HEADER OXIDOREDUCTASE 07-DEC-10 2Y1A TITLE CRYSTAL STRUCTURE OF ACHROMOBACTER CYCLOCLASTES CU NITRITE REDUCTASE TITLE 2 WITH BOUND NO COMPND MOL_ID: 1; COMPND 2 MOLECULE: COPPER-CONTAINING NITRITE REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CU-NIR; COMPND 5 EC: 1.7.2.1 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ACHROMOBACTER CYCLOCLASTES; SOURCE 3 ORGANISM_TAXID: 223 KEYWDS OXIDOREDUCTASE, DENITRIFICATION EXPDTA X-RAY DIFFRACTION AUTHOR M.A.HOUGH,S.V.ANTONYUK REVDAT 3 20-DEC-23 2Y1A 1 REMARK LINK REVDAT 2 25-MAY-11 2Y1A 1 JRNL REVDAT 1 16-FEB-11 2Y1A 0 JRNL AUTH S.V.ANTONYUK,M.A.HOUGH JRNL TITL MONITORING AND VALIDATING ACTIVE SITE REDOX STATES IN JRNL TITL 2 PROTEIN CRYSTALS. JRNL REF BIOCHIM.BIOPHYS.ACTA V.1814 778 2011 JRNL REFN ISSN 0006-3002 JRNL PMID 21215826 JRNL DOI 10.1016/J.BBAPAP.2010.12.017 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0066 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.41 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 90.0 REMARK 3 NUMBER OF REFLECTIONS : 18142 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) : 0.156 REMARK 3 R VALUE (WORKING SET) : 0.153 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 989 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) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 795 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 55.12 REMARK 3 BIN R VALUE (WORKING SET) : 0.1330 REMARK 3 BIN FREE R VALUE SET COUNT : 45 REMARK 3 BIN FREE R VALUE : 0.2040 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2565 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 234 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.99 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.201 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.170 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.094 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.192 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.923 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2639 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2324 ; 0.000 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3607 ; 1.502 ; 1.951 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5388 ; 0.683 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 335 ; 7.556 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 117 ;34.920 ;24.103 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 381 ;12.960 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;18.532 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 396 ; 0.089 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2989 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 527 ; 0.000 ; 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): 1661 ; 0.692 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 680 ; 0.202 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2675 ; 1.126 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 978 ; 1.789 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 931 ; 2.686 ; 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 : 1.40 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. U VALUES REFINED INDIVIDUALLY. STRUCTURE IN REMARK 3 SPECTROSCOPICALLY VALIDATED REDOX STATE. REMARK 4 REMARK 4 2Y1A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-DEC-10. REMARK 100 THE DEPOSITION ID IS D_1290046556. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.75 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX10.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.37 REMARK 200 MONOCHROMATOR : SI (111) DOUBLE CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19807 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 26.