HEADER OXIDOREDUCTASE 19-JUN-25 9RNZ TITLE ATOMIC RESOLUTION (1.02 A) XFEL STRUCTURE OF NITRITE-BOUND COPPER TITLE 2 NITRITE REDUCTASE FROM BRADYRHIZOBIUM SP. DETERMINED BY SERIAL TITLE 3 FEMTOSECOND ROTATION CRYSTALLOGRAPHY (SF-ROX) AT 100 K 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 DIAZOEFFICIENS USDA 110; SOURCE 3 ORGANISM_TAXID: 224911; SOURCE 4 GENE: NIRK; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS COPPER-CONTAINING NITRITE REDUCTASE, ACNIR, SF-ROX, AS-ISOLATED, SUB- KEYWDS 2 ATOMIC RESOLUTION, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR S.L.ROSE,S.V.ANTONYUK,F.M.FERRONI,H.SUGIMOTO,K.YAMASHITA,K.HIRATA, AUTHOR 2 H.AGO,G.UENO,H.MURAKAMI,R.R.EADY,T.TOSHA,M.YAMAMOTO,S.S.HASNAIN REVDAT 1 25-MAR-26 9RNZ 0 JRNL AUTH S.L.ROSE,S.ANTONYUK,F.M.FERRONI,H.SUGIMOTO,K.YAMASHITA, JRNL AUTH 2 K.HIRATA,H.AGO,G.UENO,H.MURAKAMI,R.R.EADY,T.TOSHA, JRNL AUTH 3 M.YAMAMOTO,S.S.HASNAIN JRNL TITL ACCURATE ATOMIC RESOLUTION XFEL STRUCTURES OF A JRNL TITL 2 METALLOENZYME REVEAL KEY INSIGHTS INTO ITS CATALYTIC JRNL TITL 3 MECHANISM. JRNL REF NAT COMMUN 2026 JRNL REFN ESSN 2041-1723 JRNL PMID 41794770 JRNL DOI 10.1038/S41467-026-70261-1 REMARK 2 REMARK 2 RESOLUTION. 1.02 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0425 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) : 1.02 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 16.77 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 200220 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) : NULL REMARK 3 R VALUE (WORKING SET) : 0.146 REMARK 3 FREE R VALUE : 0.161 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.079 REMARK 3 FREE R VALUE TEST SET COUNT : 10169 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) : 1.02 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 13989 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.99 REMARK 3 BIN R VALUE (WORKING SET) : 0.2950 REMARK 3 BIN FREE R VALUE SET COUNT : 749 REMARK 3 BIN FREE R VALUE : 0.3040 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2553 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 51 REMARK 3 SOLVENT ATOMS : 438 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 8.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.021 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.022 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.978 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.974 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2798 ; 0.009 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 2716 ; 0.003 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3824 ; 1.615 ; 1.832 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6229 ; 0.658 ; 1.775 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 371 ; 7.829 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 8 ;13.426 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 475 ;13.160 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 417 ; 0.097 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3235 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 603 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 475 ; 0.246 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 160 ; 0.169 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1300 ; 0.178 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 306 ; 0.226 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 