HEADER OXIDOREDUCTASE 10-DEC-13 3WNJ TITLE 1.20 A RESOLUTION CRYSTAL STRUCTURE OF DIOXYGEN BOUND COPPER- TITLE 2 CONTAINING NITRITE REDUCTASE FROM GEOBACILLUS THERMODENITRIFICANS COMPND MOL_ID: 1; COMPND 2 MOLECULE: NITRITE REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 31-352; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACILLUS THERMODENITRIFICANS; SOURCE 3 ORGANISM_TAXID: 420246; SOURCE 4 STRAIN: NG80-2; SOURCE 5 GENE: NIRK; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET22B KEYWDS GREEK KEY BETA BARREL, DISSIMILATORY NITRITE REDUCTASE, PERIPLASM- KEYWDS 2 LIKE SPACE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.FUKUDA,T.INOUE REVDAT 3 08-NOV-23 3WNJ 1 REMARK SEQADV LINK REVDAT 2 22-NOV-17 3WNJ 1 REMARK REVDAT 1 10-DEC-14 3WNJ 0 JRNL AUTH Y.FUKUDA,T.INOUE JRNL TITL CRYSTALLOGRAPHIC EVIDENCE FOR SIDE-ON DIOXYGEN TRAPPED ON JRNL TITL 2 TYPE 2 COPPER IN COPPER-CONTAINING NITRITE REDUCTASE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.73 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 91.9 REMARK 3 NUMBER OF REFLECTIONS : 114262 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) : 0.121 REMARK 3 R VALUE (WORKING SET) : 0.120 REMARK 3 FREE R VALUE : 0.146 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 6088 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) : 1.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.23 REMARK 3 REFLECTION IN BIN (WORKING SET) : 8615 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.99 REMARK 3 BIN R VALUE (WORKING SET) : 0.1790 REMARK 3 BIN FREE R VALUE SET COUNT : 466 REMARK 3 BIN FREE R VALUE : 0.2220 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2314 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 56 REMARK 3 SOLVENT ATOMS : 357 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.59 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01000 REMARK 3 B22 (A**2) : -0.01000 REMARK 3 B33 (A**2) : 0.01000 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): 0.028 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.030 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.018 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.870 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.983 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.975 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2751 ; 0.031 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3774 ; 2.439 ; 1.969 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 362 ; 8.153 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 115 ;43.787 ;25.652 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 468 ;13.026 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 4 ; 9.195 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 402 ; 0.169 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2169 ; 0.015 ; 0.022 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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): 2751 ;10.497 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 109 ;42.128 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 2964 ;19.288 ; 5.000 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 USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 3WNJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-DEC-13. REMARK 100 THE DEPOSITION ID IS D_1000096558. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-FEB-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-1A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.96 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 120357 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.1 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.07500 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) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.22 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.26300 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: 3WKO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM ACETATE, 5.5%(W/V) PEG REMARK 280 4000, 0.075M CUSO4 , PH 4.