124 GLY VAL ALA PRO VAL LYS GLY GLY PHE SER LYS GLU VAL SEQRES 6 C 124 VAL PHE ASN ALA GLU LYS GLU GLY LEU TYR VAL LEU LYS SEQRES 7 C 124 CYS ALA PRO HIS TYR GLY MET GLY MET VAL VAL LEU VAL SEQRES 8 C 124 GLN VAL GLY LYS PRO VAL ASN LEU ASP GLN ILE LYS GLU SEQRES 9 C 124 TYR LYS ALA THR GLY LEU ALA LYS LYS ARG LEU ASP GLY SEQRES 10 C 124 GLU ILE ALA LYS VAL VAL GLN HET CU A 500 1 HET CU A 501 1 HET CU B 500 1 HET CU B 501 1 HET CU C 401 1 HETNAM CU COPPER (II) ION FORMUL 4 CU 5(CU 2+) HELIX 1 AA1 GLY A 98 THR A 106 5 9 HELIX 2 AA2 MET A 135 SER A 142 1 8 HELIX 3 AA3 THR A 192 ARG A 205 1 14 HELIX 4 AA4 THR A 222 ALA A 226 5 5 HELIX 5 AA5 ASN A 301 GLU A 307 1 7 HELIX 6 AA6 ASP B 2 LEU B 6 5 5 HELIX 7 AA7 GLY B 98 ASN B 107 5 10 HELIX 8 AA8 MET B 135 SER B 142 1 8 HELIX 9 AA9 LEU B 193 GLU B 195 5 3 HELIX 10 AB1 SER B 196 THR B 206 1 11 HELIX 11 AB2 THR B 222 ALA B 226 5 5 HELIX 12 AB3 ASN B 301 GLU B 307 1 7 HELIX 13 AB4 ALA C 80 GLY C 86 5 7 HELIX 14 AB5 ASN C 98 TYR C 105 1 8 HELIX 15 AB6 GLY C 109 LYS C 121 1 13 SHEET 1 AA1 3 HIS A 8 LYS A 10 0 SHEET 2 AA1 3 VAL A 32 VAL A 45 1 O GLU A 34 N THR A 9 SHEET 3 AA1 3 THR A 52 PHE A 58 -1 O THR A 57 N GLU A 40 SHEET 1 AA2 4 HIS A 8 LYS A 10 0 SHEET 2 AA2 4 VAL A 32 VAL A 45 1 O GLU A 34 N THR A 9 SHEET 3 AA2 4 TYR A 74 ASN A 81 1 O GLN A 76 N PHE A 35 SHEET 4 AA2 4 GLU A 112 LYS A 119 -1 O PHE A 118 N VAL A 75 SHEET 1 AA3 4 LEU A 67 HIS A 70 0 SHEET 2 AA3 4 SER A 145 LEU A 151 1 O MET A 149 N LEU A 67 SHEET 3 AA3 4 GLY A 124 HIS A 129 -1 N PHE A 126 O LEU A 148 SHEET 4 AA3 4 ASP A 92 PHE A 93 -1 N ASP A 92 O HIS A 129 SHEET 1 AA4 2 LEU A 156 LYS A 157 0 SHEET 2 AA4 2 PRO A 163 LEU A 164 -1 O LEU A 164 N LEU A 156 SHEET 1 AA5 6 HIS A 211 PHE A 214 0 SHEET 2 AA5 6 ARG A 168 LEU A 177 -1 N PHE A 175 O VAL A 213 SHEET 3 AA5 6 THR A 234 GLN A 241 1 O ILE A 238 N ILE A 172 SHEET 4 AA5 6 SER A 281 THR A 288 -1 O ALA A 285 N LEU A 237 SHEET 5 AA5 6 GLY A 255 TRP A 259 -1 N TRP A 259 O ALA A 284 SHEET 6 AA5 6 GLN A 269 LEU A 272 -1 O GLN A 269 N VAL A 258 SHEET 1 AA6 4 LEU A 227 LYS A 230 0 SHEET 2 AA6 4 ALA A 311 GLU A 317 1 O LYS A 315 N LEU A 227 SHEET 3 AA6 4 GLY A 293 ASN A 299 -1 N TYR A 295 O ILE A 314 SHEET 4 AA6 4 PRO A 248 LEU A 250 -1 N HIS A 249 O LEU A 298 SHEET 1 AA7 3 HIS B 8 LYS B 10 0 SHEET 2 AA7 3 VAL B 32 VAL B 45 1 O GLU B 34 N THR B 9 SHEET 3 AA7 3 THR B 52 PHE B 58 -1 O THR B 57 N GLU B 40 SHEET 1 AA8 4 HIS B 8 LYS B 10 0 SHEET 2 AA8 4 VAL B 32 VAL B 45 1 O GLU B 34 N THR B 9 SHEET 3 AA8 4 TYR B 74 ASN B 81 1 O TYR B 74 N VAL B 33 SHEET 4 AA8 4 GLU B 112 LYS B 119 -1 O PHE B 118 N VAL B 75 SHEET 1 AA9 4 GLY B 64 HIS B 70 0 SHEET 2 AA9 4 SER B 145 LEU B 151 1 O LEU B 151 N VAL B 69 SHEET 3 AA9 4 GLY B 124 HIS B 