HEADER OXIDOREDUCTASE 05-JUN-20 6ZAX TITLE NITRITE-BOUND COPPER NITRITE REDUCTASE FROM BRADYRHIZOBIUM SP. ORS 375 TITLE 2 (TWO-DOMAIN) AT LOW DOSE (0.5 MGY) COMPND MOL_ID: 1; COMPND 2 MOLECULE: COPPER-CONTAINING NITRITE REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.7.2.1; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BRADYRHIZOBIUM SP. (STRAIN ORS 375); SOURCE 3 ORGANISM_TAXID: 566679; SOURCE 4 STRAIN: ORS 375; SOURCE 5 GENE: NIRK, BRAO375_4030011; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET26B+ KEYWDS NITRITE REDUCTASE, COPPER NITRITE REDUCTASE, COPPER-CONTAINING KEYWDS 2 NITRITE REDUCTASE, BRNIR, BR2DNIR, SUBSTRATE-BOUND, NITRITE-BOUND, KEYWDS 3 LOW DOSE, SYNCHROTRON, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR S.L.ROSE,S.V.ANTONYUK,D.SASAKI,K.YAMASHITA,K.HIRATA,G.UENO,H.AGO, AUTHOR 2 R.R.EADY,T.TOSHA,M.YAMAMOTO,S.S.HASNAIN REVDAT 3 24-JAN-24 6ZAX 1 REMARK REVDAT 2 10-FEB-21 6ZAX 1 JRNL REVDAT 1 20-JAN-21 6ZAX 0 JRNL AUTH S.L.ROSE,S.V.ANTONYUK,D.SASAKI,K.YAMASHITA,K.HIRATA,G.UENO, JRNL AUTH 2 H.AGO,R.R.EADY,T.TOSHA,M.YAMAMOTO,S.S.HASNAIN JRNL TITL AN UNPRECEDENTED INSIGHT INTO THE CATALYTIC MECHANISM OF JRNL TITL 2 COPPER NITRITE REDUCTASE FROM ATOMIC-RESOLUTION AND JRNL TITL 3 DAMAGE-FREE STRUCTURES. JRNL REF SCI ADV V. 7 2021 JRNL REFN ESSN 2375-2548 JRNL PMID 33523860 JRNL DOI 10.1126/SCIADV.ABD8523 REMARK 2 REMARK 2 RESOLUTION. 1.48 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0258 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) : 1.48 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.15 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 65659 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) : 0.148 REMARK 3 R VALUE (WORKING SET) : 0.147 REMARK 3 FREE R VALUE : 0.176 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3481 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.48 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.52 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4782 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.05 REMARK 3 BIN R VALUE (WORKING SET) : 0.3080 REMARK 3 BIN FREE R VALUE SET COUNT : 242 REMARK 3 BIN FREE R VALUE : 0.3180 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2666 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 125 REMARK 3 SOLVENT ATOMS : 494 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.13 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.058 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.062 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.046 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.315 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.979 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.969 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3144 ; 0.013 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 2799 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4318 ; 1.954 ; 1.682 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6562 ; 1.458 ; 1.601 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 404 ; 8.042 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 157 ;33.623 ;23.057 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 499 ;14.213 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;21.654 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 410 ; 0.095 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3520 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 629 ; 0.002 ; 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): 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): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6ZAX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-JUN-20. REMARK 100 THE DEPOSITION ID IS D_1292109168. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-FEB-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 65671 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.480 REMARK 200 RESOLUTION RANGE LOW (A) : 48.150 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.09400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.48 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.63800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: 6THF REMARK 200 REMARK 200 REMARK: BLUE CUBES REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6 M (NH4)2SO4 AND 50MM HEPES BUFFER REMARK 280 PH5.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 297K 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 53.78300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.78300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 53.78300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 53.78300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 53.78300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 53.78300 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 53.78300 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 53.78300 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 53.78300 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 53.78300 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 53.78300 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 53.78300 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 53.78300 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 53.78300 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 53.78300 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 53.78300 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 53.78300 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 53.78300 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: 25310 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 36900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -380.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, F, G 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 0.000000 1.000000 -53.78300 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 53.78300 REMARK 350 BIOMT3 2 0.000000 -1.000000 0.000000 107.56600 REMARK 350 BIOMT1 3 0.000000 -1.000000 0.000000 53.78300 REMARK 350 BIOMT2 3 0.000000 0.000000 -1.000000 107.56600 REMARK 350 BIOMT3 3 1.000000 0.000000 0.000000 53.78300 REMARK 350 APPLY THE FOLLOWING TO CHAINS: E REMARK 350 BIOMT1 4 -1.000000 0.000000 0.000000 53.78300 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 107.56600 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 53.78300 REMARK 350 BIOMT1 5 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT2 5 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT1 6 0.000000 1.000000 0.000000 -53.78300 REMARK 350 BIOMT2 6 0.000000 0.000000 -1.000000 53.78300 REMARK 350 BIOMT3 6 -1.000000 0.000000 0.000000 107.56600 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 S SO4 A 412 