HEADER OXIDOREDUCTASE 09-SEP-13 3WI9 TITLE CRYSTAL STRUCTURE OF COPPER NITRITE REDUCTASE FROM GEOBACILLUS TITLE 2 KAUSTOPHILUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: NITRITE REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 32-354; COMPND 5 EC: 1.7.2.1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACILLUS KAUSTOPHILUS; SOURCE 3 ORGANISM_TAXID: 235909; SOURCE 4 STRAIN: HTA426; SOURCE 5 GENE: GK0767; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA-GAMI (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-20B KEYWDS CUPREDOXIN-FOLD, TRIMER, NITRITE REDUCTION, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.FUKUDA,M.NOJIRI REVDAT 2 08-NOV-23 3WI9 1 REMARK SEQADV LINK REVDAT 1 23-JUL-14 3WI9 0 JRNL AUTH Y.FUKUDA,H.KOTEISHI,R.YONEDA,T.TAMADA,H.TAKAMI,T.INOUE, JRNL AUTH 2 M.NOJIRI JRNL TITL STRUCTURAL AND FUNCTIONAL CHARACTERIZATION OF THE JRNL TITL 2 GEOBACILLUS COPPER NITRITE REDUCTASE: INVOLVEMENT OF THE JRNL TITL 3 UNIQUE N-TERMINAL REGION IN THE INTERPROTEIN ELECTRON JRNL TITL 4 TRANSFER WITH ITS REDOX PARTNER JRNL REF BIOCHIM.BIOPHYS.ACTA V.1837 396 2014 JRNL REFN ISSN 0006-3002 JRNL PMID 24440558 JRNL DOI 10.1016/J.BBABIO.2014.01.004 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 3 NUMBER OF REFLECTIONS : 96275 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) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5038 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) : 1.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.33 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6729 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.37 REMARK 3 BIN R VALUE (WORKING SET) : 0.3490 REMARK 3 BIN FREE R VALUE SET COUNT : 339 REMARK 3 BIN FREE R VALUE : 0.3450 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2350 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 24 REMARK 3 SOLVENT ATOMS : 334 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.32 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.05000 REMARK 3 B22 (A**2) : -1.05000 REMARK 3 B33 (A**2) : 1.58000 REMARK 3 B12 (A**2) : -0.53000 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): 0.048 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.045 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.038 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.208 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.967 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2470 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3371 ; 1.296 ; 1.945 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 310 ; 7.402 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 109 ;43.177 ;25.413 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 394 ;10.657 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 4 ; 8.663 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 370 ; 0.087 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1903 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1100 ; 0.192 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1654 ; 0.304 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 274 ; 0.118 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 12 ; 0.266 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 69 ; 0.204 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 34 ; 0.115 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): 2 ; 0.167 ; 0.200 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): 1540 ; 0.749 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2516 ; 1.175 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 951 ; 1.890 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 855 ; 2.767 ; 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): 2491 ; 0.925 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 341 ; 3.516 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 2403 ; 2.834 ; 3.000 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 3WI9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-SEP-13. REMARK 100 THE DEPOSITION ID IS D_1000096368. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JUN-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL38B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SI DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 101119 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 18.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 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: 1KBW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M ACETATE, 5.5% PEG4000, 175MM REMARK 280 ZNSO4, PH 4.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K 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 57.53450 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 33.21756 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 29.16833 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 57.53450 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 33.21756 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 29.16833 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 57.53450 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 33.21756 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 29.16833 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 66.43512 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 58.33667 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 66.43512 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 58.33667 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 66.43512 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 58.33667 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: 8600 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30340 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -37.0 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 HOH A 769 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 0 REMARK 465 GLU A 1 REMARK 465 ASN A 2 REMARK 465 LYS A 3 REMARK 465 ASN A 4 REMARK 465 GLY A 5 REMARK 465 THR A 6 REMARK 465 ALA A 7 REMARK 465 ALA A 8 REMARK 465 THR A 9 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 SER 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 740 O HOH A 834 2.18 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 PHE A 213 -30.07 -134.16 REMARK 500 SER A 242 79.97 -112.13 REMARK 500 ASP A 256 15.91 55.47 REMARK 500 SER A 274 0.16 80.81 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 293 147.61 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 ZN A 404 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 42 NE2 REMARK 620 2 HIS A 83 ND1 104.4 REMARK 620 3 ACY A 408 O 103.3 109.2 REMARK 620 4 ACY A 408 OXT 158.8 82.7 55.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 403 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 83 ND1 REMARK 620 2 HIS A 83 NE2 43.5 REMARK 620 N 1 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 139.8 REMARK 620 3 HIS A 143 ND1 99.2 103.7 REMARK 620 4 MET A 148 SD 82.7 113.8 117.8 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 112.2 REMARK 620 3 HOH A 722 O 97.8 104.1 REMARK 620 4 HOH A 723 O 153.8 91.6 64.