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 57.45150 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 33.16964 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 28.00733 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 57.45150 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 33.16964 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 28.00733 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 57.45150 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 33.16964 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 28.00733 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 66.33928 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 56.01467 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 66.33928 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 56.01467 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 66.33928 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 56.01467 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: 13750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -213.0 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 653 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: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 MET A 45 SD MET A 45 CE -0.356 REMARK 500 GLU A 169 CB GLU A 169 CG -0.127 REMARK 500 TYR A 193 CD1 TYR A 193 CE1 0.091 REMARK 500 LYS A 301 CE LYS A 301 NZ 0.166 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 MET A 33 CG - SD - CE ANGL. DEV. = 17.9 DEGREES REMARK 500 MET A 45 CG - SD - CE ANGL. DEV. = -16.7 DEGREES REMARK 500 ARG A 229 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 TYR A 231 CZ - CE2 - CD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 GLU A 311 O - C - N ANGL. DEV. = -9.6 DEGREES 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 SER A 274 -1.91 78.77 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 293 142.31 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 GLU A 311 -10.29 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 NA A 407 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 40 OD2 REMARK 620 2 HOH A 649 O 61.0 REMARK 620 N 1 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 HIS A 83 ND1 101.6 REMARK 620 3 HOH A 800 O 97.0 104.6 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 401 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 95 ND1 REMARK 620 2 CYS A 135 SG 136.8 REMARK 620 3 HIS A 143 ND1 100.4 106.5 REMARK 620 4 MET A 148 SD 82.7 114.0 115.2 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 112.0 REMARK 620 3 OXY A 408 O2 117.8 105.1 REMARK 620 4 OXY A 408 O1 142.0 101.1 31.3 REMARK 620 5 HOH A 821 O 138.8 102.6 27.3 4.1 REMARK 620 6 HOH A 856 O 89.3 97.7 36.7 67.7 63.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 406 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 167 OD2 REMARK 620 2 HOH A 693 O 94.0 REMARK 620 3 HOH A 741 O 93.4 88.9 REMARK 620 4 HOH A 806 O 84.5 97.6 173.3 REMARK 620 5 HOH A 843 O 159.3 105.9 92.6 87.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 406 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 167 OD1 REMARK 620 2 HOH A 741 O 97.4 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 405 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 239 OE2 REMARK 620 2 HOH A 628 O 104.2 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 405 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 239 OE2 REMARK 620 2 HOH A 813 O 84.8 REMARK 620 3 HOH A 814 O 114.7 130.9 REMARK 620 4 HOH A 853 O 116.0 67.5 63.4 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU 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 OXY 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 EDO A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 411 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 412 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 413 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 414 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY A 415 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY A 416 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY A 417 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY A 418 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3WNI RELATED DB: PDB DBREF 3WNJ A 2 323 UNP A4IL26 A4IL26_GEOTN 31 352 SEQADV 3WNJ MET A 1 UNP A4IL26 EXPRESSION TAG SEQRES 1 A 323 MET GLU SER LYS ASN LYS THR ALA ALA THR GLN GLN SER SEQRES 2 A 323 GLU PRO ASN VAL ILE ALA ALA HIS LYS GLY VAL ASN GLN SEQRES 3 A 323 ALA PRO VAL PRO LEU LYS MET GLU ARG VAL GLY PRO HIS SEQRES 4 A 323 ASP VAL HIS ILE GLU MET THR ALA GLN ILE THR ASP ILE SEQRES 5 A 323 GLU ILE ASP LYS GLY LYS ILE TYR LYS ALA TRP THR PHE SEQRES 6 A 323 ASN GLY GLN ALA PRO GLY PRO LEU VAL VAL VAL ASN GLU SEQRES 7 A 323 GLY ASP THR ILE HIS PHE THR LEU LYS ASN MET ASP PRO SEQRES 8 A 323 VAL VAL PRO HIS SER MET ASP PHE HIS ALA VAL HIS ALA SEQRES 9 A 323 SER PRO SER LYS ASP PHE ILE ASP VAL MET PRO ASN LYS SEQRES 10 A 323 SER GLY THR PHE THR TYR PRO ALA ASN LYS PRO GLY VAL SEQRES 11 A 323 PHE MET TYR HIS CYS GLY THR LYS PRO VAL LEU GLN HIS SEQRES 12 A 323 ILE ALA ASN GLY MET HIS GLY VAL ILE ILE VAL LYS PRO SEQRES 13 A 323 LYS ASN GLY TYR PRO THR ASP LYS GLU VAL ASP ARG GLU SEQRES 14 A 323 TYR VAL LEU ILE GLN ASN GLU TRP TYR LYS TYR ASN ASP SEQRES 15 A 323 MET ASN ASP PHE GLN ASN GLY VAL PRO SER TYR VAL VAL