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.100 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.2 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 58.4 REMARK 200 DATA REDUNDANCY IN SHELL : 1.80 REMARK 200 R MERGE FOR SHELL (I) : 0.08000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.700 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: PDB ENTRY 2BW4 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6M AMMONIUM SULPHATE, 100MM SODIUM REMARK 280 ACETATE PH 4.75 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 47.62000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.62000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 47.62000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 47.62000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 47.62000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 47.62000 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 47.62000 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 47.62000 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 47.62000 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 47.62000 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 47.62000 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 47.62000 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 47.62000 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 47.62000 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 47.62000 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 47.62000 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 47.62000 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 47.62000 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: 16760 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33340 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -261.4 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 0.000000 -1.000000 0.000000 47.62000 REMARK 350 BIOMT2 2 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT3 2 1.000000 0.000000 0.000000 -47.62000 REMARK 350 BIOMT1 3 0.000000 0.000000 1.000000 47.62000 REMARK 350 BIOMT2 3 -1.000000 0.000000 0.000000 47.62000 REMARK 350 BIOMT3 3 0.000000 -1.000000 0.000000 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 ALA A 1 REMARK 465 ALA A 2 REMARK 465 GLY A 3 REMARK 465 ALA A 4 REMARK 465 ALA A 5 REMARK 465 PRO A 6 REMARK 465 VAL A 7 REMARK 465 MET A 340 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 THR A 212 O REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ASP A 8 OD1 OD2 REMARK 480 LYS A 16 CD CE NZ REMARK 480 LYS A 49 CE NZ REMARK 480 LYS A 187 NZ REMARK 480 GLU A 189 CB CG CD OE1 OE2 REMARK 480 LYS A 194 CD CE NZ REMARK 480 LYS A 195 CD CE NZ REMARK 480 GLU A 197 CB CG CD OE1 OE2 REMARK 480 LYS A 208 CG CD CE NZ REMARK 480 LYS A 321 CD CE NZ REMARK 480 LYS A 336 CG CD CE NZ 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 OE1 GLU A 313 O HOH A 2209 2.02 REMARK 500 NZ LYS A 21 O HOH A 2016 2.11 REMARK 500 OH TYR A 196 OD2 ASP A 205 2.13 REMARK 500 OD2 ASP A 251 O HOH A 2180 2.17 REMARK 500 O VAL A 17 O HOH A 2011 2.18 REMARK 500 N ASP A 205 O HOH A 2156 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 2180 O HOH A 2180 6555 1.26 REMARK 500 REMARK 500 REMARK: NULL 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 ASP A 8 CG ASP A 8 OD1 -0.200 REMARK 500 LYS A 187 CE LYS A 187 NZ 0.226 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 ASP A 8 OD1 - CG - OD2 ANGL. DEV. = 14.0 DEGREES REMARK 500 ASP A 8 CB - CG - OD2 ANGL. DEV. = -14.2 DEGREES REMARK 500 ASP A 98 CB - CG - OD1 ANGL. DEV. = 6.7 DEGREES REMARK 500 LYS A 187 CD - CE - NZ ANGL. DEV. = -41.1 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 ALA A 105 49.52 39.22 REMARK 500 ALA A 137 72.27 -158.58 REMARK 500 LEU A 227 48.54 -105.80 