HEADER OXIDOREDUCTASE 05-JUN-20 6ZAT TITLE NITRITE-BOUND COPPER NITRITE REDUCTASE FROM BRADYRHIZOBIUM SP. ORS 375 TITLE 2 (TWO-DOMAIN) AT 1.0 A RESOLUTION (UNRESTRAINED FULL MATRIX REFINEMENT TITLE 3 BY SHELX) 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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: DE3; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-26B(+) KEYWDS NITRITE REDUCTASE, COPPER NITRITE REDUCTASE, COPPER-CONTAINING, KEYWDS 2 BRNIR, BR2DNIR, NITRITE-BOUND, SUBSTRATE-BOUND, OXIDOREDUCTASE, KEYWDS 3 ATOMIC RESOLUTION 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 6ZAT 1 REMARK REVDAT 2 10-FEB-21 6ZAT 1 JRNL REVDAT 1 20-JAN-21 6ZAT 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. 1.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.126 REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 0.126 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 8133 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.100 REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 0.100 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 5719 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 108958 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 : 107 REMARK 3 SOLVENT ATOMS : 700 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 3350.3 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 2485.0 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 139 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.019 REMARK 3 ANGLE DISTANCES (A) : NULL REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANISOTROPIC REFINEMENT REDUCED FREE R REMARK 3 (NO CUTOFF) BY 4% REMARK 4 REMARK 4 6ZAT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-JUN-20. REMARK 100 THE DEPOSITION ID IS D_1292109153. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-DEC-19 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 : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.86999 REMARK 200 MONOCHROMATOR : SI111 REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 216881 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.000 REMARK 200 RESOLUTION RANGE LOW (A) : 53.390 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.07900 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) : 1.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 1.20100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: REFMAC 5.8.0258 REMARK 200 STARTING MODEL: 6THF REMARK 200 REMARK 200 REMARK: BLUE BIG CUBES REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6/1.8 M (NH4)2SO4 AND 50MM HEPES REMARK 280 BUFFER PH 5/ PH 5.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K 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 53.39300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.39300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 53.39300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 53.39300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 53.39300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 53.39300 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 53.39300 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 53.39300 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 53.39300 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 53.39300 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 53.39300 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 