LIES ON A SPECIAL POSITION. REMARK 375 O3 SO4 A 412 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 737 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 ASP A 2 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 154 CG - CD - NE ANGL. DEV. = -14.4 DEGREES REMARK 500 ARG A 154 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 169 NE - CZ - NH2 ANGL. DEV. = -3.0 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 LYS A 5 49.92 -105.29 REMARK 500 GLN A 24 -85.27 -77.75 REMARK 500 ALA A 131 71.94 -159.81 REMARK 500 THR A 340 53.72 -117.47 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 299 THR A 300 148.71 REMARK 500 HIS A 301 ASN A 302 142.36 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 991 DISTANCE = 5.93 ANGSTROMS REMARK 525 HOH A 992 DISTANCE = 6.48 ANGSTROMS REMARK 525 HOH A 993 DISTANCE = 6.61 ANGSTROMS REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 SO4 A 413 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 406 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 89 ND1 REMARK 620 2 CYS A 130 SG 131.7 REMARK 620 3 HIS A 140 ND1 100.6 111.8 REMARK 620 4 MET A 145 SD 84.4 111.9 113.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 407 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 94 NE2 REMARK 620 2 HIS A 129 NE2 103.6 REMARK 620 3 HIS A 301 NE2 69.5 92.7 REMARK 620 4 NO2 A 409 N 128.8 113.4 138.2 REMARK 620 5 NO2 A 409 O1 162.8 90.6 120.3 34.2 REMARK 620 6 NO2 A 409 O2 96.5 105.5 159.4 41.3 69.9 REMARK 620 N 1 2 3 4 5 DBREF 6ZAX A 2 341 UNP H0SLX7 H0SLX7_BRAS3 25 364 SEQADV 6ZAX MET A 1 UNP H0SLX7 INITIATING METHIONINE SEQADV 6ZAX GLU A 342 UNP H0SLX7 EXPRESSION TAG SEQADV 6ZAX ASN A 343 UNP H0SLX7 EXPRESSION TAG SEQADV 6ZAX LEU A 344 UNP H0SLX7 EXPRESSION TAG SEQADV 6ZAX TYR A 345 UNP H0SLX7 EXPRESSION TAG SEQADV 6ZAX PHE A 346 UNP H0SLX7 EXPRESSION TAG SEQADV 6ZAX GLN A 347 UNP H0SLX7 EXPRESSION TAG SEQRES 1 A 347 MET ASP ASP LEU LYS LEU PRO ARG GLN ARG VAL ASP LEU SEQRES 2 A 347 VAL ALA PRO PRO PHE VAL HIS VAL HIS GLU GLN ALA THR SEQRES 3 A 347 LYS GLN GLY PRO LYS ILE MET GLU PHE LYS LEU VAL VAL SEQRES 4 A 347 GLN GLU LYS LYS MET VAL ILE ASP GLU LYS GLY THR THR SEQRES 5 A 347 PHE GLN ALA MET THR PHE ASN GLY SER MET PRO GLY PRO SEQRES 6 A 347 LEU MET VAL VAL HIS GLU GLY ASP TYR VAL GLU VAL THR SEQRES 7 A 347 LEU VAL ASN PRO ALA THR ASN THR MET PRO HIS ASN ILE SEQRES 8 A 347 ASP PHE HIS SER ALA THR GLY ALA LEU GLY GLY GLY ALA SEQRES 9 A 347 LEU THR LEU ILE ASN PRO GLY GLU GLN VAL VAL LEU ARG SEQRES 10 A 347 TRP LYS ALA THR ARG THR GLY VAL PHE VAL TYR HIS CYS SEQRES 11 A 347 ALA PRO GLY GLY PRO MET ILE PRO TRP HIS VAL VAL SER SEQRES 12 A 347 GLY MET ASN GLY ALA VAL MET VAL LEU PRO ARG ASP GLY SEQRES 13 A 347 LEU ASN ASP GLY HIS GLY HIS SER LEU ARG TYR ASP ARG SEQRES 14 A 347 ILE TYR TYR ILE GLY GLU GLN ASP LEU TYR VAL PRO ARG SEQRES 15 A 347 ASP GLU LYS GLY ASN PHE LYS SER TYR ASP SER PRO GLY SEQRES 16 A 347 GLU ALA TYR SER ASP THR GLU GLU VAL MET ARG LYS LEU SEQRES 17 A 347 THR PRO THR HIS VAL VAL PHE ASN GLY LYS ALA GLY ALA SEQRES 18 A 347 LEU THR GLY LYS ASN ALA LEU ASN ALA ASN VAL GLY GLU SEQRES 19 A 347 ASN VAL LEU ILE VAL HIS SER GLN ALA ASN ARG ASP SER SEQRES 20 A 347 ARG PRO HIS LEU ILE GLY GLY HIS GLY ASP TYR VAL TRP SEQRES 21 A 347 GLU THR GLY LYS PHE SER ASN ALA PRO GLU THR GLY LEU SEQRES 22 A 347 GLU THR TRP PHE ILE ARG GLY