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 405 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 167 OD1 REMARK 620 2 HOH A 555 O 92.6 REMARK 620 3 HOH A 582 O 99.9 86.4 REMARK 620 4 HOH A 594 O 92.6 174.8 92.3 REMARK 620 5 HOH A 668 O 176.6 87.8 83.5 87.0 REMARK 620 6 HOH A 685 O 86.4 86.8 171.0 93.9 90.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 407 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 239 OE1 REMARK 620 2 GLU A 239 OE2 48.4 REMARK 620 3 HOH A 727 O 88.9 107.4 REMARK 620 4 HOH A 742 O 94.0 66.5 167.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 406 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 726 O REMARK 620 2 HOH A 740 O 167.9 REMARK 620 3 HOH A 790 O 52.8 128.8 REMARK 620 4 HOH A 834 O 115.4 63.5 65.5 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 ZN A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 410 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3WIA RELATED DB: PDB DBREF 3WI9 A 1 323 UNP Q5L1X8 Q5L1X8_GEOKA 32 354 SEQADV 3WI9 MET A 0 UNP Q5L1X8 EXPRESSION TAG SEQRES 1 A 324 MET GLU ASN LYS ASN GLY THR ALA ALA THR THR GLN GLN SEQRES 2 A 324 SER ALA ALA ASN MET LEU ALA ALA HIS LYS GLY VAL ASN SEQRES 3 A 324 GLN ALA PRO VAL PRO LEU LYS MET GLU ARG VAL GLY PRO SEQRES 4 A 324 HIS ASP VAL HIS ILE GLU MET THR ALA GLN ILE THR ASP SEQRES 5 A 324 ILE GLU ILE ASP LYS GLY LYS ILE TYR LYS ALA TRP THR SEQRES 6 A 324 PHE ASN GLY GLN ALA PRO GLY PRO LEU VAL VAL VAL ASN SEQRES 7 A 324 GLU GLY ASP THR ILE HIS PHE THR LEU LYS ASN MET ASP SEQRES 8 A 324 PRO VAL VAL PRO HIS SER MET ASP PHE HIS ALA VAL HIS SEQRES 9 A 324 ALA SER PRO SER LYS ASP PHE ILE ASP VAL MET PRO ASN SEQRES 10 A 324 LYS SER GLY THR PHE THR TYR PRO ALA ASN LYS PRO GLY SEQRES 11 A 324 VAL PHE MET TYR HIS CYS GLY THR LYS PRO VAL LEU GLN SEQRES 12 A 324 HIS ILE ALA ASN GLY MET HIS GLY VAL ILE ILE VAL LYS SEQRES 13 A 324 PRO LYS ASN GLY TYR PRO THR ASP LYS GLU VAL ASP ARG SEQRES 14 A 324 GLU TYR VAL LEU ILE GLN ASN GLU TRP TYR LYS TYR ASN SEQRES 15 A 324 ASP MET ASN ASP PHE GLN ASN GLY VAL PRO SER TYR VAL SEQRES 16 A 324 VAL PHE SER SER LYS ALA LEU LYS PRO GLY ASP PRO ASN SEQRES 17 A 324 THR ASN GLY ASP THR PHE THR LEU LYS GLU LYS PRO LEU SEQRES 18 A 324 LEU ALA LYS VAL GLY GLU LYS ILE ARG LEU TYR ILE ASN SEQRES 19 A 324 ASN VAL GLY PRO ASN GLU VAL SER SER PHE HIS VAL VAL SEQRES 20 A 324 GLY THR VAL PHE ASP ASP VAL TYR LEU ASP GLY ASN PRO SEQRES 21 A 324 ASN ASN HIS LEU GLN GLY MET GLN THR VAL MET LEU PRO SEQRES 22 A 324 ALA SER GLY GLY ALA VAL VAL GLU PHE THR VAL THR ARG SEQRES 23 A 324 PRO GLY THR TYR PRO ILE VAL THR HIS GLN PHE ASN HIS SEQRES 24 A 324 ALA GLN LYS GLY ALA VAL ALA MET LEU LYS VAL THR GLU SEQRES 25 A 324 THR GLY GLU ASP ASP GLY SER GLU THR SER GLY HIS HET CU A 401 1 HET CU A 402 1 HET ZN A 403 1 HET ZN A 404 1 HET ZN A 405 1 HET NA A 406 1 HET NA A 407 1 HET ACY A 408 4 HET MPD A 409 8 HET SO4 A 410 5 HETNAM CU COPPER (II) ION HETNAM ZN ZINC ION HETNAM NA SODIUM ION HETNAM ACY ACETIC ACID HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM SO4 SULFATE ION FORMUL 2 CU 2(CU 2+) FORMUL 4 ZN 3(ZN 2+) FORMUL 7 NA 2(NA 1+) FORMUL 9 ACY C2 H4 O2 FORMUL 10 MPD C6 H14 O2 FORMUL 11 SO4 O4 S 2- FORMUL 12 HOH *334(H2 O) HELIX 1 1 THR A 10 LYS A 22 1 13 HELIX 2 2 SER A 105 PHE A 110 1 6 HELIX 3 3 PRO A 139 ASN A 146 1 8 HELIX 4 4 THR A 162 VAL A 166 5 5 HELIX 5 5 ASP A 182 GLY A 189 1 8 HELIX 