53.39300 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 53.39300 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 53.39300 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 53.39300 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 53.39300 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 53.39300 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 53.39300 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: 26490 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 34990 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -478.0 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 -53.39300 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 53.39300 REMARK 350 BIOMT3 2 0.000000 -1.000000 0.000000 106.78600 REMARK 350 BIOMT1 3 0.000000 -1.000000 0.000000 53.39300 REMARK 350 BIOMT2 3 0.000000 0.000000 -1.000000 106.78600 REMARK 350 BIOMT3 3 1.000000 0.000000 0.000000 53.39300 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 516 LIES ON A SPECIAL POSITION. REMARK 375 O3 SO4 A 516 LIES ON A SPECIAL POSITION. REMARK 375 S EPE A 520 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1085 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 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 GLU A 342 CD GLU A 342 OE2 0.081 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 8 NE - CZ - NH1 ANGL. DEV. = 5.1 DEGREES REMARK 500 ARG A 8 NE - CZ - NH2 ANGL. DEV. = -4.6 DEGREES REMARK 500 GLN A 9 CA - CB - CG ANGL. DEV. = 17.8 DEGREES REMARK 500 GLN A 9 CB - CG - CD ANGL. DEV. = 17.0 DEGREES REMARK 500 PHE A 53 N - CA - CB ANGL. DEV. = 11.4 DEGREES REMARK 500 PHE A 53 N - CA - CB ANGL. DEV. = -13.2 DEGREES REMARK 500 MET A 87 CA - CB - CG ANGL. DEV. = 19.9 DEGREES REMARK 500 ASP A 92 CB - CG - OD2 ANGL. DEV. = -6.9 DEGREES REMARK 500 ARG A 117 NE - CZ - NH1 ANGL. DEV. = -6.7 DEGREES REMARK 500 ARG A 117 NE - CZ - NH2 ANGL. DEV. = 7.8 DEGREES REMARK 500 ARG A 154 CG - CD - NE ANGL. DEV. = -15.2 DEGREES REMARK 500 ARG A 154 CD - NE - CZ ANGL. DEV. = 15.2 DEGREES REMARK 500 ARG A 154 NE - CZ - NH1 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG A 169 NE - CZ - NH1 ANGL. DEV. = 5.3 DEGREES REMARK 500 ARG A 169 NE - CZ - NH2 ANGL. DEV. = -9.1 DEGREES REMARK 500 ARG A 182 NH1 - CZ - NH2 ANGL. DEV. = -8.1 DEGREES REMARK 500 ARG A 182 NE - CZ - NH1 ANGL. DEV. = 5.1 DEGREES REMARK 500 LYS A 218 CA - CB - CG ANGL. DEV. = 17.8 DEGREES REMARK 500 PHE A 346 CB - CG - CD2 ANGL. DEV. = -4.7 DEGREES REMARK 500 PHE A 346 CD1 - CG - CD2 ANGL. DEV. = 8.0 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 73.74 -102.25 REMARK 500 GLN A 24 -76.05 -77.42 REMARK 500 ALA A 131 72.33 -158.73 REMARK 500 ALA A 131 66.09 -158.73 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 300 147.82 REMARK 500 HIS A 301 ASN A 302 143.79 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 A1279 DISTANCE = 5.82 ANGSTROMS REMARK 525 HOH A1281 DISTANCE = 5.86 ANGSTROMS REMARK 525 HOH A1282 DISTANCE = 5.87 ANGSTROMS REMARK 525 HOH A1284 DISTANCE = 5.92 ANGSTROMS REMARK 525 HOH A1286 DISTANCE = 5.97 ANGSTROMS REMARK 525 HOH A1288 DISTANCE = 6.10 ANGSTROMS REMARK 525 HOH A1292 DISTANCE = 6.29 ANGSTROMS REMARK 525 HOH A1293 DISTANCE = 6.31 ANGSTROMS REMARK 525 HOH A1294 DISTANCE = 6.41 ANGSTROMS REMARK 525 HOH A1296 DISTANCE = 6.50 ANGSTROMS REMARK 525 HOH A1297 DISTANCE = 6.51 ANGSTROMS