HEADER OXIDOREDUCTASE 19-JUN-25 9RO1 TITLE ATOMIC RESOLUTION (1.00 A) XFEL STRUCTURE OF AS-ISOLATED COPPER TITLE 2 NITRITE REDUCTASE FROM BRADYRHIZOBIUM SP. AT HIGH PH (7.3) DETERMINED TITLE 3 BY SERIAL 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 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, BRJNIR, SF-ROX, AS-ISOLATED, KEYWDS 2 SUB-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 9RO1 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. 1.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0431 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) : 1.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 16.77 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 212404 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) : 0.135 REMARK 3 FREE R VALUE : 0.157 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.076 REMARK 3 FREE R VALUE TEST SET COUNT : 10781 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) : 1.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.03 REMARK 3 REFLECTION IN BIN (WORKING SET) : 14781 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.47 REMARK 3 BIN R VALUE (WORKING SET) : 0.3110 REMARK 3 BIN FREE R VALUE SET COUNT : 793 REMARK 3 BIN FREE R VALUE : 0.3420 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 : 50 REMARK 3 SOLVENT ATOMS : 484 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): 0.019 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.020 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 : 0.982 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): 2818 ; 0.014 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 2747 ; 0.002 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3860 ; 1.898 ; 1.829 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6301 ; 0.690 ; 1.767 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 376 ; 7.972 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 7 ;16.058 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 482 ;12.312 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 425 ; 0.113 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3254 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 598 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 470 ; 0.229 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 132 ; 0.190 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1319 ; 0.178 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 320 ; 0.223 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 5 ; 0.144 ; 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 ; 0.035 ; 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): 1383 ; 9.129 ; 1.194 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1383 ; 9.125 ; 1.194 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1740 ;11.039 ; 2.146 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1741 ;11.049 ; 2.149 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1435 ; 8.135 ; 1.412 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1416 ; 8.054 ; 1.389 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2099 ;10.662 ; 2.488 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2070 ;10.566 ; 2.447 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): 5565 ; 7.349 ; 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 9RO1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-JUN-25. REMARK 100 THE DEPOSITION ID IS D_1292148754. 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 : 212579 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 20.