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 HIS A 306 ASN A 307 146.24 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 95 ND1 REMARK 620 2 CYS A 136 SG 131.6 REMARK 620 3 HIS A 145 ND1 101.4 103.7 REMARK 620 4 MET A 150 SD 84.9 108.7 129.5 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 100 NE2 REMARK 620 2 HIS A 135 NE2 105.0 REMARK 620 3 HIS A 306 NE2 100.0 110.6 REMARK 620 4 NO A 502 N 144.7 104.5 87.5 REMARK 620 5 NO A 502 O 109.7 111.4 118.8 40.1 REMARK 620 N 1 2 3 4 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 NO A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 508 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2BWI RELATED DB: PDB REMARK 900 ATOMIC RESOLUTION STRUCTURE OF NITRITE -SOAKED ACHROMOBACTER REMARK 900 CYCLOCLASTES CU NITRITE REDUCTASE REMARK 900 RELATED ID: 1NIE RELATED DB: PDB REMARK 900 RELATED ID: 1NIA RELATED DB: PDB REMARK 900 RELATED ID: 1NID RELATED DB: PDB REMARK 900 RELATED ID: 2BW5 RELATED DB: PDB REMARK 900 ATOMIC RESOLUTION STRUCTURE OF NO-BOUND ALCALIGENES CYCLOCLASTES CU REMARK 900 NITRITE REDUCTASE REMARK 900 RELATED ID: 2AVF RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF C-TERMINAL DESUNDECAPEPTIDE NITRITEREDUCTASE REMARK 900 FROM ACHROMOBACTER CYCLOCLASTES REMARK 900 RELATED ID: 1NIF RELATED DB: PDB REMARK 900 RELATED ID: 2BWD RELATED DB: PDB REMARK 900 ATOMIC RESOLUTION STRUCTURE OF ACHROMOBACTER CYCLOCLASTES CU REMARK 900 NITRITE REDUCTASE WITH ENDOGENOUSLY BOUND NITRATE AND NO REMARK 900 RELATED ID: 2NRD RELATED DB: PDB REMARK 900 RELATED ID: 1KCB RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A NO-FORMING NITRITE REDUCTASE MUTANT:AN REMARK 900 ANALOG OF A TRANSITION STATE IN ENZYMATIC REACTION REMARK 900 RELATED ID: 1RZP RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF C-TERMINAL DESPENTAPEPTIDE NITRITEREDUCTASE REMARK 900 FROM ACHROMOBACTER CYCLOCLASTES AT PH6.2 REMARK 900 RELATED ID: 1NIC RELATED DB: PDB REMARK 900 RELATED ID: 1NIB RELATED DB: PDB REMARK 900 RELATED ID: 1RZQ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF C-TERMINAL DESPENTAPEPTIDE NITRITEREDUCTASE REMARK 900 FROM ACHROMOBACTER CYCLOCLASTES AT PH5.0 REMARK 900 RELATED ID: 2BW4 RELATED DB: PDB REMARK 900 ATOMIC RESOLUTION STRUCTURE OF RESTING STATE OF THE ALCALIGENES REMARK 900 CYCLOCLASTES CU NITRITE REDUCTASE DBREF 2Y1A A 1 340 UNP P25006 NIR_ACHCY 39 378 SEQRES 1 A 340 ALA ALA GLY ALA ALA PRO VAL ASP ILE SER THR LEU PRO SEQRES 2 A 340 ARG VAL LYS VAL ASP LEU VAL LYS PRO PRO PHE VAL HIS SEQRES 3 A 340 ALA HIS ASP GLN VAL ALA LYS THR GLY PRO ARG VAL VAL SEQRES 4 A 340 GLU PHE THR MET THR ILE GLU GLU LYS LYS LEU VAL ILE SEQRES 5 A 340 ASP ARG GLU GLY THR GLU ILE HIS ALA MET THR PHE ASN SEQRES 6 A 340 GLY SER VAL PRO GLY PRO LEU MET VAL VAL HIS GLU ASN SEQRES 7 A 340 ASP TYR VAL GLU LEU ARG LEU ILE ASN PRO ASP THR ASN SEQRES 8 A 340 THR LEU LEU HIS ASN ILE ASP PHE HIS ALA ALA THR GLY SEQRES 9 A 340 ALA LEU GLY GLY GLY ALA LEU THR GLN VAL ASN PRO GLY SEQRES 10 A 340 GLU GLU THR THR LEU ARG PHE LYS ALA THR LYS PRO GLY SEQRES 11 A 340 VAL PHE VAL TYR HIS CYS ALA PRO GLU GLY MET VAL PRO SEQRES 12 A 340 TRP HIS VAL THR SER GLY MET ASN GLY ALA ILE MET VAL SEQRES 13 A 340 LEU PRO ARG ASP GLY LEU LYS ASP GLU LYS GLY GLN PRO SEQRES 14 A 340 LEU THR TYR ASP LYS ILE TYR TYR VAL GLY GLU GLN ASP SEQRES 15 A 340 PHE TYR VAL PRO LYS ASP GLU ALA GLY ASN TYR LYS LYS SEQRES 16 A 340 TYR GLU THR PRO GLY GLU ALA TYR GLU ASP ALA VAL LYS SEQRES 17 A 340 ALA MET ARG THR LEU THR PRO THR HIS ILE VAL PHE ASN SEQRES 18 A 340 GLY ALA VAL GLY ALA LEU THR GLY ASP HIS ALA LEU THR SEQRES 19 A 340 ALA ALA VAL GLY GLU ARG VAL LEU VAL VAL HIS SER GLN SEQRES 20 A 340 ALA ASN ARG ASP THR ARG PRO HIS LEU ILE GLY GLY HIS SEQRES 21 A 340 GLY ASP TYR