REMARK 525 HOH A1299 DISTANCE = 6.58 ANGSTROMS REMARK 525 HOH A1300 DISTANCE = 6.64 ANGSTROMS REMARK 525 HOH A1303 DISTANCE = 6.78 ANGSTROMS REMARK 525 HOH A1306 DISTANCE = 6.81 ANGSTROMS REMARK 525 HOH A1307 DISTANCE = 6.89 ANGSTROMS REMARK 525 HOH A1309 DISTANCE = 7.02 ANGSTROMS REMARK 525 HOH A1312 DISTANCE = 7.13 ANGSTROMS REMARK 525 HOH A1313 DISTANCE = 7.19 ANGSTROMS REMARK 525 HOH A1317 DISTANCE = 7.44 ANGSTROMS REMARK 525 HOH A1322 DISTANCE = 8.18 ANGSTROMS REMARK 525 HOH A1324 DISTANCE = 8.36 ANGSTROMS 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 89 ND1 REMARK 620 2 CYS A 130 SG 129.5 REMARK 620 3 HIS A 140 ND1 103.3 117.3 REMARK 620 4 MET A 145 SD 82.0 108.4 110.3 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 89 ND1 REMARK 620 2 CYS A 130 SG 131.2 REMARK 620 3 HIS A 140 ND1 92.0 106.1 REMARK 620 4 MET A 145 SD 89.8 122.9 110.4 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 HIS A 94 NE2 REMARK 620 2 HIS A 129 NE2 105.5 REMARK 620 3 HIS A 301 NE2 69.2 93.8 REMARK 620 4 NO2 A 503 N 133.4 117.7 121.2 REMARK 620 5 NO2 A 503 N 128.8 95.9 155.5 35.2 REMARK 620 6 NO2 A 503 O1 162.9 87.8 121.6 30.7 36.9 REMARK 620 7 NO2 A 503 O1 159.3 89.5 125.0 28.4 33.0 4.0 REMARK 620 8 NO2 A 503 O2 102.7 139.2 123.8 31.4 43.3 60.5 57.4 REMARK 620 9 NO2 A 503 O2 95.9 102.8 160.3 59.5 33.3 70.2 66.3 44.9 REMARK 620 N 1 2 3 4 5 6 7 8 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 NO2 A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 509 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 510 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 511 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 512 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 513 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 514 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 515 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 516 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NO2 A 517 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NO2 A 518 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EPE A 519 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EPE A 520 DBREF 6ZAT A 2 341 UNP H0SLX7 H0SLX7_BRAS3 25 364 SEQADV 6ZAT MET A 1 UNP H0SLX7 INITIATING METHIONINE SEQADV 6ZAT GLU A 342 UNP H0SLX7 EXPRESSION TAG SEQADV 6ZAT ASN A 343 UNP H0SLX7 EXPRESSION TAG SEQADV 6ZAT LEU A 344 UNP H0SLX7 EXPRESSION TAG SEQADV 6ZAT TYR A 345 UNP H0SLX7 EXPRESSION TAG SEQADV 6ZAT PHE A 346 UNP H0SLX7 EXPRESSION TAG SEQADV 6ZAT 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 CU A 501 2 HET CU A 502 1 HET NO2 A 503 6 HET GOL A 504 6 HET SO4 A 505 5 HET SO4 A 506 5 HET SO4 A 507 5 HET SO4 A 508 5 HET SO4 A 509 5 HET SO4 A 510 5 HET SO4 A 511 5 HET SO4 A 512 5 HET SO4 A 513 5 HET SO4 A 514 5 HET SO4 A 515 5 HET SO4 A 516 5 HET NO2 A 517 3 HET NO2 A 518 6 HET EPE A 519 15 HET EPE A 520 15 HETNAM CU COPPER (II) ION HETNAM NO2 NITRITE ION HETNAM GOL GLYCEROL HETNAM SO4 SULFATE ION HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN EPE HEPES FORMUL 2 CU 2(CU 2+) FORMUL 4 NO2 3(N O2 1-) FORMUL 5 GOL C3 H8 O3 FORMUL 6 SO4 12(O4 S 2-) FORMUL 20 EPE 2(C8 H18 N2 O4 S) FORMUL 22 HOH *700(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 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 LEU A 116 N VAL A 77 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 ALA A 286 N ILE