5 ; 0.132 ; 0.200 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): 1 ; 0.009 ; 0.200 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): 1371 ; 6.197 ; 1.259 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1371 ; 6.194 ; 1.258 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1722 ; 8.984 ; 2.264 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1723 ; 8.982 ; 2.266 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1427 ; 4.670 ; 1.489 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1412 ; 4.534 ; 1.468 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2082 ; 7.009 ; 2.631 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2059 ; 6.867 ; 2.590 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): 5514 ; 2.968 ; 3.000 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 BULK SOLVENT 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: NULL REMARK 4 REMARK 4 9RNZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-MAR-26. REMARK 100 THE DEPOSITION ID IS D_1292148751. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-JUN-22 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : FREE ELECTRON LASER REMARK 200 BEAMLINE : BL2 REMARK 200 X-RAY GENERATOR MODEL : SACLA BEAMLINE BL2 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.954 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300-HS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTFEL REMARK 200 DATA SCALING SOFTWARE : CRYSTFEL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 212451 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.000 REMARK 200 RESOLUTION RANGE LOW (A) : 17.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 20.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.3000 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) : 1.01 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASES REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.8 M AMMONIUM SULPHATE, 100 MM TRIS REMARK 280 (PH 7.3), VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 32.17500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 32.17500 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 32.17500 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 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 -0.500000 -0.866025 0.000000 -51.94500 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 89.97138 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -103.89000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 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 848 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1001 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1007 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 ASP A 2 REMARK 465 ASP A 3 REMARK 465 ALA A 337 REMARK 465 ASN A 338 REMARK 465 THR A 339 REMARK 465 ASN A 340 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 C1 GLC A 505 O2 FRU A 506 1.83 REMARK 500 O HOH A 621 O HOH A 672 2.00 REMARK 500 O HOH A 620 O HOH A 820 2.04 REMARK 500 OE2 GLU A 261 O HOH A 602 2.11 REMARK 500 O HOH A 672 O HOH A 990 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OE1 GLU A 184 O HOH A 807 1554 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 184 CD GLU A 184 OE1 0.158 REMARK 500 GLU A 184 CD GLU A 184 OE2 0.073 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 GLN A 24 -91.53 -83.39 REMARK 500 ALA A 131 72.51 -160.93 