HEADER OXIDOREDUCTASE 18-DEC-24 9HS0 TITLE COPPER-CONTAINING NITRITE REDUCTASE (NIRK) FROM BRADYRHIZOBIUM TITLE 2 JAPONICUM USDA110 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; COMPND 6 OTHER_DETAILS: SIGNAL PEPTIDE: MLPMFTRRAALISAAATALMLATPALA SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BRADYRHIZOBIUM DIAZOEFFICIENS USDA 110; SOURCE 3 ORGANISM_TAXID: 224911; SOURCE 4 STRAIN: USDA110; SOURCE 5 GENE: NIRK; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21GOLD(DE3) KEYWDS COPPER-BINDING PROTEIN, REDUCTASE, NIRK, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR C.TOLMIE,F.M.FERRONI,D.J.OPPERMAN REVDAT 1 11-JUN-25 9HS0 0 JRNL AUTH C.S.RAMIREZ,C.TOLMIE,M.G.RIVAS,P.J.GONZALEZ,D.H.MURGIDA, JRNL AUTH 2 D.J.OPPERMAN,C.D.BRONDINO,F.M.FERRONI JRNL TITL STRUCTURAL INSIGHTS INTO THE COPPER-CONTAINING NITRITE JRNL TITL 2 REDUCTASE FROM BRADYRHIZOBIUM JAPONICUM USDA110 AND ITS ROLE JRNL TITL 3 IN THE LOW NITRITE REDUCTASE ACTIVITY OF RHIZOBIA. JRNL REF ARCH.BIOCHEM.BIOPHYS. V. 770 10467 2025 JRNL REFN ESSN 1096-0384 JRNL PMID 40381977 JRNL DOI 10.1016/J.ABB.2025.110467 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0430 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.27 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 91925 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.091 REMARK 3 R VALUE (WORKING SET) : 0.090 REMARK 3 FREE R VALUE : 0.109 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 4731 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) : 1.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.33 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6731 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.82 REMARK 3 BIN R VALUE (WORKING SET) : 0.1330 REMARK 3 BIN FREE R VALUE SET COUNT : 305 REMARK 3 BIN FREE R VALUE : 0.1670 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2559 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 572 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.27 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.028 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.027 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.013 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.699 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.986 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.983 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2817 ; 0.015 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 2665 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3861 ; 2.012 ; 1.825 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6178 ; 0.727 ; 1.755 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 380 ; 7.882 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 7 ;12.538 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 474 ;11.008 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 415 ; 0.116 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3358 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 600 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1424 ; 4.677 ; 1.001 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1424 ; 4.681 ; 1.