HEADER OXIDOREDUCTASE 05-MAR-15 5AKR TITLE ATOMIC RESOLUTION STRUCTURE OF NITRITE BOUND STATE OF THE TITLE 2 ACHROMOBACTER CYCLOCLASTES CU NITRITE REDUCTASE AT 0.87 A TITLE 3 RESOLUTION 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, CATALYSIS, NITRITE REDUCTASES, OXIDATION-REDUCTION, KEYWDS 2 SUBSTRATE SPECIFICITY EXPDTA X-RAY DIFFRACTION AUTHOR M.P.BLAKELEY,S.S.HASNAIN,S.V.ANTONYUK REVDAT 2 29-JUL-15 5AKR 1 JRNL REVDAT 1 08-JUL-15 5AKR 0 JRNL AUTH M.P.BLAKELEY,S.S.HASNAIN,S.V.ANTONYUK JRNL TITL SUB-ATOMIC RESOLUTION X-RAY CRYSTALLOGRAPHY AND NEUTRON JRNL TITL 2 CRYSTALLOGRAPHY: PROMISE, CHALLENGES AND POTENTIAL. JRNL REF IUCRJ V. 2 464 2015 JRNL REFN ISSN 2052-2525 JRNL PMID 26175905 JRNL DOI 10.1107/S2052252515011239 REMARK 2 REMARK 2 RESOLUTION. 0.87 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU, REMARK 3 STEINER,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) : 0.87 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 17.41 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.78 REMARK 3 NUMBER OF REFLECTIONS : 214835 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) : 0.10984 REMARK 3 R VALUE (WORKING SET) : 0.10892 REMARK 3 FREE R VALUE : 0.12714 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.0 REMARK 3 FREE R VALUE TEST SET COUNT : 11344 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) : 0.870 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 0.893 REMARK 3 REFLECTION IN BIN (WORKING SET) : 16002 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.58 REMARK 3 BIN R VALUE (WORKING SET) : 0.280 REMARK 3 BIN FREE R VALUE SET COUNT : 873 REMARK 3 BIN FREE R VALUE : 0.291 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2882 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 36 REMARK 3 SOLVENT ATOMS : 668 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 10.996 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00 REMARK 3 B22 (A**2) : 0.00 REMARK 3 B33 (A**2) : 0.00 REMARK 3 B12 (A**2) : 0.00 REMARK 3 B13 (A**2) : 0.00 REMARK 3 B23 (A**2) : 0.00 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.014 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.015 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.009 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.323 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.989 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.984 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3023 ; 0.017 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2167 ; 0.008 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4153 ; 1.998 ; 1.966 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5032 ; 1.946 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 404 ; 8.213 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 134 ;35.199 ;24.254 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 495 ;11.927 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;18.051 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 454 ; 0.118 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3416 ; 0.013 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 605 ; 0.007 ; 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): 1473 ; 1.216 ; 0.716 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1465 ; 1.142 ; 0.711 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1854 ; 1.461 ; 1.078 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1550 ; 2.680 ; 0.903 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): 5190 ; 4.250 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 98 ;57.360 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 5679 ;20.477 ; 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 ADDED IN THE RIDING REMARK 3 POSITIONS IF THEY WERE VISIBLE IN FO-FC ELECTRON DENSITY AT 2 SIGMA REMARK 3 VALUES REFINED INDIVIDUALLY. REMARK 4 REMARK 4 5AKR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-MAY-15. REMARK 100 THE PDBE ID CODE IS EBI-63202. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JUL-08 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) : 0.92 REMARK 200 MONOCHROMATOR : SI111 REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL2000 REMARK 200 DATA SCALING SOFTWARE : HKL2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 231231 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.87 REMARK 200 RESOLUTION RANGE LOW (A) : 23.00 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NONE REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.2 REMARK 200 R MERGE (I) : 0.06 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 32.00 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.87 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.7 REMARK 200 R MERGE FOR SHELL (I) : 0.46 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.00 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 (%): 34.7 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.86 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 47.47400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.47400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 47.47400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 47.47400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 47.47400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 47.47400 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 47.47400 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 47.47400 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 47.47400 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 47.47400 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 47.47400 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 47.47400 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 47.47400 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 47.47400 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 47.47400 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 47.47400 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 47.47400 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 47.47400 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: 16930 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 34870 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -108.0 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 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 0.000000 1.000000 -47.47400 REMARK 350 BIOMT3 2 -1.000000 0.000000 0.000000 47.47400 REMARK 350 BIOMT1 3 0.000000 0.000000 -1.000000 47.47400 REMARK 350 BIOMT2 3 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 1.000000 0.000000 47.47400 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 A2009 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2019 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2057 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2059 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2147 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2171 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2175 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2331 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2517 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2672 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 -37 REMARK 465 THR A -36 REMARK 465 GLU A -35 REMARK 465 GLN A -34 REMARK 465 LEU A -33 REMARK 465 GLN A -32 REMARK 465 MET A -31 REMARK 465 THR A -30 REMARK 465 ARG A -29 REMARK 465 ARG A -28 REMARK 465 THR A -27 REMARK 465 MET A -26 REMARK 465 LEU A -25 REMARK 465 ALA A -24 REMARK 465 GLY A -23 REMARK 465 ALA A -22 REMARK 465 ALA A -21 REMARK 465 LEU A -20 REMARK 465 ALA A -19 REMARK 465 GLY A -18 REMARK 465 ALA A -17 REMARK 465 VAL A -16 REMARK 465 ALA A -15 REMARK 465 PRO A -14 REMARK 465 LEU A -13 REMARK 465 LEU A -12 REMARK 465 HIS A -11 REMARK 465 THR A -10 REMARK 465 ALA A -9 REMARK 465 GLN A -8 REMARK 465 ALA A -7 REMARK 465 HIS A -6 REMARK 465 ALA A -5 REMARK 465 ALA A -4 REMARK 465 GLY A -3 REMARK 465 ALA A -2 REMARK 465 ALA A -1 REMARK 465 ALA A 0 REMARK 465 ALA A 1 REMARK 465 ALA A 2 REMARK 465 GLY A 3 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 B ASP A 8 OG1 THR A 11 2.13 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 NH1A ARG A 84 OE2B GLU A 197 9555 2.16 REMARK 500 NH1A ARG A 84 CD B GLU A 197 9555 2.04 REMARK 500 NH1A ARG A 84 OE1B GLU A 197 9555 2.03 REMARK 500 CD B GLN A 168 O B HOH A 2647 8555 1.83 REMARK 500 OE1B GLN A 168 O B HOH A 2647 8555 2.17 REMARK 500 OE1B GLN A 168 O A HOH A 2647 8555 1.22 REMARK 500 NE2B GLN A 168 O B HOH A 2647 8555 1.15 REMARK 500 CD B GLU A 197 O C HOH A 2693 5555 1.27 REMARK 500 OE1B GLU A 197 O C HOH A 2693 5555 1.41 REMARK 500 OE2B GLU A 197 O HOH A 2066 5555 1.54 REMARK 500 OE2B GLU A 197 O C HOH A 2693 5555 1.18 REMARK 500 O8 A MLI A 514 O B HOH A 2561 10545 1.90 REMARK 500 O HOH A 2014 O HOH A 2675 11455 0.64 REMARK 500 O A HOH A 2037 O HOH A 2297 9555 2.13 REMARK 500 O HOH A 2056 O B HOH A 2677 8555 1.43 REMARK 500 O HOH A 2097 O A HOH A 2412 10545 1.70 REMARK 500 O HOH A 2097 O C HOH A 2420 10545 1.84 REMARK 500 O HOH A 2173 O A HOH A 2387 7555 1.33 REMARK 500 O HOH A 2173 O B HOH A 2387 7555 0.60 REMARK 500 O HOH A 2217 O HOH A 2535 10545 2.11 REMARK 500 O HOH A 2255 O HOH A 2640 7555 1.93 REMARK 500 O A HOH A 2326 O C HOH A 2686 10545 1.44 REMARK 500 O B HOH A 2367 O B HOH A 2561 10545 2.20 REMARK 500 O HOH A 2445 O C HOH A 2679 3555 0.79 REMARK 500 O HOH A 2473 O HOH A 2633 7555 2.12 REMARK 500 O B HOH A 2561 O B HOH A 2561 7555 1.27 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 LYS A 195 C A TYR A 196 N A 0.163 REMARK 500 TRP A 281 CG A TRP A 281 CD1A 0.146 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 ARG A 84 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 ASP A 98 CB - CG - OD1 ANGL. DEV. = 6.6 DEGREES REMARK 500 ARG A 253 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 253 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 TRP A 281 CD1 - CG - CD2 ANGL. DEV. = -5.0 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 137 70.54 -158.87 REMARK 500 MET A 141 37.42 -143.54 REMARK 500 LEU A 227 45.42 -101.77 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 HIS A 306 ASN A 307 143.03 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 TRP A 281 -11.62 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 501 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 95 ND1 REMARK 620 2 CYS A 136 SG 127.9 REMARK 620 3 HIS A 145 ND1 100.7 106.6 REMARK 620 4 MET A 150 SD 86.7 108.1 128.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 502 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 NO2 A 508 O2 REMARK 620 2 HOH A2698 O 34.2 REMARK 620 3 HIS A 135 NE2 96.2 109.3 REMARK 620 4 NO2 A 508 O1 62.6 34.7 90.8 REMARK 620 5 HIS A 100 NE2 142.9 110.5 112.1 92.3 REMARK 620 6 NO2 A 508 N 34.9 3.2 112.4 36.7 109.1 REMARK 620 7 HIS A 306 NE2 88.6 110.5 113.2 144.8 101.1 108.3 REMARK 620 N 1 2 3 4 5 6 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 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MLI A 512 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MLI A 514 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 515 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 601 DBREF 5AKR A -37 340 UNP P25006 NIR_ACHCY 1 378 SEQRES 1 A 378 MET THR GLU GLN LEU GLN MET THR ARG ARG THR MET LEU SEQRES 2 A 378 ALA GLY ALA ALA LEU ALA GLY ALA VAL ALA PRO LEU LEU SEQRES 3 A 378 HIS THR ALA GLN ALA HIS ALA ALA GLY ALA ALA ALA ALA SEQRES 4 A 