REMARK 500 LEU A 222 47.29 -106.91 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 300 149.58 REMARK 500 HIS A 301 ASN A 302 142.74 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 117 0.08 SIDE CHAIN REMARK 500 ARG A 154 0.09 SIDE CHAIN REMARK 500 ARG A 279 0.13 SIDE CHAIN 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 A1034 DISTANCE = 6.23 ANGSTROMS REMARK 525 HOH A1035 DISTANCE = 6.23 ANGSTROMS REMARK 525 HOH A1036 DISTANCE = 6.73 ANGSTROMS REMARK 525 HOH A1037 DISTANCE = 6.79 ANGSTROMS REMARK 525 HOH A1038 DISTANCE = 7.57 ANGSTROMS REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 GLC A 505 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 135.8 REMARK 620 3 HIS A 140 ND1 98.5 110.3 REMARK 620 4 MET A 145 SD 84.3 113.9 110.7 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 104.7 REMARK 620 3 HIS A 301 NE2 69.5 93.4 REMARK 620 4 NO2 A 503 N 131.7 99.5 149.7 REMARK 620 5 NO2 A 503 O1 162.3 89.3 121.2 32.7 REMARK 620 6 NO2 A 503 O2 98.4 109.1 156.8 33.6 66.3 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 9RN0 RELATED DB: PDB REMARK 900 SAME PROTEIN BUT FROM DIFFERENT ORGANISM. CONTAINS SAME SUBSTRATE REMARK 900 RELATED ID: 9RLL RELATED DB: PDB REMARK 900 SAME PROTEIN BUT FROM DIFFERENT ORGANISM. DOES NOT CONTAIN SUBSTRATE DBREF 9RNZ A 2 340 UNP Q89EJ6 Q89EJ6_BRADU 29 367 SEQRES 1 A 339 ASP ASP LEU LYS LEU PRO ARG GLN LYS VAL GLU LEU VAL SEQRES 2 A 339 ALA PRO PRO PHE VAL HIS ALA HIS GLU GLN ALA THR LYS SEQRES 3 A 339 GLN GLY PRO LYS ILE VAL GLU PHE LYS LEU THR ILE GLU SEQRES 4 A 339 GLU LYS LYS VAL VAL ILE ASP GLU LYS GLY THR THR PHE SEQRES 5 A 339 GLN ALA MET THR PHE ASN GLY SER MET PRO GLY PRO LEU SEQRES 6 A 339 MET VAL VAL HIS GLU GLY ASP TYR VAL GLU THR THR LEU SEQRES 7 A 339 VAL ASN PRO ALA THR ASN THR MET PRO HIS ASN ILE ASP SEQRES 8 A 339 PHE HIS SER ALA THR GLY ALA LEU GLY GLY GLY ALA LEU SEQRES 9 A 339 THR LEU ILE ASN PRO GLY GLU GLN VAL VAL LEU ARG TRP SEQRES 10 A 339 LYS ALA THR LYS THR GLY VAL PHE VAL TYR HIS CYS ALA SEQRES 11 A 339 PRO GLY GLY PRO MET ILE PRO TRP HIS VAL VAL SER GLY SEQRES 12 A 339 MET ASN GLY ALA VAL MET VAL LEU PRO ARG ASP GLY LEU SEQRES 13 A 339 ASN ASP GLY LYS GLY HIS ALA LEU LYS TYR ASP LYS VAL SEQRES 14 A 339 TYR TYR VAL GLY GLU GLN ASP MET TYR VAL PRO ARG ASP SEQRES 15 A 339 GLU LYS GLY ASN PHE LYS SER TYR ASP SER PRO GLY GLU SEQRES 16 A 339 ALA PHE THR ASP THR GLU GLU MET MET LYS LYS LEU ILE SEQRES 17 A 339 PRO SER HIS VAL VAL PHE ASN GLY LYS VAL GLY ALA LEU SEQRES 18 A 339 THR GLY LYS ASN ALA LEU THR ALA ASN VAL GLY GLU ASN SEQRES 19 A 339 VAL LEU ILE VAL HIS SER GLN ALA ASN ARG ASP SER ARG SEQRES 20 A 339 PRO HIS LEU ILE GLY GLY HIS GLY ASP TYR VAL TRP GLU SEQRES 21 A 339 THR GLY LYS PHE GLY ASN ALA PRO GLU VAL GLY LEU GLU SEQRES 22 A 339 THR TRP PHE ILE ARG GLY GLY SER ALA GLY ALA ALA MET SEQRES 23 A 339 TYR LYS PHE MET GLN PRO GLY ILE TYR ALA TYR VAL THR SEQRES 24 A 339 HIS ASN LEU ILE GLU ALA ALA ASP LEU GLY ALA THR ALA SEQRES 25 A 339 HIS PHE LYS VAL GLU GLY LYS TRP ASN ASP ASP LEU MET SEQRES 26 A 339 THR GLN VAL LYS ALA PRO ALA GLU ILE PRO ALA ASN THR SEQRES 27 A 339 ASN HET CU A 501 1 HET CU A 502 1 HET NO2 A 503 3 HET NO2 A 504 3 HET GLC A 505 21 HET FRU A 506 24 HET SO4 A 507 5 HET SO4 A 508 5 HET SO4 A 509 5 HET SO4 A 510 5 HETNAM CU COPPER (II) ION HETNAM NO2 NITRITE ION HETNAM GLC ALPHA-D-GLUCOPYRANOSE HETNAM FRU BETA-D-FRUCTOFURANOSE