HEADER OXIDOREDUCTASE 05-JUN-20 6ZAV TITLE NO-BOUND COPPER NITRITE REDUCTASE FROM BRADYRHIZOBIUM SP. ORS 375 TITLE 2 (TWO-DOMAIN) AT 1.19 A RESOLUTION (UNRESTRAINED, FULL MATRIX TITLE 3 REFINEMENT BY SHELX) CAVEAT 6ZAV GLC D 1 HAS WRONG CHIRALITY AT ATOM C2 FRU D 2 HAS WRONG CAVEAT 2 6ZAV CHIRALITY AT ATOM C4 FRU E 2 HAS WRONG CHIRALITY AT ATOM C4 CAVEAT 3 6ZAV FRU E 2 HAS WRONG CHIRALITY AT ATOM C5 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: PET-26B(+) KEYWDS NITRITE REDUCTASE, COPPER NITRITE REDUCTASE, COPPER-CONTAINING KEYWDS 2 NITRITE REDUCTASE, BRNIR, BR2DNIR, NO-BOUND, PRODUCT-BOUND, KEYWDS 3 OXIDOREDUCTASE, 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 6ZAV 1 REMARK REVDAT 2 10-FEB-21 6ZAV 1 JRNL REVDAT 1 20-JAN-21 6ZAV 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. 1.19 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELX REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.19 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) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 125178 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)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2663 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 157 REMARK 3 SOLVENT ATOMS : 501 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL 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) : NULL 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 6ZAV 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_1292109167. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-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 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 166484 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.190 REMARK 200 RESOLUTION RANGE LOW (A) : 48.060 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.19 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.50 REMARK 200 R MERGE FOR SHELL (I) : 1.22300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.400 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: 6THF REMARK 200 REMARK 200 REMARK: BLUE CUBS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6/1.8 M (NH4)2SO3 AND 50MM HEPES REMARK 280 BUFFER PH 5/ PH 5.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 291K 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 53.73350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.73350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 53.73350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 53.73350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 53.73350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 53.73350 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 53.73350 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 53.73350 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 53.73350 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 53.73350 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 53.73350 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 53.73350 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 53.73350 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 53.73350 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 53.73350 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 53.73350 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 53.73350 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 53.73350 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: 28730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 35640 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -349.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, D, E 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 -53.73350 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 53.73350 REMARK 350 BIOMT3 2 0.000000 -1.000000 0.000000 107.46700 REMARK 350 BIOMT1 3 0.000000 -1.000000 0.000000 53.73350 REMARK 350 BIOMT2 3 0.000000 0.000000 -1.000000 107.46700 REMARK 350 BIOMT3 3 1.000000 0.000000 0.000000 53.73350 REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 4 -1.000000 0.000000 0.000000 53.73350 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 107.46700 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 53.73350 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 -53.73350 REMARK 350 BIOMT2 6 0.000000 0.000000 -1.000000 53.73350 REMARK 350 BIOMT3 6 -1.000000 0.000000 0.000000 107.46700 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 N4 EPE A 509 LIES ON A SPECIAL POSITION. REMARK 375 S EPE A 509 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1059 