HEADER OXIDOREDUCTASE 20-NOV-19 6THF TITLE CRYSTAL STRUCTURE OF TWO-DOMAIN CU NITRITE REDUCTASE FROM TITLE 2 BRADYRHIZOBIUM SP. ORS 375 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. ORS 375; SOURCE 3 ORGANISM_TAXID: 566679; SOURCE 4 GENE: NIRK, BRAO375_4030011; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET-26B(+) KEYWDS TWO-DOMAIN, COPPER-CONTAINING NITRITE REDUCTASE, BRADYRHIZOBIUM SP. KEYWDS 2 ORS 375, ELECTRON TRANSFER, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR D.SASAKI,T.F.WATANABE,R.R.EADY,R.C.GARRATT,S.V.ANTONYUK,S.S.HASNAIN REVDAT 3 24-JAN-24 6THF 1 REMARK REVDAT 2 13-JAN-21 6THF 1 JRNL LINK REVDAT 1 22-APR-20 6THF 0 JRNL AUTH D.SASAKI,T.F.WATANABE,R.R.EADY,R.C.GARRATT,S.V.ANTONYUK, JRNL AUTH 2 S.S.HASNAIN JRNL TITL REVERSE PROTEIN ENGINEERING OF A NOVEL 4-DOMAIN COPPER JRNL TITL 2 NITRITE REDUCTASE REVEALS FUNCTIONAL REGULATION BY JRNL TITL 3 PROTEIN-PROTEIN INTERACTION. JRNL REF FEBS J. V. 288 262 2021 JRNL REFN ISSN 1742-464X JRNL PMID 32255260 JRNL DOI 10.1111/FEBS.15324 REMARK 2 REMARK 2 RESOLUTION. 1.47 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.47 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.93 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 65827 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) : 0.142 REMARK 3 R VALUE (WORKING SET) : 0.141 REMARK 3 FREE R VALUE : 0.157 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 3384 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) : 1.47 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.51 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4781 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2510 REMARK 3 BIN FREE R VALUE SET COUNT : 269 REMARK 3 BIN FREE R VALUE : 0.2450 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2617 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 66 REMARK 3 SOLVENT ATOMS : 494 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.52 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): 0.052 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.052 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.039 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.082 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.979 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.976 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2817 ; 0.013 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2642 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3852 ; 1.667 ; 1.968 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6108 ; 0.984 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 363 ; 7.237 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 123 ;37.046 ;24.472 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 445 ;11.495 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;21.128 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 422 ; 0.100 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3187 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 635 ; 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 : NULL 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 6THF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-NOV-19. REMARK 100 THE DEPOSITION ID IS D_1292105422. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JUN-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9159 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS 1.10.4 REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 69285 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.470 REMARK 200 RESOLUTION RANGE LOW (A) : 106.930 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.08100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.47 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.60 REMARK 200 R MERGE FOR SHELL (I) : 1.01800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP 11.4.06 REMARK 200 STARTING MODEL: 5I6K REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.2 M AMMONIUM SULFATE, 0.05 M MES REMARK 280 PH6.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 53.46450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.46450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 53.46450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 53.46450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 53.46450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 53.46450 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 53.46450 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 53.46450 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 53.46450 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 53.46450 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 53.46450 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 53.46450 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 53.46450 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 53.46450 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 53.46450 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 53.46450 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 53.46450 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 53.46450 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: 17640 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 36530 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -359.0 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 0.000000 1.000000 -53.46450 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 53.46450 REMARK 350 BIOMT3 2 0.000000 -1.000000 0.000000 106.92900 REMARK 350 BIOMT1 3 0.000000 -1.000000 0.000000 53.46450 REMARK 350 BIOMT2 3 0.000000 0.000000 -1.000000 106.92900 REMARK 350 BIOMT3 3 1.000000 0.000000 0.000000 53.46450 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 861 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 465 ASN A 343 REMARK 465 LEU A 344 REMARK 465 TYR A 345 REMARK 465 PHE A 346 REMARK 465 GLN A 347 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 92 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG A 154 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 279 NE - CZ - NH1 ANGL. DEV. = -4.0 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 70.97 -108.70 REMARK 500 GLN A 24 -83.63 -78.22 REMARK 500 ALA A 131 70.45 -159.34 REMARK 500 ALA A 131 68.83 -159.34 REMARK 500 ASN A 341 9.33 33.16 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 301 ASN A 302 144.70 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 = 5.98 ANGSTROMS REMARK 525 HOH A 992 DISTANCE = 7.29 ANGSTROMS REMARK 525 HOH A 993 DISTANCE = 7.96 ANGSTROMS REMARK 525 HOH A 994 DISTANCE = 8.79 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 HOH A 596 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 411 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 89 ND1 REMARK 620 2 CYS A 130 SG 129.7 REMARK 620 3 HIS A 140 ND1 100.4 111.8 REMARK 620 4 MET A 145 SD 85.7 113.2 113.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 412 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 94 NE2 REMARK 620 2 HIS A 129 NE2 109.8 REMARK 620 3 HIS A 301 NE2 69.6 93.8 REMARK 620 4 HOH A 509 O 110.1 108.5 155.7 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 MES A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MES A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CU A 411 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CU A 412 DBREF 6THF A 2 341 UNP H0SLX7 H0SLX7_BRAS3 25 364 SEQADV 6THF MET A 1 UNP H0SLX7 INITIATING METHIONINE SEQADV 6THF GLU A 342 UNP H0SLX7 EXPRESSION TAG SEQADV 6THF ASN A 343 UNP H0SLX7 EXPRESSION TAG SEQADV 6THF LEU A 344 UNP H0SLX7 EXPRESSION TAG SEQADV 6THF TYR A 345 UNP H0SLX7 EXPRESSION TAG SEQADV 6THF PHE A 346 UNP H0SLX7 EXPRESSION TAG SEQADV 6THF 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 MES A 401 12 HET MES A 402 12 HET SO4 A 403 5 HET SO4 A 404 5 HET SO4 A 405 5 HET SO4 A 406 5 HET SO4 A 407 5 HET SO4 A 408 5 HET SO4 A 409 5 HET SO4 A 410 5 HET CU A 411 1 HET CU A 412 1 HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID HETNAM SO4 SULFATE ION HETNAM CU COPPER (II) ION FORMUL 2 MES 2(C6 H13 N O4 S) FORMUL 4 SO4 8(O4 S 2-) FORMUL 12 CU 2(CU 2+) FORMUL 14 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 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 THR A 57 N GLN A 40 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 TYR A 74 N MET A 33 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 2 LEU A 157 ASN A 158 0 SHEET 2 AA4 2 SER A 164 LEU A 165 -1 O LEU A 165 N LEU A 157 SHEET 1 AA5 6 HIS A 212 PHE A 215 0 SHEET 2 AA5 6 ARG A 169 LEU A 178 -1 N LEU A 178 O HIS A 212 SHEET 3 AA5 6 ASN A 235 GLN A 242 1 O VAL A 239 N ILE A 173 SHEET 4 AA5 6 SER A 282 LYS A 289 -1 O TYR A 288 N VAL A 236 SHEET 5 AA5 6 GLY A 256 TRP A 260 -1 N TYR A 258 O LEU A 287 SHEET 6 AA5 6 GLU A 270 LEU A 273 -1 O GLU A 270 N VAL A 259 SHEET 1 AA6 4 LEU A 228 ASN A 231 0 SHEET 2 AA6 4 THR A 312 GLU A 318 1 O HIS A 314 N LEU A 228 SHEET 3 AA6 4 GLY A 294 THR A 300 -1 N TYR A 298 O ALA A 313 SHEET 4 AA6 4 PRO A 249 ILE A 252 -1 N ILE A 252 O ALA A 297 LINK ND1 HIS A 89 CU CU A 411 1555 1555 2.07 LINK NE2 HIS A 94 CU CU A 412 1555 1555 2.03 LINK NE2 HIS A 129 CU CU A 412 1555 1555 2.05 LINK SG CYS A 130 CU CU A 411 1555 1555 2.19 LINK ND1 HIS A 140 CU CU A 411 1555 1555 2.05 LINK SD MET A 145 CU CU A 411 1555 1555 2.50 LINK NE2 HIS A 301 CU CU A 412 1555 12565 2.07 LINK CU CU A 412 O HOH A 509 1555 1555 1.79 CISPEP 1 PRO A 16 PRO A 17 0 9.15 CISPEP 2 PRO A 16 PRO A 17 0 8.85 CISPEP 3 MET A 62 PRO A 63 0 -11.04 SITE 1 AC1 4 GLU A 261 GLU A 270 ARG A 279 HOH A 731 SITE 1 AC2 10 HIS A 22 GLN A 24 ARG A 166 TYR A 167 SITE 2 AC2 10 ARG A 169 ILE A 170 HOH A 555 HOH A 605 SITE 3 AC2 10 HOH A 758 HOH A 786 SITE 1 AC3 11 HIS A 161 SER A 266 ASN A 267 ALA A 268 SITE 2 AC3 11 HOH A 525 HOH A 536 HOH A 616 HOH A 660 SITE 3 AC3 11 HOH A 662 HOH A 703 HOH A 790 SITE 1 AC4 5 ASP A 183 GLU A 184 LYS A 189 HOH A 711 SITE 2 AC4 5 HOH A 737 SITE 1 AC5 5 VAL A 329 LYS A 330 ALA A 331 HOH A 639 SITE 2 AC5 5 HOH A 723 SITE 1 AC6 4 HIS A 163 SER A 164 HOH A 505 HOH A 739 SITE 1 AC7 6 LYS A 43 THR A 52 SER A 190 LYS A 289 SITE 2 AC7 6 HOH A 501 HOH A 502 SITE 1 AC8 4 LYS A 36 GLN A 113 HOH A 527 HOH A 668 SITE 1 AC9 7 ASP A 3 LEU A 4 ARG A 117 HOH A 508 SITE 2 AC9 7 HOH A 607 HOH A 632 HOH A 683 SITE 1 AD1 9 ARG A 169 LYS A 225 ASN A 226 ASN A 229 SITE 2 AD1 9 HOH A 665 HOH A 736 HOH A 819 HOH A 820 SITE 3 AD1 9 HOH A 864 SITE 1 AD2 4 HIS A 89 CYS A 130 HIS A 140 MET A 145 SITE 1 AD3 5 ASP A 92 HIS A 94 HIS A 129 HIS A 301 SITE 2 AD3 5 HOH A 509 CRYST1 106.929 106.929 106.929 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 0.009352 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009352 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009352 0.00000