SEQRES 16 A 323 PHE SER SER LYS ALA LEU LYS PRO GLY ASP PRO ASN THR SEQRES 17 A 323 ASN GLY ASP THR PHE THR LEU LYS GLU LYS PRO LEU LEU SEQRES 18 A 323 ALA LYS VAL GLY GLU LYS ILE ARG LEU TYR ILE ASN ASN SEQRES 19 A 323 VAL GLY PRO ASN GLU VAL SER SER PHE HIS VAL VAL GLY SEQRES 20 A 323 THR VAL PHE ASP ASP VAL TYR LEU ASP GLY ASN PRO ASN SEQRES 21 A 323 ASN HIS LEU GLN GLY MET GLN THR VAL MET LEU PRO ALA SEQRES 22 A 323 SER GLY GLY ALA VAL VAL GLU PHE THR VAL THR ARG PRO SEQRES 23 A 323 GLY THR TYR PRO ILE VAL THR HIS GLN PHE ASN HIS ALA SEQRES 24 A 323 GLN LYS GLY ALA VAL ALA MET LEU LYS VAL THR GLU THR SEQRES 25 A 323 GLY GLU ASP ASP GLY THR GLU THR SER GLY HIS HET CU A 401 1 HET CU A 402 1 HET CU A 403 1 HET CU A 404 1 HET CU A 405 2 HET CU A 406 2 HET NA A 407 1 HET OXY A 408 2 HET MPD A 409 16 HET EDO A 410 4 HET EDO A 411 4 HET SO4 A 412 5 HET SO4 A 413 5 HET SO4 A 414 5 HET ACY A 415 4 HET ACY A 416 4 HET ACY A 417 4 HET ACY A 418 4 HETNAM CU COPPER (II) ION HETNAM NA SODIUM ION HETNAM OXY OXYGEN MOLECULE HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM EDO 1,2-ETHANEDIOL HETNAM SO4 SULFATE ION HETNAM ACY ACETIC ACID HETSYN EDO ETHYLENE GLYCOL FORMUL 2 CU 6(CU 2+) FORMUL 8 NA NA 1+ FORMUL 9 OXY O2 FORMUL 10 MPD C6 H14 O2 FORMUL 11 EDO 2(C2 H6 O2) FORMUL 13 SO4 3(O4 S 2-) FORMUL 16 ACY 4(C2 H4 O2) FORMUL 20 HOH *357(H2 O) HELIX 1 1 ILE A 18 LYS A 22 5 5 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 THR A 85 N ILE A 43 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 PHE A 131 O ILE A 152 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 SER A 198 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 LEU A 263 N VAL A 253 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 39 CU CU A 404 1555 1555 1.93 LINK OD2 ASP A 40 NA A NA A 407 1555 1555 2.23 LINK NE2 HIS A 42 CU CU A 403 1555 1555 2.02 LINK ND1 HIS A 83 CU CU A 403 1555 1555 1.96 LINK ND1 HIS A 95 CU CU A 401 1555 1555 2.03 LINK NE2 HIS A 100 CU CU A 402 1555 1555 1.92 LINK NE2 HIS A 134 CU CU A 402 1555 1555 2.03 LINK SG CYS A 135 CU CU A 401 1555 1555 2.19 LINK ND1 HIS A 143 CU CU A 401 1555 1555 2.09 LINK SD AMET A 148 CU CU A 401 1555 1555 2.61 LINK OD2 ASP A 167 CU A CU A 406 1555 1555 2.09 LINK OD1 ASP A 167 CU B CU A 406 1555 1555 2.09 LINK OE2AGLU A 239 CU A CU A 405 1555 1555 2.05 LINK OE2BGLU A 239 CU B CU A 405 1555 1555 2.63 LINK CU CU A 402 O2 AOXY A 408 1555 1555 2.13 LINK CU CU A 402 O1 AOXY A 408 1555 1555 2.40 LINK CU CU A 402 O BHOH A 821 1555 1555 2.21 LINK CU CU A 402 O BHOH A 856 1555 1555 2.19 LINK CU CU A 403 O HOH A 800 1555 1555 2.36 LINK CU A CU A 405 O HOH A 628 1555 1555 1.78 LINK CU B CU A 405 O HOH A 813 1555 1555 2.53 LINK CU B CU A 405 O HOH A 814 1555 1555 1.79 LINK CU B CU A 405 O BHOH A 853 1555 1555 2.24 LINK CU A CU A 406 O HOH A 693 1555 1555 2.43 LINK CU A CU A 406 O HOH A 741 1555 1555 1.79 LINK CU B CU A 406 O HOH A 741 1555 1555 2.42 LINK CU A CU A 406 O HOH A 806 1555 1555 2.37 LINK CU A CU A 406 O HOH A 843 1555 1555 2.00 LINK NA A NA A 407 O HOH A 649 1555 1555 3.17 CISPEP 1 ALA A 69 PRO A 70 0 -12.61 CISPEP 2 LYS A 138 PRO A 139 0 -5.03 CISPEP 3 LYS A 138 PRO A 139 0 -4.30 CISPEP 4 GLY A 236 PRO A 237 0 20.81 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 294 OXY A 408 SITE 2 AC2 6 HOH A 821 HOH A 856 SITE 1 AC3 5 HIS A 42 GLU A 53 HIS A 83 HOH A 704 SITE 2 AC3 5 HOH A 800 SITE 1 AC4 1 HIS A 39 SITE 1 AC5 6 GLU A 239 HOH A 628 HOH A 770 HOH A 813 SITE 2 AC5 6 HOH A 814 HOH A 853 SITE 1 AC6 5 ASP A 167 HOH A 693 HOH A 741 HOH A 806 SITE 2 AC6 5 HOH A 843 SITE 1 AC7 3 ASP A 40 HOH A 815 HOH A 835 SITE 1 AC8 11 ASP A 98 HIS A 100 HIS A 134 HIS A 244 SITE 2 AC8 11 VAL A 246 HIS A 294 PHE A 296 CU A 402 SITE 3 AC8 11 HOH A 783 HOH A 821 HOH A 856 SITE 1 AC9 8 ASP A 163 VAL A 166 ASP A 167 ARG A 168 SITE 2 AC9 8 GLU A 169 ARG A 229 HOH A 719 HOH A 803 SITE 1 BC1 4 LYS A 138 PRO A 139 GLN A 300 HOH A 560 SITE 1 BC2 7 ASN A 158 GLY A 159 TYR A 160 ASP A 163 SITE 2 BC2 7 LYS A 164 HOH A 724 HOH A 778 SITE 1 BC3 3 HIS A 262 LEU A 263 HOH A 750 SITE 1 BC4 2 MET A 270 HOH A 850 SITE 1 BC5 5 LYS A 22 GLY A 23 LYS A 61 HOH A 683 SITE 2 BC5 5 HOH A 852 SITE 1 BC6 4 PRO A 290 HOH A 716 HOH A 783 HOH A 857 SITE 1 BC7 5 ASP A 55 LYS A 56 THR A 212 PHE A 213 SITE 2 BC7 5 HOH A 583 SITE 1 BC8 8 LYS A 127 PRO A 128 ASN A 258 ASN A 260 SITE 2 BC8 8 HOH A 572 HOH A 754 HOH A 804 HOH A 805 SITE 1 BC9 6 ARG A 168 LYS A 223 THR A 312 GLU A 314 SITE 2 BC9 6 HOH A 840 HOH A 841 CRYST1 114.903 114.903 84.022 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 0.008703 0.005025 0.000000 0.00000 SCALE2 0.000000 0.010049 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011902 0.00000