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1803 ; 6.923 ; 1.822 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1804 ; 6.929 ; 1.824 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1393 ; 5.459 ; 1.173 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1394 ; 5.463 ; 1.174 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2046 ; 7.318 ; 2.079 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 12013 ;16.999 ;16.980 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 11188 ;11.605 ;13.900 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 5482 ; 4.896 ; 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 REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 9HS0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-DEC-24. REMARK 100 THE DEPOSITION ID IS D_1292143909. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JAN-17 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.928190 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 121035 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.190 REMARK 200 RESOLUTION RANGE LOW (A) : 35.290 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 200 DATA REDUNDANCY : 7.700 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.2000 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) : 1.25 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.20300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS PH 8.0, 30% W/V PEG 400, 8 REMARK 280 -15 MG/ML BJNIRK, VAPOR DIFFUSION, TEMPERATURE 289K 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 52.90400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.90400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 52.90400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.90400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 52.90400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 52.90400 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 52.90400 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 52.90400 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 52.90400 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 52.90400 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 52.90400 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 52.90400 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 52.90400 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 52.90400 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 52.90400 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 52.90400 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 52.90400 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 52.90400 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: 13090 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 34240 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -109.0 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 -105.80800 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 105.80800 REMARK 350 BIOMT3 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT1 3 0.000000 1.000000 0.000000 -105.80800 REMARK 350 BIOMT2 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT3 3 1.000000 0.000000 0.000000 105.80800 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 923 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 980 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1014 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1019 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1030 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1045 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1048 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 -26 REMARK 465 LEU A -25 REMARK 465 PRO A -24 REMARK 465 MET A -23 REMARK 465 PHE A -22 REMARK 465 THR A -21 REMARK 465 ARG A -20 REMARK 465 ARG A -19 REMARK 465 ALA A -18 REMARK 465 