129 -1 N PHE B 126 O LEU B 148 SHEET 4 AA9 4 ASP B 92 PHE B 93 -1 N ASP B 92 O HIS B 129 SHEET 1 AB1 2 LEU B 156 LYS B 157 0 SHEET 2 AB1 2 PRO B 163 LEU B 164 -1 O LEU B 164 N LEU B 156 SHEET 1 AB2 6 HIS B 211 PHE B 214 0 SHEET 2 AB2 6 ARG B 168 LEU B 177 -1 N LEU B 177 O HIS B 211 SHEET 3 AB2 6 THR B 234 GLN B 241 1 O ILE B 238 N ILE B 172 SHEET 4 AB2 6 SER B 281 THR B 288 -1 O ALA B 285 N LEU B 237 SHEET 5 AB2 6 GLY B 255 TRP B 259 -1 N TRP B 257 O LEU B 286 SHEET 6 AB2 6 GLN B 269 LEU B 272 -1 O GLN B 269 N VAL B 258 SHEET 1 AB3 4 LEU B 227 LYS B 230 0 SHEET 2 AB3 4 ALA B 311 GLU B 317 1 O LYS B 315 N LEU B 227 SHEET 3 AB3 4 GLY B 293 ASN B 299 -1 N TYR B 297 O GLY B 312 SHEET 4 AB3 4 PRO B 248 LEU B 250 -1 N HIS B 249 O LEU B 298 SHEET 1 AB4 4 THR C 16 GLN C 20 0 SHEET 2 AB4 4 GLU C 2 LYS C 10 -1 N ASN C 9 O MET C 17 SHEET 3 AB4 4 THR C 31 VAL C 35 1 O LYS C 33 N HIS C 3 SHEET 4 AB4 4 VAL C 65 ASN C 68 -1 O PHE C 67 N VAL C 32 SHEET 1 AB5 5 PHE C 23 VAL C 26 0 SHEET 2 AB5 5 VAL C 88 VAL C 93 1 O GLN C 92 N VAL C 26 SHEET 3 AB5 5 LEU C 74 LYS C 78 -1 N TYR C 75 O VAL C 91 SHEET 4 AB5 5 ASN C 42 SER C 45 -1 N GLU C 44 O LYS C 78 SHEET 5 AB5 5 LYS C 58 PHE C 61 -1 O GLY C 59 N ALA C 43 LINK ND1 HIS A 89 CU CU A 500 1555 1555 2.22 LINK NE2 HIS A 94 CU CU A 501 1555 1555 2.08 LINK NE2 HIS A 129 CU CU A 501 1555 1555 2.25 LINK SG CYS A 130 CU CU A 500 1555 1555 2.23 LINK ND1 HIS A 139 CU CU A 500 1555 1555 2.01 LINK SD MET A 144 CU CU A 500 1555 1555 2.57 LINK NE2 HIS A 300 CU CU A 501 1555 9555 2.20 LINK ND1 HIS B 89 CU CU B 500 1555 1555 2.19 LINK NE2 HIS B 94 CU CU B 501 1555 1555 2.00 LINK NE2 HIS B 129 CU CU B 501 1555 1555 2.24 LINK SG CYS B 130 CU CU B 500 1555 1555 2.18 LINK ND1 HIS B 139 CU CU B 500 1555 1555 2.05 LINK SD MET B 144 CU CU B 500 1555 1555 2.59 LINK NE2 HIS B 300 CU CU B 501 1555 6445 2.25 LINK ND1 HIS C 41 CU CU C 401 1555 1555 2.36 LINK SG CYS C 79 CU CU C 401 1555 1555 2.11 LINK ND1 HIS C 82 CU CU C 401 1555 1555 2.20 LINK SD MET C 87 CU CU C 401 1555 1555 2.46 CISPEP 1 PRO A 16 PRO A 17 0 7.22 CISPEP 2 MET A 62 PRO A 63 0 -13.39 CISPEP 3 PRO B 16 PRO B 17 0 6.47 CISPEP 4 MET B 62 PRO B 63 0 -4.89 CISPEP 5 GLN C 20 PRO C 21 0 4.17 SITE 1 AC1 4 HIS A 89 CYS A 130 HIS A 139 MET A 144 SITE 1 AC2 5 ASP A 92 HIS A 94 HIS A 129 HIS A 249 SITE 2 AC2 5 HIS A 300 SITE 1 AC3 4 HIS B 89 CYS B 130 HIS B 139 MET B 144 SITE 1 AC4 4 ASP B 92 HIS B 94 HIS B 129 HIS B 300 SITE 1 AC5 4 HIS C 41 CYS C 79 HIS C 82 MET C 87 CRYST1 153.226 153.226 153.226 90.00 90.00 90.00 P 21 3 24 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 0.006526 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006526 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006526 0.00000