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.1000 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 (%): 54.66 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 32.23500 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 32.23500 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 32.23500 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 -51.91000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 89.91076 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -103.82000 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 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 O HOH A 764 O HOH A 779 1.56 REMARK 500 O HOH A 671 O HOH A 865 1.72 REMARK 500 O HOH A 796 O HOH A 881 1.99 REMARK 500 O HOH A 736 O HOH A 779 2.10 REMARK 500 O HOH A 754 O HOH A 814 2.19 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 O HOH A 650 O HOH A 908 4464 1.94 REMARK 500 O HOH A 748 O HOH A 761 4464 1.98 REMARK 500 O HOH A 687 O HOH A 687 2565 2.15 REMARK 500 O HOH A 908 O HOH A 940 4465 2.16 REMARK 500 O HOH A 783 O HOH A 923 3455 2.18 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 LYS A 27 CD - CE - NZ ANGL. DEV. = 15.4 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 GLN A 24 -92.36 -84.31 REMARK 500 ALA A 131 72.57 -159.53 REMARK 500 ALA A 131 71.23 -159.53 REMARK 500 PRO A 132 35.81 -97.45 REMARK 500 LEU A 208 -1.88 82.33 REMARK 500 LEU A 222 49.27 -108.56 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 300 149.76 REMARK 500 HIS A 301 ASN A 302 142.76 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 0.10 SIDE CHAIN REMARK 500 ARG A 182 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 A 971 DISTANCE = 5.83 ANGSTROMS REMARK 525 HOH A 972 DISTANCE = 5.95 ANGSTROMS REMARK 525 HOH A 973 DISTANCE = 6.09 ANGSTROMS REMARK 525 HOH A 974 DISTANCE = 6.25 ANGSTROMS REMARK 525 HOH A 975 DISTANCE = 6.38 ANGSTROMS REMARK 525 HOH A 976 DISTANCE = 6.40 ANGSTROMS REMARK 525 HOH A 977 DISTANCE = 6.80 ANGSTROMS REMARK 525 HOH A 978 DISTANCE = 7.39 ANGSTROMS REMARK 525 HOH A 979 DISTANCE = 7.46 ANGSTROMS REMARK 525 HOH A 980 DISTANCE = 7.67 ANGSTROMS REMARK 525 HOH A 981 DISTANCE = 7.69 ANGSTROMS REMARK 525 HOH A 982 DISTANCE = 8.10 ANGSTROMS REMARK 525 HOH A 983 DISTANCE = 9.15 ANGSTROMS REMARK 525 HOH A 984 DISTANCE = 11.33 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 403 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 401 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 89 ND1 REMARK 620 2 CYS A 130 SG 136.4 REMARK 620 3 HIS A 140 ND1 98.7 111.5 REMARK 620 4 MET A 145 SD 82.1 112.5 111.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 402 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 94 NE2 REMARK 620 2 HIS A 129 NE2 104.9 REMARK 620 3 HIS A 301 NE2 68.5 93.2 REMARK 620 4 HOH A 512 O 104.9 109.0 157.8 REMARK 620 5 HOH A 809 O 158.4 96.1 115.7 62.7 REMARK 620 N 1 2 3 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 9RNZ RELATED DB: PDB REMARK 900 SAME PROTEIN BUT SUBSTRATE REMARK 900 RELATED ID: 9RN0 RELATED DB: PDB REMARK 900 SAME PROTEIN FROM DIFFERENT ORGANISM BUT WITH SUBSTRATE REMARK 900 RELATED ID: 9RLL RELATED DB: PDB REMARK 900 SAME PROTEIN FROM DIFFERENT ORGANISM AND WITHOUT SUBSTRATE BUT LOW REMARK 900 PH DBREF 9RO1 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 401 1 HET CU A 402 1 HET GLC A 403 21 HET FRU A 404 24 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 HETNAM CU COPPER (II) 