ALA A -17 REMARK 465 LEU A -16 REMARK 465 ILE A -15 REMARK 465 SER A -14 REMARK 465 ALA A -13 REMARK 465 ALA A -12 REMARK 465 ALA A -11 REMARK 465 THR A -10 REMARK 465 ALA A -9 REMARK 465 LEU A -8 REMARK 465 MET A -7 REMARK 465 LEU A -6 REMARK 465 ALA A -5 REMARK 465 THR A -4 REMARK 465 PRO A -3 REMARK 465 ALA A -2 REMARK 465 LEU A -1 REMARK 465 ALA A 0 REMARK 465 ALA A 1 REMARK 465 ALA A 337 REMARK 465 ASN A 338 REMARK 465 THR A 339 REMARK 465 ASN A 340 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 LYS A 27 NZ REMARK 470 LYS A 166 CE NZ REMARK 470 GLU A 184 CD OE1 OE2 REMARK 470 LYS A 185 CG CD CE NZ 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 OE2 GLU A 270 O HOH A 868 5465 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 34 CD GLU A 34 OE2 -0.074 REMARK 500 GLU A 270 CD GLU A 270 OE1 -0.091 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 182 NE - CZ - NH2 ANGL. DEV. = 6.4 DEGREES REMARK 500 GLU A 270 OE1 - CD - OE2 ANGL. DEV. = -17.2 DEGREES REMARK 500 MET A 287 CG - SD - CE ANGL. DEV. = -21.8 DEGREES REMARK 500 THR A 327 CA - CB - OG1 ANGL. DEV. = 12.9 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 71.71 -104.88 REMARK 500 GLN A 24 -94.94 -84.85 REMARK 500 ALA A 131 68.82 -158.16 REMARK 500 ALA A 131 68.87 -158.16 REMARK 500 PRO A 132 37.53 -94.16 REMARK 500 LEU A 208 -3.58 81.20 REMARK 500 LEU A 222 42.84 -109.18 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 300 149.24 REMARK 500 HIS A 301 ASN A 302 142.31 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 154 0.10 SIDE CHAIN REMARK 500 ARG A 182 0.08 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 A1032 DISTANCE = 5.81 ANGSTROMS REMARK 525 HOH A1033 DISTANCE = 5.83 ANGSTROMS REMARK 525 HOH A1034 DISTANCE = 5.90 ANGSTROMS REMARK 525 HOH A1035 DISTANCE = 5.96 ANGSTROMS REMARK 525 HOH A1036 DISTANCE = 5.96 ANGSTROMS REMARK 525 HOH A1037 DISTANCE = 6.09 ANGSTROMS REMARK 525 HOH A1038 DISTANCE = 6.20 ANGSTROMS REMARK 525 HOH A1039 DISTANCE = 6.36 ANGSTROMS REMARK 525 HOH A1040 DISTANCE = 6.37 ANGSTROMS REMARK 525 HOH A1041 DISTANCE = 6.40 ANGSTROMS REMARK 525 HOH A1042 DISTANCE = 6.52 ANGSTROMS REMARK 525 HOH A1043 DISTANCE = 6.67 ANGSTROMS REMARK 525 HOH A1044 DISTANCE = 6.78 ANGSTROMS REMARK 525 HOH A1045 DISTANCE = 6.87 ANGSTROMS REMARK 525 HOH A1046 DISTANCE = 6.94 ANGSTROMS REMARK 525 HOH A1047 DISTANCE = 7.11 ANGSTROMS REMARK 525 HOH A1048 DISTANCE = 7.31 ANGSTROMS REMARK 525 HOH A1049 DISTANCE = 7.38 ANGSTROMS REMARK 525 HOH A1050 DISTANCE = 7.48 ANGSTROMS REMARK 525 HOH A1051 DISTANCE = 7.48 ANGSTROMS REMARK 525 HOH A1052 DISTANCE = 7.69 ANGSTROMS REMARK 525 HOH A1053 DISTANCE = 7.99 ANGSTROMS REMARK 525 HOH A1054 DISTANCE = 8.14 ANGSTROMS REMARK 525 HOH A1055 DISTANCE = 8.26 ANGSTROMS REMARK 525 HOH A1056 DISTANCE = 8.33 ANGSTROMS REMARK 525 HOH A1057 DISTANCE = 8.56 ANGSTROMS REMARK 525 HOH A1058 DISTANCE = 8.59 ANGSTROMS REMARK 525 HOH A1059 DISTANCE = 8.72 ANGSTROMS REMARK 525 HOH A1060 DISTANCE = 8.83 ANGSTROMS REMARK 525 HOH A1061 DISTANCE = 8.97 ANGSTROMS REMARK 525 HOH A1062 DISTANCE = 9.01 ANGSTROMS REMARK 525 HOH A1063 DISTANCE = 9.75 ANGSTROMS REMARK 525 HOH A1064 DISTANCE = 9.76 ANGSTROMS REMARK 525 HOH A1065 DISTANCE = 10.15 ANGSTROMS REMARK 525 HOH A1066 DISTANCE = 10.41 ANGSTROMS REMARK 525 HOH A1067 DISTANCE = 10.47 ANGSTROMS REMARK 525 HOH A1068 DISTANCE = 10.68 ANGSTROMS REMARK 525 HOH A1069 DISTANCE = 11.07 ANGSTROMS REMARK 525 HOH A1070 DISTANCE = 11.56 ANGSTROMS REMARK 525 