6 6 PHE A 213 LYS A 218 1 6 HELIX 7 7 GLN A 295 LYS A 301 1 7 SHEET 1 A 3 LYS A 32 GLY A 37 0 SHEET 2 A 3 ASP A 40 ASP A 55 -1 O HIS A 42 N GLU A 34 SHEET 3 A 3 LYS A 58 PHE A 65 -1 O TYR A 60 N ILE A 52 SHEET 1 B 4 LYS A 32 GLY A 37 0 SHEET 2 B 4 ASP A 40 ASP A 55 -1 O HIS A 42 N GLU A 34 SHEET 3 B 4 ASP A 80 ASN A 88 1 O HIS A 83 N VAL A 41 SHEET 4 B 4 SER A 118 ALA A 125 -1 O PHE A 121 N PHE A 84 SHEET 1 C 4 VAL A 74 ASN A 77 0 SHEET 2 C 4 HIS A 149 LYS A 155 1 O ILE A 153 N VAL A 74 SHEET 3 C 4 GLY A 129 HIS A 134 -1 N GLY A 129 O VAL A 154 SHEET 4 C 4 ASP A 98 PHE A 99 -1 N ASP A 98 O HIS A 134 SHEET 1 D 6 TYR A 193 LYS A 199 0 SHEET 2 D 6 ARG A 168 TRP A 177 -1 N ASN A 175 O VAL A 195 SHEET 3 D 6 LYS A 227 GLY A 236 1 O TYR A 231 N LEU A 172 SHEET 4 D 6 GLY A 276 THR A 282 -1 O PHE A 281 N ILE A 228 SHEET 5 D 6 PHE A 250 LEU A 255 -1 N TYR A 254 O VAL A 278 SHEET 6 D 6 HIS A 262 MET A 266 -1 O MET A 266 N PHE A 250 SHEET 1 E 5 LEU A 220 LYS A 223 0 SHEET 2 E 5 VAL A 304 THR A 310 1 O LYS A 308 N LEU A 220 SHEET 3 E 5 GLY A 287 THR A 293 -1 N GLY A 287 O VAL A 309 SHEET 4 E 5 SER A 241 VAL A 245 -1 N HIS A 244 O VAL A 292 SHEET 5 E 5 VAL A 269 LEU A 271 -1 O LEU A 271 N SER A 241 LINK NE2 HIS A 42 ZN ZN A 404 1555 1555 2.06 LINK ND1BHIS A 83 ZN ZN A 403 1555 1555 2.00 LINK NE2AHIS A 83 ZN ZN A 403 1555 1555 2.09 LINK ND1BHIS A 83 ZN ZN A 404 1555 1555 2.03 LINK ND1 HIS A 95 CU CU A 401 1555 1555 2.07 LINK NE2 HIS A 100 CU CU A 402 1555 1555 1.95 LINK NE2 HIS A 134 CU CU A 402 1555 1555 2.08 LINK SG CYS A 135 CU CU A 401 1555 1555 2.13 LINK ND1 HIS A 143 CU CU A 401 1555 1555 2.03 LINK SD MET A 148 CU CU A 401 1555 1555 2.61 LINK OD1 ASP A 167 ZN ZN A 405 1555 1555 2.21 LINK OE1 GLU A 239 NA NA A 407 1555 1555 2.38 LINK OE2 GLU A 239 NA NA A 407 1555 1555 2.82 LINK CU CU A 402 O HOH A 722 1555 1555 1.92 LINK CU CU A 402 O HOH A 723 1555 1555 2.53 LINK ZN ZN A 404 O ACY A 408 1555 1555 1.97 LINK ZN ZN A 404 OXT ACY A 408 1555 1555 2.61 LINK ZN ZN A 405 O HOH A 555 1555 1555 2.07 LINK ZN ZN A 405 O HOH A 582 1555 1555 2.19 LINK ZN ZN A 405 O HOH A 594 1555 1555 2.08 LINK ZN ZN A 405 O HOH A 668 1555 1555 2.14 LINK ZN ZN A 405 O HOH A 685 1555 1555 2.21 LINK NA NA A 406 O HOH A 726 1555 1555 2.72 LINK NA NA A 406 O HOH A 740 1555 1555 2.15 LINK NA NA A 406 O HOH A 790 1555 1555 2.20 LINK NA NA A 406 O HOH A 834 1555 1555 1.99 LINK NA NA A 407 O HOH A 727 1555 1555 2.05 LINK NA NA A 407 O HOH A 742 1555 1555 2.22 CISPEP 1 ALA A 69 PRO A 70 0 -6.16 CISPEP 2 LYS A 138 PRO A 139 0 -6.13 CISPEP 3 GLY A 236 PRO A 237 0 14.56 SITE 1 AC1 4 HIS A 95 CYS A 135 HIS A 143 MET A 148 SITE 1 AC2 6 HIS A 100 HIS A 134 HIS A 244 HIS A 294 SITE 2 AC2 6 HOH A 722 HOH A 723 SITE 1 AC3 6 VAL A 36 HIS A 42 GLU A 53 HIS A 83 SITE 2 AC3 6 ZN A 404 HOH A 636 SITE 1 AC4 5 HIS A 42 GLU A 53 HIS A 83 ZN A 403 SITE 2 AC4 5 ACY A 408 SITE 1 AC5 6 ASP A 167 HOH A 555 HOH A 582 HOH A 594 SITE 2 AC5 6 HOH A 668 HOH A 685 SITE 1 AC6 5 ASP A 40 HOH A 726 HOH A 740 HOH A 790 SITE 2 AC6 5 HOH A 834 SITE 1 AC7 4 GLU A 239 HOH A 727 HOH A 741 HOH A 742 SITE 1 AC8 8 HIS A 42 GLU A 53 LYS A 56 GLY A 57 SITE 2 AC8 8 HIS A 83 ZN A 404 HOH A 569 HOH A 629 SITE 1 AC9 5 ASP A 163 ASP A 167 GLU A 169 HOH A 739 SITE 2 AC9 5 HOH A 825 SITE 1 BC1 5 LYS A 22 GLY A 23 LYS A 61 HOH A 812 SITE 2 BC1 5 HOH A 832 CRYST1 115.069 115.069 87.505 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 0.010035 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011428 0.00000