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASP A 3 CG OD1 OD2 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 ARG A 117 CD ARG A 117 NE -0.154 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 12 CB - CG - OD1 ANGL. DEV. = -6.0 DEGREES REMARK 500 PHE A 53 N - CA - CB ANGL. DEV. = -11.4 DEGREES REMARK 500 ASP A 92 CB - CG - OD1 ANGL. DEV. = 10.2 DEGREES REMARK 500 ARG A 117 CD - NE - CZ ANGL. DEV. = 13.1 DEGREES REMARK 500 ARG A 117 NE - CZ - NH1 ANGL. DEV. = -6.6 DEGREES REMARK 500 ARG A 117 NE - CZ - NH2 ANGL. DEV. = 4.6 DEGREES REMARK 500 ARG A 122 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 ARG A 154 CG - CD - NE ANGL. DEV. = -17.0 DEGREES REMARK 500 ARG A 154 NE - CZ - NH1 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG A 154 NE - CZ - NH2 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 166 NE - CZ - NH1 ANGL. DEV. = -7.9 DEGREES REMARK 500 HIS A 240 CG - ND1 - CE1 ANGL. DEV. = 14.2 DEGREES REMARK 500 HIS A 240 ND1 - CE1 - NE2 ANGL. DEV. = -8.8 DEGREES REMARK 500 ARG A 248 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG A 248 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG A 279 NE - CZ - NH1 ANGL. DEV. = -4.3 DEGREES REMARK 500 ARG A 279 NE - CZ - NH2 ANGL. DEV. = 3.5 DEGREES REMARK 500 PHE A 346 CB - CG - CD1 ANGL. DEV. = -5.6 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 77.04 -106.01 REMARK 500 GLN A 24 -88.51 -85.39 REMARK 500 ALA A 131 66.87 -157.41 REMARK 500 ALA A 131 71.97 -157.41 REMARK 500 PRO A 132 35.32 -94.38 REMARK 500 ALA A 311 62.11 -100.63 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 302 143.86 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 89 ND1 REMARK 620 2 CYS A 130 SG 130.2 REMARK 620 3 HIS A 140 ND1 101.7 110.6 REMARK 620 4 MET A 145 SD 85.3 112.9 113.9 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 110.1 REMARK 620 3 HIS A 301 NE2 72.6 97.8 REMARK 620 4 NO A 503 N 138.2 95.6 137.2 REMARK 620 5 NO A 503 O 107.2 103.4 157.2 32.7 REMARK 620 N 1 2 3 4 DBREF 6ZAV A 2 341 UNP H0SLX7 H0SLX7_BRAS3 25 364 SEQADV 6ZAV MET A 1 UNP H0SLX7 INITIATING METHIONINE SEQADV 6ZAV GLU A 342 UNP H0SLX7 EXPRESSION TAG SEQADV 6ZAV ASN A 343 UNP H0SLX7 EXPRESSION TAG SEQADV 6ZAV LEU A 344 UNP H0SLX7 EXPRESSION TAG SEQADV 6ZAV TYR A 345 UNP H0SLX7 EXPRESSION TAG SEQADV 6ZAV PHE A 346 UNP H0SLX7 EXPRESSION TAG SEQADV 6ZAV 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 B 1 11 HET FRU B 2 12 HET GLC C 1 11 HET FRU C 2 12 HET GLC D 1 11 HET FRU D 2 12 HET GLC E 1 11 HET FRU E 2 12 HET CU A 501 1 HET CU A 502 1 HET NO A 503 2 HET SO4 A 504 5 HET SO4 A 505 5 HET SO4 A 506 5 HET SO4 A 507 5 HET SO4 A 508 5 HET EPE A 509 15 HET SO4 A 510 5 HET SO4 A 511 5 HET SO4 A 512 5 HET NO A 513 2 HET NO A 514 2 HET NO A 515 2 HETNAM GLC ALPHA-D-GLUCOPYRANOSE HETNAM FRU BETA-D-FRUCTOFURANOSE HETNAM CU COPPER (II) ION HETNAM NO NITRIC OXIDE HETNAM SO4 SULFATE ION HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETSYN GLC ALPHA-D-GLUCOSE; D-GLUCOSE; GLUCOSE HETSYN FRU BETA-D-FRUCTOSE; D-FRUCTOSE; FRUCTOSE HETSYN NO NITROGEN MONOXIDE HETSYN EPE HEPES FORMUL 2 GLC 4(C6 H12 O6) FORMUL 2 FRU 4(C6 H12 O6) FORMUL 6 CU 2(CU 2+) FORMUL 8 NO 4(N O) FORMUL 9 SO4 8(O4 S 2-) FORMUL 14 EPE C8 H18 N2 O4 S FORMUL 21 HOH *501(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 PRO A 336 GLY A 338 5 3 HELIX 7 AA7 SER A 339 LEU A 344 1 6 HELIX 8 AA8 TYR A 345 GLN A 347 5 3 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 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 GLN A 176 O VAL A 214 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 C1 GLC B 1 O2 FRU B 2 1555 1555 1.49 LINK C1 GLC C 1 O2 FRU C 2 1555 1555 1.46 LINK C1 AGLC D 1 O2 AFRU D 2 1555 1555 1.50 LINK C1 BGLC E 1 O2 BFRU E 2 1555 1555 1.51 LINK ND1 HIS A 89 CU CU A 501 1555 1555 2.10 LINK NE2 HIS A 94 CU CU A 502 1555 1555 1.99 LINK NE2 HIS A 129 CU CU A 502 1555 1555 1.97 LINK SG CYS A 130 CU CU A 501 1555 1555 2.20 LINK ND1 HIS A 140 CU CU A 501 1555 1555 2.11 LINK SD MET A 145 CU CU A 501 1555 1555 2.49 LINK NE2 HIS A 301 CU CU A 502 1555 12565 2.01 LINK CU CU A 502 N A NO A 503 1555 1555 2.17 LINK CU CU A 502 O A NO A 503 1555 1555 2.07 CISPEP 1 PRO A 16 PRO A 17 0 7.00 CISPEP 2 PRO A 16 PRO A 17 0 7.99 CISPEP 3 MET A 62 PRO A 63 0 -7.34 CISPEP 4 MET A 62 PRO A 63 0 -6.71 CISPEP 5 MET A 62 PRO A 63 0 -8.72 CRYST1 107.467 107.467 107.467 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 0.009305 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009305 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009305 0.00000