378 ALA GLY ALA ALA PRO VAL ASP ILE SER THR LEU PRO ARG SEQRES 5 A 378 VAL LYS VAL ASP LEU VAL LYS PRO PRO PHE VAL HIS ALA SEQRES 6 A 378 HIS ASP GLN VAL ALA LYS THR GLY PRO ARG VAL VAL GLU SEQRES 7 A 378 PHE THR MET THR ILE GLU GLU LYS LYS LEU VAL ILE ASP SEQRES 8 A 378 ARG GLU GLY THR GLU ILE HIS ALA MET THR PHE ASN GLY SEQRES 9 A 378 SER VAL PRO GLY PRO LEU MET VAL VAL HIS GLU ASN ASP SEQRES 10 A 378 TYR VAL GLU LEU ARG LEU ILE ASN PRO ASP THR ASN THR SEQRES 11 A 378 LEU LEU HIS ASN ILE ASP PHE HIS ALA ALA THR GLY ALA SEQRES 12 A 378 LEU GLY GLY GLY ALA LEU THR GLN VAL ASN PRO GLY GLU SEQRES 13 A 378 GLU THR THR LEU ARG PHE LYS ALA THR LYS PRO GLY VAL SEQRES 14 A 378 PHE VAL TYR HIS CYS ALA PRO GLU GLY MET VAL PRO TRP SEQRES 15 A 378 HIS VAL THR SER GLY MET ASN GLY ALA ILE MET VAL LEU SEQRES 16 A 378 PRO ARG ASP GLY LEU LYS ASP GLU LYS GLY GLN PRO LEU SEQRES 17 A 378 THR TYR ASP LYS ILE TYR TYR VAL GLY GLU GLN ASP PHE SEQRES 18 A 378 TYR VAL PRO LYS ASP GLU ALA GLY ASN TYR LYS LYS TYR SEQRES 19 A 378 GLU THR PRO GLY GLU ALA TYR GLU ASP ALA VAL LYS ALA SEQRES 20 A 378 MET ARG THR LEU THR PRO THR HIS ILE VAL PHE ASN GLY SEQRES 21 A 378 ALA VAL GLY ALA LEU THR GLY ASP HIS ALA LEU THR ALA SEQRES 22 A 378 ALA VAL GLY GLU ARG VAL LEU VAL VAL HIS SER GLN ALA SEQRES 23 A 378 ASN ARG ASP THR ARG PRO HIS LEU ILE GLY GLY HIS GLY SEQRES 24 A 378 ASP TYR VAL TRP ALA THR GLY LYS PHE ARG ASN PRO PRO SEQRES 25 A 378 ASP LEU ASP GLN GLU THR TRP LEU ILE PRO GLY GLY THR SEQRES 26 A 378 ALA GLY ALA ALA PHE TYR THR PHE ARG GLN PRO GLY VAL SEQRES 27 A 378 TYR ALA TYR VAL ASN HIS ASN LEU ILE GLU ALA PHE GLU SEQRES 28 A 378 LEU GLY ALA ALA GLY HIS PHE LYS VAL THR GLY GLU TRP SEQRES 29 A 378 ASN ASP ASP LEU MET THR SER VAL VAL LYS PRO ALA SER SEQRES 30 A 378 MET HET CU A 501 1 HET CU A 502 1 HET ACT A 505 4 HET ACT A 506 8 HET NO2 A 508 3 HET MLI A 512 7 HET MLI A 514 7 HET SO4 A 515 5 HET ACT A 601 4 HETNAM MLI MALONATE ION HETNAM SO4 SULFATE ION HETNAM NO2 NITRITE ION HETNAM CU COPPER (II) ION HETNAM ACT ACETATE ION FORMUL 2 MLI 2(C3 H2 O4 2-) FORMUL 3 SO4 O4 S 2- FORMUL 4 NO2 N O2 1- FORMUL 5 CU 2(CU 2+) FORMUL 6 ACT 3(C2 H3 O2 1-) FORMUL 7 HOH *568(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 SER A 148 1 8 HELIX 4 4 THR A 198 THR A 212 1 15 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 MET A 73 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 CU CU A 501 ND1 HIS A 95 1555 1555 2.05 LINK CU CU A 501 SG CYS A 136 1555 1555 2.23 LINK CU CU A 501 ND1 HIS A 145 1555 1555 2.04 LINK CU CU A 501 SD MET A 150 1555 1555 2.47 LINK CU CU A 502 NE2 HIS A 100 1555 1555 2.00 LINK CU CU A 502 NE2 HIS A 135 1555 1555 2.01 LINK CU CU A 502 O AHOH A2698 1555 1555 2.23 LINK CU CU A 502 NE2 HIS A 306 1555 10545 1.99 LINK CU CU A 502 O2 BNO2 A 508 1555 1555 2.26 LINK CU CU A 502 O1 BNO2 A 508 1555 1555 2.26 LINK CU CU A 502 N BNO2 A 508 1555 1555 2.14 CISPEP 1 PRO A 22 PRO A 23 0 10.12 CISPEP 2 VAL A 68 PRO A 69 0 -5.87 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 HOH A2698 SITE 1 AC3 3 THR A 228 GLY A 229 HIS A 319 SITE 1 AC4 5 PHE A 312 HIS A 319 HOH A2468 HOH A2471 SITE 2 AC4 5 HOH A2473 SITE 1 AC5 8 ALA A 27 HIS A 28 GLN A 30 ILE A 175 SITE 2 AC5 8 HOH A2264 HOH A2481 HOH A2483 HOH A2611 SITE 1 AC6 6 ARG A 250 ASP A 251 ARG A 253 ASN A 307 SITE 2 AC6 6 GLU A 310 HOH A2369 SITE 1 AC7 9 PRO A 158 ARG A 159 ASP A 160 HOH A2241 SITE 2 AC7 9 HOH A2246 HOH A2494 HOH A2500 HOH A2524 SITE 3 AC7 9 HOH A2622 SITE 1 AC8 7 THR A 198 PRO A 199 GLY A 200 VAL A 237 SITE 2 AC8 7 GLY A 238 HOH A2361 HOH A2685 CRYST1 94.948 94.948 94.948 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 0.010532 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010532 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010532 0.00000 MASTER 544 0 9 6 28 0 14 6 0 0 0 30 END