HOH A1071 DISTANCE = 13.92 ANGSTROMS REMARK 525 HOH A1072 DISTANCE = 15.70 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 401 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 89 ND1 REMARK 620 2 CYS A 130 SG 129.6 REMARK 620 3 HIS A 140 ND1 100.0 111.9 REMARK 620 4 MET A 145 SD 85.1 113.7 113.9 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 108.9 REMARK 620 3 HIS A 301 NE2 70.7 95.4 REMARK 620 4 HOH A 510 O 106.7 107.8 155.9 REMARK 620 N 1 2 3 DBREF 9HS0 A -26 340 UNP Q89EJ6 Q89EJ6_BRADU 1 367 SEQRES 1 A 367 MET LEU PRO MET PHE THR ARG ARG ALA ALA LEU ILE SER SEQRES 2 A 367 ALA ALA ALA THR ALA LEU MET LEU ALA THR PRO ALA LEU SEQRES 3 A 367 ALA ALA ASP ASP LEU LYS LEU PRO ARG GLN LYS VAL GLU SEQRES 4 A 367 LEU VAL ALA PRO PRO PHE VAL HIS ALA HIS GLU GLN ALA SEQRES 5 A 367 THR LYS GLN GLY PRO LYS ILE VAL GLU PHE LYS LEU THR SEQRES 6 A 367 ILE GLU GLU LYS LYS VAL VAL ILE ASP GLU LYS GLY THR SEQRES 7 A 367 THR PHE GLN ALA MET THR PHE ASN GLY SER MET PRO GLY SEQRES 8 A 367 PRO LEU MET VAL VAL HIS GLU GLY ASP TYR VAL GLU THR SEQRES 9 A 367 THR LEU VAL ASN PRO ALA THR ASN THR MET PRO HIS ASN SEQRES 10 A 367 ILE ASP PHE HIS SER ALA THR GLY ALA LEU GLY GLY GLY SEQRES 11 A 367 ALA LEU THR LEU ILE ASN PRO GLY GLU GLN VAL VAL LEU SEQRES 12 A 367 ARG TRP LYS ALA THR LYS THR GLY VAL PHE VAL TYR HIS SEQRES 13 A 367 CYS ALA PRO GLY GLY PRO MET ILE PRO TRP HIS VAL VAL SEQRES 14 A 367 SER GLY MET ASN GLY ALA VAL MET VAL LEU PRO ARG ASP SEQRES 15 A 367 GLY LEU ASN ASP GLY LYS GLY HIS ALA LEU LYS TYR ASP SEQRES 16 A 367 LYS VAL TYR TYR VAL GLY GLU GLN ASP MET TYR VAL PRO SEQRES 17 A 367 ARG ASP GLU LYS GLY ASN PHE LYS SER TYR ASP SER PRO SEQRES 18 A 367 GLY GLU ALA PHE THR ASP THR GLU GLU MET MET LYS LYS SEQRES 19 A 367 LEU ILE PRO SER HIS VAL VAL PHE ASN GLY LYS VAL GLY SEQRES 20 A 367 ALA LEU THR GLY LYS ASN ALA LEU THR ALA ASN VAL GLY SEQRES 21 A 367 GLU ASN VAL LEU ILE VAL HIS SER GLN ALA ASN ARG ASP SEQRES 22 A 367 SER ARG PRO HIS LEU ILE GLY GLY HIS GLY ASP TYR VAL SEQRES 23 A 367 TRP GLU THR GLY LYS PHE GLY ASN ALA PRO GLU VAL GLY SEQRES 24 A 367 LEU GLU THR TRP PHE ILE ARG GLY GLY SER ALA GLY ALA SEQRES 25 A 367 ALA MET TYR LYS PHE MET GLN PRO GLY ILE TYR ALA TYR SEQRES 26 A 367 VAL THR HIS ASN LEU ILE GLU ALA ALA ASP LEU GLY ALA SEQRES 27 A 367 THR ALA HIS PHE LYS VAL GLU GLY LYS TRP ASN ASP ASP SEQRES 28 A 367 LEU MET THR GLN VAL LYS ALA PRO ALA GLU ILE PRO ALA SEQRES 29 A 367 ASN THR ASN HET CU A 401 1 HET CU A 402 1 HETNAM CU COPPER (II) ION FORMUL 2 CU 2(CU 2+) FORMUL 4 HOH *572(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 401 1555 1555 2.04 LINK NE2 HIS A 94 CU CU A 402 1555 1555 2.00 LINK NE2 HIS A 129 CU CU A 402 1555 1555 2.02 LINK SG CYS A 130 CU CU A 401 1555 1555 2.24 LINK ND1 HIS A 140 CU CU A 401 1555 1555 2.06 LINK SD MET A 145 CU CU A 401 1555 1555 2.51 LINK NE2 HIS A 301 CU CU A 402 1555 5465 2.03 LINK CU CU A 402 O HOH A 510 1555 1555 1.97 CISPEP 1 PRO A 16 PRO A 17 0 9.95 CISPEP 2 PRO A 16 PRO A 17 0 11.73 CISPEP 3 MET A 62 PRO A 63 0 -8.86 CRYST1 105.808 105.808 105.808 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 0.009451 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009451 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009451 0.00000 CONECT 743 2724 CONECT 791 2725 CONECT 1055 2725 CONECT 1061 2724 CONECT 1143 2724 CONECT 1177 2724 CONECT 2724 743 1061 1143 1177 CONECT 2725 791 1055 2738 CONECT 2738 2725 MASTER 530 0 2 5 23 0 0 6 3133 1 9 29 END