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 GLC C6 H12 O6 FORMUL 5 FRU C6 H12 O6 FORMUL 6 SO4 5(O4 S 2-) FORMUL 11 HOH *484(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 VAL A 80 N ILE A 39 SHEET 4 AA2 4 GLU A 112 LYS A 119 -1 O TRP A 118 N VAL A 75 SHEET 1 AA3 4 MET A 67 HIS A 70 0 SHEET 2 AA3 4 ASN A 146 LEU A 152 1 O MET A 150 N MET A 67 SHEET 3 AA3 4 GLY A 124 HIS A 129 -1 N GLY A 124 O VAL A 151 SHEET 4 AA3 4 ASP A 92 PHE A 93 -1 N ASP A 92 O HIS A 129 SHEET 1 AA4 6 HIS A 212 PHE A 215 0 SHEET 2 AA4 6 LYS A 169 MET A 178 -1 N MET A 178 O HIS A 212 SHEET 3 AA4 6 ASN A 235 GLN A 242 1 O VAL A 239 N VAL A 173 SHEET 4 AA4 6 SER A 282 LYS A 289 -1 O ALA A 286 N ILE A 238 SHEET 5 AA4 6 GLY A 256 TRP A 260 -1 N TRP A 260 O ALA A 285 SHEET 6 AA4 6 GLU A 270 LEU A 273 -1 O GLU A 270 N VAL A 259 SHEET 1 AA5 4 LEU A 228 ASN A 231 0 SHEET 2 AA5 4 THR A 312 GLU A 318 1 O HIS A 314 N LEU A 228 SHEET 3 AA5 4 GLY A 294 THR A 300 -1 N TYR A 298 O ALA A 313 SHEET 4 AA5 4 PRO A 249 ILE A 252 -1 N ILE A 252 O ALA A 297 LINK ND1 HIS A 89 CU CU A 401 1555 1555 1.95 LINK NE2 HIS A 94 CU CU A 402 1555 1555 2.00 LINK NE2 HIS A 129 CU CU A 402 1555 1555 2.03 LINK SG CYS A 130 CU CU A 401 1555 1555 2.13 LINK ND1 HIS A 140 CU CU A 401 1555 1555 1.95 LINK SD AMET A 145 CU CU A 401 1555 1555 2.55 LINK NE2 HIS A 301 CU CU A 402 1555 3455 2.00 LINK CU CU A 402 O HOH A 512 1555 1555 1.88 LINK CU CU A 402 O HOH A 809 1555 1555 2.20 CISPEP 1 PRO A 16 PRO A 17 0 8.23 CISPEP 2 PRO A 16 PRO A 17 0 9.54 CISPEP 3 MET A 62 PRO A 63 0 -7.96 CRYST1 103.820 103.820 64.470 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 0.009632 0.005561 0.000000 0.00000 SCALE2 0.000000 0.011122 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015511 0.00000 CONECT 1471 5408 CONECT 1556 5409 CONECT 2093 5409 CONECT 2106 5408 CONECT 2258 5408 CONECT 2328 5408 CONECT 5408 1471 2106 2258 2328 CONECT 5409 1556 2093 5493 5796 CONECT 5410 5411 5419 CONECT 5411 5410 5412 5416 5421 CONECT 5412 5411 5413 5417 5422 CONECT 5413 5412 5414 5418 5423 CONECT 5414 5413 5415 5419 5424 CONECT 5415 5414 5420 5425 5426 CONECT 5416 5411 5427 CONECT 5417 5412 5428 CONECT 5418 5413 5429 CONECT 5419 5410 5414 CONECT 5420 5415 5430 CONECT 5421 5411 CONECT 5422 5412 CONECT 5423 5413 CONECT 5424 5414 CONECT 5425 5415 CONECT 5426 5415 CONECT 5427 5416 CONECT 5428 5417 CONECT 5429 5418 CONECT 5430 5420 CONECT 5431 5432 5437 5443 5444 CONECT 5432 5431 5433 5438 5441 CONECT 5433 5432 5434 5439 5445 CONECT 5434 5433 5435 5440 5446 CONECT 5435 5434 5436 5441 5447 CONECT 5436 5435 5442 5448 5449 CONECT 5437 5431 5450 CONECT 5438 5432 5451 CONECT 5439 5433 5452 CONECT 5440 5434 5453 CONECT 5441 5432 5435 CONECT 5442 5436 5454 CONECT 5443 5431 CONECT 5444 5431 CONECT 5445 5433 CONECT 5446 5434 CONECT 5447 5435 CONECT 5448 5436 CONECT 5449 5436 CONECT 5450 5437 CONECT 5451 5438 CONECT 5452 5439 CONECT 5453 5440 CONECT 5454 5442 CONECT 5455 5456 5457 5458 5459 CONECT 5456 5455 CONECT 5457 5455 CONECT 5458 5455 CONECT 5459 5455 CONECT 5460 5461 5462 5463 5464 CONECT 5461 5460 CONECT 5462 5460 CONECT 5463 5460 CONECT 5464 5460 CONECT 5465 5466 5467 5468 5469 CONECT 5466 5465 CONECT 5467 5465 CONECT 5468 5465 CONECT 5469 5465 CONECT 5470 5471 5472 5473 5474 CONECT 5471 5470 CONECT 5472 5470 CONECT 5473 5470 CONECT 5474 5470 CONECT 5475 5476 5477 5478 5479 CONECT 5476 5475 CONECT 5477 5475 CONECT 5478 5475 CONECT 5479 5475 CONECT 5493 5409 CONECT 5796 5409 MASTER 437 0 9 5 21 0 0 6 3087 1 80 27 END