GLY SER ALA GLY ALA ALA SEQRES 23 A 347 LEU TYR LYS PHE LEU GLN PRO GLY ILE TYR ALA TYR VAL SEQRES 24 A 347 THR HIS ASN LEU ILE GLU ALA ALA ASN LEU GLY ALA THR SEQRES 25 A 347 ALA HIS PHE LYS VAL GLU GLY LYS TRP ASN ASP ASP LEU SEQRES 26 A 347 MET THR GLN VAL LYS ALA PRO ALA ASP ILE PRO THR GLY SEQRES 27 A 347 SER THR ASN GLU ASN LEU TYR PHE GLN HET GLC E 1 11 HET FRU E 2 12 HET GLC F 1 11 HET FRU F 2 12 HET GLC G 1 11 HET FRU G 2 12 HET SO4 A 401 5 HET SO4 A 402 5 HET SO4 A 403 5 HET SO4 A 404 5 HET SO4 A 405 5 HET CU A 406 1 HET CU A 407 1 HET GOL A 408 6 HET NO2 A 409 3 HET SO4 A 410 5 HET SO4 A 411 5 HET SO4 A 412 5 HET SO4 A 413 5 HETNAM GLC ALPHA-D-GLUCOPYRANOSE HETNAM FRU BETA-D-FRUCTOFURANOSE HETNAM SO4 SULFATE ION HETNAM CU COPPER (II) ION HETNAM GOL GLYCEROL HETNAM NO2 NITRITE ION HETSYN GLC ALPHA-D-GLUCOSE; D-GLUCOSE; GLUCOSE HETSYN FRU BETA-D-FRUCTOSE; D-FRUCTOSE; FRUCTOSE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GLC 3(C6 H12 O6) FORMUL 2 FRU 3(C6 H12 O6) FORMUL 5 SO4 9(O4 S 2-) FORMUL 10 CU 2(CU 2+) FORMUL 12 GOL C3 H8 O3 FORMUL 13 NO2 N O2 1- FORMUL 18 HOH *494(H2 O) HELIX 1 AA1 GLY A 98 THR A 106 5 9 HELIX 2 AA2 PRO A 135 SER A 143 1 9 HELIX 3 AA3 SER A 193 LYS A 207 1 15 HELIX 4 AA4 THR A 223 ALA A 227 5 5 HELIX 5 AA5 ASN A 302 LEU A 309 1 8 HELIX 6 AA6 THR A 340 LEU A 344 5 5 SHEET 1 AA1 3 ARG A 8 ARG A 10 0 SHEET 2 AA1 3 ILE A 32 VAL A 45 1 O GLU A 34 N GLN A 9 SHEET 3 AA1 3 THR A 52 PHE A 58 -1 O PHE A 53 N MET A 44 SHEET 1 AA2 4 ARG A 8 ARG A 10 0 SHEET 2 AA2 4 ILE A 32 VAL A 45 1 O GLU A 34 N GLN A 9 SHEET 3 AA2 4 TYR A 74 ASN A 81 1 O VAL A 80 N VAL A 39 SHEET 4 AA2 4 GLU A 112 LYS A 119 -1 O TRP A 118 N VAL A 75 SHEET 1 AA3 4 LEU A 66 HIS A 70 0 SHEET 2 AA3 4 ASN A 146 LEU A 152 1 O MET A 150 N MET A 67 SHEET 3 AA3 4 GLY A 124 HIS A 129 -1 N GLY A 124 O VAL A 151 SHEET 4 AA3 4 ASP A 92 PHE A 93 -1 N ASP A 92 O HIS A 129 SHEET 1 AA4 6 HIS A 212 PHE A 215 0 SHEET 2 AA4 6 ARG A 169 LEU A 178 -1 N LEU A 178 O HIS A 212 SHEET 3 AA4 6 ASN A 235 GLN A 242 1 O VAL A 239 N ILE A 173 SHEET 4 AA4 6 SER A 282 LYS A 289 -1 O TYR A 288 N VAL A 236 SHEET 5 AA4 6 GLY A 256 TRP A 260 -1 N TYR A 258 O LEU A 287 SHEET 6 AA4 6 GLU A 270 LEU A 273 -1 O GLU A 270 N VAL A 259 SHEET 1 AA5 4 LEU A 228 ASN A 231 0 SHEET 2 AA5 4 THR A 312 GLU A 318 1 O HIS A 314 N LEU A 228 SHEET 3 AA5 4 GLY A 294 THR A 300 -1 N TYR A 296 O PHE A 315 SHEET 4 AA5 4 PRO A 249 LEU A 251 -1 N HIS A 250 O VAL A 299 LINK C1 AGLC E 1 O2 AFRU E 2 1555 1555 1.42 LINK C1 AGLC F 1 O2 AFRU F 2 1555 1555 1.42 LINK C1 AGLC G 1 O2 AFRU G 2 1555 1555 1.43 LINK ND1 HIS A 89 CU CU A 406 1555 1555 2.02 LINK NE2 HIS A 94 CU CU A 407 1555 1555 2.01 LINK NE2 HIS A 129 CU CU A 407 1555 1555 2.06 LINK SG CYS A 130 CU CU A 406 1555 1555 2.16 LINK ND1 HIS A 140 CU CU A 406 1555 1555 1.96 LINK SD MET A 145 CU CU A 406 1555 1555 2.54 LINK NE2 HIS A 301 CU CU A 407 1555 12565 2.05 LINK CU CU A 407 N BNO2 A 409 1555 1555 1.78 LINK CU CU A 407 O1 BNO2 A 409 1555 1555 2.33 LINK CU CU A 407 O2 BNO2 A 409 1555 1555 1.92 CISPEP 1 PRO A 16 PRO A 17 0 7.78 CISPEP 2 PRO A 16 PRO A 17 0 6.96 CISPEP 3 MET A 62 PRO A 63 0 -9.12 CRYST1 107.566 107.566 107.566 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 0.009297 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009297 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009297 0.00000