A 238 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 A CU A 501 1555 1555 2.04 LINK ND1 HIS A 89 CU B CU A 501 1555 1555 2.06 LINK NE2 HIS A 94 CU CU A 502 1555 1555 2.00 LINK NE2 HIS A 129 CU CU A 502 1555 1555 2.03 LINK SG CYS A 130 CU A CU A 501 1555 1555 2.19 LINK SG CYS A 130 CU B CU A 501 1555 1555 2.14 LINK ND1 HIS A 140 CU A CU A 501 1555 1555 1.95 LINK ND1 HIS A 140 CU B CU A 501 1555 1555 2.28 LINK SD MET A 145 CU A CU A 501 1555 1555 2.66 LINK SD MET A 145 CU B CU A 501 1555 1555 2.34 LINK NE2 HIS A 301 CU CU A 502 1555 12565 2.01 LINK CU CU A 502 N ANO2 A 503 1555 1555 2.43 LINK CU CU A 502 N BNO2 A 503 1555 1555 2.36 LINK CU CU A 502 O1 ANO2 A 503 1555 1555 2.22 LINK CU CU A 502 O1 BNO2 A 503 1555 1555 2.14 LINK CU CU A 502 O2 ANO2 A 503 1555 1555 2.13 LINK CU CU A 502 O2 BNO2 A 503 1555 1555 1.96 CISPEP 1 PRO A 16 PRO A 17 0 7.80 CISPEP 2 MET A 62 PRO A 63 0 -8.08 SITE 1 AC1 4 HIS A 89 CYS A 130 HIS A 140 MET A 145 SITE 1 AC2 5 ASP A 92 HIS A 94 HIS A 129 HIS A 301 SITE 2 AC2 5 NO2 A 503 SITE 1 AC3 11 ASP A 92 HIS A 94 HIS A 129 HIS A 250 SITE 2 AC3 11 ILE A 252 HIS A 301 LEU A 303 CU A 502 SITE 3 AC3 11 HOH A 618 HOH A 671 HOH A 731 SITE 1 AC4 6 THR A 223 GLY A 224 ALA A 227 HIS A 314 SITE 2 AC4 6 LYS A 316 HOH A 605 SITE 1 AC5 4 ASP A 183 GLU A 184 LYS A 189 HOH A 668 SITE 1 AC6 5 LYS A 330 ALA A 331 HOH A 614 HOH A 828 SITE 2 AC6 5 HOH A 889 SITE 1 AC7 9 HIS A 163 SER A 164 ASP A 192 HOH A 609 SITE 2 AC7 9 HOH A 709 HOH A 760 HOH A 906 HOH A 981 SITE 3 AC7 9 HOH A1064 SITE 1 AC8 10 LYS A 43 THR A 52 SER A 190 LYS A 289 SITE 2 AC8 10 NO2 A 517 HOH A 612 HOH A 616 HOH A 739 SITE 3 AC8 10 HOH A1072 HOH A1134 SITE 1 AC9 6 ASP A 3 LEU A 4 ARG A 117 HOH A 627 SITE 2 AC9 6 HOH A 890 HOH A 951 SITE 1 AD1 5 LYS A 320 TRP A 321 HOH A 622 HOH A 654 SITE 2 AD1 5 HOH A 748 SITE 1 AD2 13 HIS A 161 SER A 266 ALA A 268 HOH A 611 SITE 2 AD2 13 HOH A 692 HOH A 706 HOH A 750 HOH A 794 SITE 3 AD2 13 HOH A 859 HOH A 873 HOH A1053 HOH A1170 SITE 4 AD2 13 HOH A1270 SITE 1 AD3 13 GLU A 23 GLN A 24 ALA A 25 GLN A 40 SITE 2 AD3 13 ARG A 166 GLN A 347 HOH A 634 HOH A 640 SITE 3 AD3 13 HOH A 647 HOH A 929 HOH A1010 HOH A1083 SITE 4 AD3 13 HOH A1162 SITE 1 AD4 8 ALA A 15 TYR A 345 PHE A 346 HOH A 606 SITE 2 AD4 8 HOH A 915 HOH A 945 HOH A1030 HOH A1233 SITE 1 AD5 8 LYS A 36 THR A 78 GLN A 113 SER A 339 SITE 2 AD5 8 HOH A 619 HOH A 631 HOH A 691 HOH A 969 SITE 1 AD6 8 ARG A 169 LYS A 225 ASN A 226 ASN A 231 SITE 2 AD6 8 HOH A 602 HOH A 633 HOH A 893 HOH A1224 SITE 1 AD7 3 LYS A 207 HOH A 624 HOH A 957 SITE 1 AD8 7 LYS A 43 THR A 52 PHE A 53 GLN A 54 SITE 2 AD8 7 SER A 190 TYR A 191 SO4 A 508 SITE 1 AD9 10 ASN A 244 ARG A 245 ASP A 246 ARG A 248 SITE 2 AD9 10 ASN A 302 HOH A 601 HOH A 603 HOH A 607 SITE 3 AD9 10 HOH A 938 HOH A 974 SITE 1 AE1 17 THR A 121 ARG A 122 TYR A 258 LEU A 291 SITE 2 AE1 17 LEU A 325 HOH A 646 HOH A 657 HOH A 736 SITE 3 AE1 17 HOH A 898 HOH A1034 HOH A1086 HOH A1112 SITE 4 AE1 17 HOH A1123 HOH A1139 HOH A1209 HOH A1256 SITE 5 AE1 17 HOH A1324 SITE 1 AE2 9 GLU A 261 GLU A 270 ARG A 279 HOH A 687 SITE 2 AE2 9 HOH A 692 HOH A 933 HOH A1068 HOH A1100 SITE 3 AE2 9 HOH A1246 CRYST1 106.786 106.786 106.786 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 0.009365 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009365 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009365 0.00000