HEADER OXIDOREDUCTASE 20-NOV-19 6THE TITLE CRYSTAL STRUCTURE OF CORE DOMAIN OF FOUR-DOMAIN HEME-CUPREDOXIN-CU TITLE 2 NITRITE REDUCTASE FROM BRADYRHIZOBIUM SP. ORS 375 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: SYNTHETIC VARIANT OF FOUR-DOMAIN CU-CONTAINING NITRITE COMPND 7 REDUCTASE FROM BRADYRHIZOBIUM SP. ORS 375 WHERE BOTH CYTOCHROME AND COMPND 8 CUPREDOXIN DOMAINS ARE TRUNCATED. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BRADYRHIZOBIUM SP. ORS 375; SOURCE 3 ORGANISM_TAXID: 566679; SOURCE 4 GENE: BRAO375_2740002; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET-26B(+) KEYWDS FOUR DOMAIN NIR, COPPER-HEME CONTAINING NITRITE REDUCTASE, KEYWDS 2 BRADYRHIZOBIUM SP. ORS 375, ELECTRON TRANSFER, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR D.SASAKI,T.F.WATANABE,R.R.EADY,R.C.GARRATT,S.V.ANTONYUK,S.S.HASNAIN REVDAT 3 24-JAN-24 6THE 1 REMARK REVDAT 2 13-JAN-21 6THE 1 JRNL LINK REVDAT 1 22-APR-20 6THE 0 JRNL AUTH D.SASAKI,T.F.WATANABE,R.R.EADY,R.C.GARRATT,S.V.ANTONYUK, JRNL AUTH 2 S.S.HASNAIN JRNL TITL REVERSE PROTEIN ENGINEERING OF A NOVEL 4-DOMAIN COPPER JRNL TITL 2 NITRITE REDUCTASE REVEALS FUNCTIONAL REGULATION BY JRNL TITL 3 PROTEIN-PROTEIN INTERACTION. JRNL REF FEBS J. V. 288 262 2021 JRNL REFN ISSN 1742-464X JRNL PMID 32255260 JRNL DOI 10.1111/FEBS.15324 REMARK 2 REMARK 2 RESOLUTION. 2.87 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0238 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) : 2.87 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.57 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.7 REMARK 3 NUMBER OF REFLECTIONS : 6726 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) : 0.226 REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 330 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) : 2.87 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 459 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.03 REMARK 3 BIN R VALUE (WORKING SET) : 0.2730 REMARK 3 BIN FREE R VALUE SET COUNT : 24 REMARK 3 BIN FREE R VALUE : 0.3270 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2250 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 62 REMARK 3 SOLVENT ATOMS : 55 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.88 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.416 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.325 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 17.321 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.893 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.875 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2355 ; 0.002 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3191 ; 0.653 ; 1.636 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 298 ; 5.870 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 105 ;28.341 ;22.667 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 341 ;13.663 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;10.431 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 294 ; 0.050 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1806 ; 0.002 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL 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 : NULL 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6THE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-NOV-19. REMARK 100 THE DEPOSITION ID IS D_1292105421. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-FEB-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9686 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : XIA2 0.5.769, DIALS 1.12.5, REMARK 200 AIMLESS 0.7.3 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7073 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.870 REMARK 200 RESOLUTION RANGE LOW (A) : 39.570 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.2 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : 0.21900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 3.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.87 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.48100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP 11.6.04 REMARK 200 STARTING MODEL: 2DV6 REMARK 200 REMARK 200 REMARK: TRIANGULAR PYRAMID REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% (W/V) PEG 8,000, 20% (V/V) 1,5 REMARK 280 -PENTANEDIOL, 0.1 M MOPSO/BIS-TRIS PH6.5, 0.005 M YTTRIUM (III) REMARK 280 CHLORIDE HEXAHYDRATE, 0.005 M ERBIUM (III) CHLORIDE HEXAHYDRATE, REMARK 280 0.005 M TERBIUM (III) CHLORIDE HEXAHYDRATE, 0.005 M YTTERBIUM REMARK 280 (III) CHLORIDE HEXAHYDRATE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 Z,X,Y REMARK 290 6555 Z,-X,-Y REMARK 290 7555 -Z,-X,Y REMARK 290 8555 -Z,X,-Y REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z,-X REMARK 290 11555 Y,-Z,-X REMARK 290 12555 -Y,-Z,X REMARK 290 13555 X+1/2,Y+1/2,Z+1/2 REMARK 290 14555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 15555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 16555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 17555 Z+1/2,X+1/2,Y+1/2 REMARK 290 18555 Z+1/2,-X+1/2,-Y+1/2 REMARK 290 19555 -Z+1/2,-X+1/2,Y+1/2 REMARK 290 20555 -Z+1/2,X+1/2,-Y+1/2 REMARK 290 21555 Y+1/2,Z+1/2,X+1/2 REMARK 290 22555 -Y+1/2,Z+1/2,-X+1/2 REMARK 290 23555 Y+1/2,-Z+1/2,-X+1/2 REMARK 290 24555 -Y+1/2,-Z+1/2,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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 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 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 0.00000 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 0.00000 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 0.00000 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 62.57050 