VAL TRP ALA THR GLY LYS PHE ARG ASN PRO SEQRES 22 A 340 PRO ASP LEU ASP GLN GLU THR TRP LEU ILE PRO GLY GLY SEQRES 23 A 340 THR ALA GLY ALA ALA PHE TYR THR PHE ARG GLN PRO GLY SEQRES 24 A 340 VAL TYR ALA TYR VAL ASN HIS ASN LEU ILE GLU ALA PHE SEQRES 25 A 340 GLU LEU GLY ALA ALA GLY HIS PHE LYS VAL THR GLY GLU SEQRES 26 A 340 TRP ASN ASP ASP LEU MET THR SER VAL VAL LYS PRO ALA SEQRES 27 A 340 SER MET HET CU A 500 1 HET CU A 501 1 HET NO A 502 2 HET ACT A 503 4 HET ACT A 504 4 HET SO4 A 505 5 HET SO4 A 506 5 HET SO4 A 507 5 HET SO4 A 508 5 HETNAM CU COPPER (II) ION HETNAM NO NITRIC OXIDE HETNAM ACT ACETATE ION HETNAM SO4 SULFATE ION HETSYN NO NITROGEN MONOXIDE FORMUL 2 CU 2(CU 2+) FORMUL 4 NO N O FORMUL 5 ACT 2(C2 H3 O2 1-) FORMUL 7 SO4 4(O4 S 2-) FORMUL 11 HOH *234(H2 O) HELIX 1 1 ASP A 8 LEU A 12 5 5 HELIX 2 2 GLY A 104 THR A 112 5 9 HELIX 3 3 MET A 141 THR A 147 1 7 HELIX 4 4 THR A 198 ARG A 211 1 14 HELIX 5 5 THR A 228 ALA A 232 5 5 HELIX 6 6 ASN A 307 GLU A 313 1 7 SHEET 1 AA 2 ARG A 14 LYS A 16 0 SHEET 2 AA 2 VAL A 38 VAL A 51 1 O VAL A 38 N VAL A 15 SHEET 1 AB 2 GLU A 58 PHE A 64 0 SHEET 2 AB 2 VAL A 38 VAL A 51 -1 O GLU A 46 N THR A 63 SHEET 1 AC 4 GLU A 118 LYS A 125 0 SHEET 2 AC 4 TYR A 80 ASN A 87 -1 O VAL A 81 N PHE A 124 SHEET 3 AC 4 VAL A 38 VAL A 51 1 O VAL A 39 N GLU A 82 SHEET 4 AC 4 GLU A 58 PHE A 64 -1 O ILE A 59 N LEU A 50 SHEET 1 AD 4 GLU A 118 LYS A 125 0 SHEET 2 AD 4 TYR A 80 ASN A 87 -1 O VAL A 81 N PHE A 124 SHEET 3 AD 4 VAL A 38 VAL A 51 1 O VAL A 39 N GLU A 82 SHEET 4 AD 4 ARG A 14 LYS A 16 1 O VAL A 15 N GLU A 40 SHEET 1 AE 4 LEU A 72 HIS A 76 0 SHEET 2 AE 4 ASN A 151 LEU A 157 1 O ALA A 153 N MET A 73 SHEET 3 AE 4 GLY A 130 HIS A 135 -1 O GLY A 130 N VAL A 156 SHEET 4 AE 4 ASP A 98 PHE A 99 -1 O ASP A 98 N HIS A 135 SHEET 1 AF 2 LEU A 162 LYS A 163 0 SHEET 2 AF 2 PRO A 169 LEU A 170 -1 O LEU A 170 N LEU A 162 SHEET 1 AG 6 HIS A 217 PHE A 220 0 SHEET 2 AG 6 LYS A 174 PHE A 183 -1 O GLN A 181 N VAL A 219 SHEET 3 AG 6 ARG A 240 GLN A 247 1 O LEU A 242 N TYR A 176 SHEET 4 AG 6 THR A 287 THR A 294 -1 O THR A 287 N GLN A 247 SHEET 5 AG 6 GLY A 261 TRP A 265 -1 N ASP A 262 O PHE A 292 SHEET 6 AG 6 ASP A 275 GLN A 278 -1 O ASP A 275 N VAL A 264 SHEET 1 AH 4 LEU A 233 ALA A 236 0 SHEET 2 AH 4 ALA A 317 THR A 323 1 O HIS A 319 N LEU A 233 SHEET 3 AH 4 GLY A 299 ASN A 305 -1 O GLY A 299 N VAL A 322 SHEET 4 AH 4 PRO A 254 ILE A 257 -1 O HIS A 255 N VAL A 304 LINK ND1 HIS A 95 CU CU A 500 1555 1555 2.06 LINK NE2 HIS A 100 CU CU A 501 1555 1555 2.06 LINK NE2 HIS A 135 CU CU A 501 1555 1555 2.09 LINK SG CYS A 136 CU CU A 500 1555 1555 2.29 LINK ND1 HIS A 145 CU CU A 500 1555 1555 2.05 LINK SD MET A 150 CU CU A 500 1555 1555 2.43 LINK NE2 HIS A 306 CU CU A 501 6555 1555 2.03 LINK CU CU A 501 N NO A 502 1555 1555 2.14 LINK CU CU A 501 O NO A 502 1555 1555 2.13 CISPEP 1 PRO A 22 PRO A 23 0 10.50 CISPEP 2 VAL A 68 PRO A 69 0 -2.71 SITE 1 AC1 4 HIS A 95 CYS A 136 HIS A 145 MET A 150 SITE 1 AC2 4 HIS A 100 HIS A 135 HIS A 306 NO A 502 SITE 1 AC3 7 ASP A 98 HIS A 100 HIS A 135 HIS A 255 SITE 2 AC3 7 ILE A 257 HIS A 306 CU A 501 SITE 1 AC4 9 TRP A 265 THR A 267 GLY A 268 LYS A 269 SITE 2 AC4 9 ASN A 272 ASP A 275 GLN A 278 HOH A2187 SITE 3 AC4 9 HOH A2230 SITE 1 AC5 4 HIS A 60 GLU A 197 THR A 198 PRO A 199 SITE 1 AC6 3 LYS A 33 ASP A 188 GLU A 189 SITE 1 AC7 4 LYS A 125 THR A 127 ARG A 296 HOH A2224 SITE 1 AC8 4 LYS A 128 ARG A 271 HOH A2231 HOH A2232 SITE 1 AC9 5 THR A 228 GLY A 229 ASP A 230 HIS A 231 SITE 2 AC9 5 HOH A2234 CRYST1 95.240 95.240 95.240 90.00 90.00 90.00 P 21 3 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 0.010500 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010500 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010500 0.00000