HETNAM SO4 SULFATE ION HETSYN GLC ALPHA-D-GLUCOSE; D-GLUCOSE; GLUCOSE HETSYN FRU BETA-D-FRUCTOSE; D-FRUCTOSE; FRUCTOSE FORMUL 2 CU 2(CU 2+) FORMUL 4 NO2 2(N O2 1-) FORMUL 6 GLC C6 H12 O6 FORMUL 7 FRU C6 H12 O6 FORMUL 8 SO4 4(O4 S 2-) FORMUL 12 HOH *438(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 206 1 14 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 LYS 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 VAL A 44 SHEET 1 AA2 4 ARG A 8 LYS 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 VAL 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 ALA 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 LYS A 169 MET A 178 -1 N MET A 178 O HIS A 212 SHEET 3 AA5 6 ASN A 235 GLN A 242 1 O VAL A 239 N VAL 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 TRP A 260 O ALA A 285 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 501 1555 1555 1.96 LINK NE2 HIS A 94 CU CU A 502 1555 1555 2.01 LINK NE2 HIS A 129 CU CU A 502 1555 1555 2.04 LINK SG CYS A 130 CU CU A 501 1555 1555 2.14 LINK ND1 HIS A 140 CU CU A 501 1555 1555 1.97 LINK SD AMET A 145 CU CU A 501 1555 1555 2.48 LINK NE2 HIS A 301 CU CU A 502 1555 3455 2.02 LINK CU CU A 502 N ANO2 A 503 1555 1555 2.25 LINK CU CU A 502 O1 ANO2 A 503 1555 1555 2.23 LINK CU CU A 502 O2 ANO2 A 503 1555 1555 1.93 CISPEP 1 PRO A 16 PRO A 17 0 8.67 CISPEP 2 PRO A 16 PRO A 17 0 8.41 CISPEP 3 MET A 62 PRO A 63 0 -9.15 CRYST1 103.890 103.890 64.350 90.00 90.00 120.00 P 63 6 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 0.009626 0.005557 0.000000 0.00000 SCALE2 0.000000 0.011115 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015540 0.00000 CONECT 1433 5358 CONECT 1527 5359 CONECT 2064 5359 CONECT 2077 5358 CONECT 2214 5358 CONECT 2284 5358 CONECT 5358 1433 2077 2214 2284 CONECT 5359 1527 2064 5360 5361 CONECT 5359 5362 CONECT 5360 5359 5361 5362 CONECT 5361 5359 5360 CONECT 5362 5359 5360 CONECT 5363 5364 5365 CONECT 5364 5363 CONECT 5365 5363 CONECT 5366 5367 5375 CONECT 5367 5366 5368 5372 5377 CONECT 5368 5367 5369 5373 5378 CONECT 5369 5368 5370 5374 5379 CONECT 5370 5369 5371 5375 5380 CONECT 5371 5370 5376 5381 5382 CONECT 5372 5367 5383 CONECT 5373 5368 5384 CONECT 5374 5369 5385 CONECT 5375 5366 5370 CONECT 5376 5371 5386 CONECT 5377 5367 CONECT 5378 5368 CONECT 5379 5369 CONECT 5380 5370 CONECT 5381 5371 CONECT 5382 5371 CONECT 5383 5372 CONECT 5384 5373 CONECT 5385 5374 CONECT 5386 5376 CONECT 5387 5388 5393 5399 5400 CONECT 5388 5387 5389 5394 5397 CONECT 5389 5388 5390 5395 5401 CONECT 5390 5389 5391 5396 5402 CONECT 5391 5390 5392 5397 5403 CONECT 5392 5391 5398 5404 5405 CONECT 5393 5387 5406 CONECT 5394 5388 5407 CONECT 5395 5389 5408 CONECT 5396 5390 5409 CONECT 5397 5388 5391 CONECT 5398 5392 5410 CONECT 5399 5387 CONECT 5400 5387 CONECT 5401 5389 CONECT 5402 5390 CONECT 5403 5391 CONECT 5404 5392 CONECT 5405 5392 CONECT 5406 5393 CONECT 5407 5394 CONECT 5408 5395 CONECT 5409 5396 CONECT 5410 5398 CONECT 5411 5412 5413 5414 5415 CONECT 5412 5411 CONECT 5413 5411 CONECT 5414 5411 CONECT 5415 5411 CONECT 5416 5417 5418 5419 5420 CONECT 5417 5416 CONECT 5418 5416 CONECT 5419 5416 CONECT 5420 5416 CONECT 5421 5422 5423 5424 5425 CONECT 5422 5421 CONECT 5423 5421 CONECT 5424 5421 CONECT 5425 5421 CONECT 5426 5427 5428 5429 5430 CONECT 5427 5426 CONECT 5428 5426 CONECT 5429 5426 CONECT 5430 5426 MASTER 430 0 10 5 23 0 0 6 3042 1 80 27 END