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 62.57050 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 62.57050 REMARK 290 SMTRY1 14 -1.000000 0.000000 0.000000 62.57050 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 62.57050 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 62.57050 REMARK 290 SMTRY1 15 -1.000000 0.000000 0.000000 62.57050 REMARK 290 SMTRY2 15 0.000000 1.000000 0.000000 62.57050 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 62.57050 REMARK 290 SMTRY1 16 1.000000 0.000000 0.000000 62.57050 REMARK 290 SMTRY2 16 0.000000 -1.000000 0.000000 62.57050 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 62.57050 REMARK 290 SMTRY1 17 0.000000 0.000000 1.000000 62.57050 REMARK 290 SMTRY2 17 1.000000 0.000000 0.000000 62.57050 REMARK 290 SMTRY3 17 0.000000 1.000000 0.000000 62.57050 REMARK 290 SMTRY1 18 0.000000 0.000000 1.000000 62.57050 REMARK 290 SMTRY2 18 -1.000000 0.000000 0.000000 62.57050 REMARK 290 SMTRY3 18 0.000000 -1.000000 0.000000 62.57050 REMARK 290 SMTRY1 19 0.000000 0.000000 -1.000000 62.57050 REMARK 290 SMTRY2 19 -1.000000 0.000000 0.000000 62.57050 REMARK 290 SMTRY3 19 0.000000 1.000000 0.000000 62.57050 REMARK 290 SMTRY1 20 0.000000 0.000000 -1.000000 62.57050 REMARK 290 SMTRY2 20 1.000000 0.000000 0.000000 62.57050 REMARK 290 SMTRY3 20 0.000000 -1.000000 0.000000 62.57050 REMARK 290 SMTRY1 21 0.000000 1.000000 0.000000 62.57050 REMARK 290 SMTRY2 21 0.000000 0.000000 1.000000 62.57050 REMARK 290 SMTRY3 21 1.000000 0.000000 0.000000 62.57050 REMARK 290 SMTRY1 22 0.000000 -1.000000 0.000000 62.57050 REMARK 290 SMTRY2 22 0.000000 0.000000 1.000000 62.57050 REMARK 290 SMTRY3 22 -1.000000 0.000000 0.000000 62.57050 REMARK 290 SMTRY1 23 0.000000 1.000000 0.000000 62.57050 REMARK 290 SMTRY2 23 0.000000 0.000000 -1.000000 62.57050 REMARK 290 SMTRY3 23 -1.000000 0.000000 0.000000 62.57050 REMARK 290 SMTRY1 24 0.000000 -1.000000 0.000000 62.57050 REMARK 290 SMTRY2 24 0.000000 0.000000 -1.000000 62.57050 REMARK 290 SMTRY3 24 1.000000 0.000000 0.000000 62.57050 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: 15280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -282.0 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 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT3 3 1.000000 0.000000 0.000000 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 ER ER3 A 509 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 PRO A 2 REMARK 465 GLN A 3 REMARK 465 THR A 4 REMARK 465 VAL A 5 REMARK 465 VAL A 6 REMARK 465 GLU A 7 REMARK 465 GLY A 307 REMARK 465 VAL A 308 REMARK 465 ALA A 309 REMARK 465 LEU A 310 REMARK 465 PRO A 311 REMARK 465 GLY A 312 REMARK 465 ALA A 313 REMARK 465 GLY A 314 REMARK 465 HIS A 315 REMARK 465 GLU A 316 REMARK 465 ASN A 317 REMARK 465 LEU A 318 REMARK 465 TYR A 319 REMARK 465 PHE A 320 REMARK 465 GLN A 321 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 TYR A 165 68.73 -103.81 REMARK 500 SER A 201 -72.82 -114.53 REMARK 500 LEU A 203 -71.62 -86.50 REMARK 500 THR A 246 -53.05 -121.20 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 655 DISTANCE = 6.12 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 YB A 503 YB REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 13 OE2 REMARK 620 2 9JE A 519 O01 16.7 REMARK 620 3 9JE A 519 O07 16.4 5.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 YB A 505 YB REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG A 63 N REMARK 620 2 HOH A 650 O 147.2 REMARK 620 N 1 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 84 ND1 REMARK 620 2 CYS A 125 SG 130.0 REMARK 620 3 HIS A 133 ND1 104.8 105.0 REMARK 620 4 MET A 138 SD 83.6 110.2 124.6 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 89 NE2 REMARK 620 2 HIS A 124 NE2 107.1 REMARK 620 3 HIS A 281 NE2 69.8 96.9 REMARK 620 4 HOH A 610 O 129.3 105.9 141.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 TB A 510 TB REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 154 OD2 REMARK 620 2 GLU A 177 OE1 24.9 REMARK 620 3 GLU A 177 OE2 23.6 2.4 REMARK 620 4 9JE A 520 O07 132.6 149.9 147.5 REMARK 620 5 9JE A 520 O01 101.0 76.9 77.7 108.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ER3 A 507 ER REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 167 OD2 REMARK 620 2 GLU A 177 OE1 90.8 REMARK 620 3 9JE A 520 O07 70.0 84.3 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CU A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CU A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue YB A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue YB A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ER3 A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ER3 A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ER3 A 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TB A 510 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue YT3 A 511 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue YT3 A 512 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 513 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 9JE A 514 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 9JE A 515 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 9JE A 516 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 9JE A 517 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 9JE A 518 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 9JE A 519 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 9JE A 520 DBREF 6THE A 2 315 UNP H0SHH5 H0SHH5_BRAS3 385 698 SEQADV 6THE MET A 1 UNP H0SHH5 INITIATING METHIONINE SEQADV 6THE GLU A 316 UNP H0SHH5 EXPRESSION TAG SEQADV 6THE ASN A 317 UNP H0SHH5 EXPRESSION TAG SEQADV 6THE LEU A 318 UNP H0SHH5 EXPRESSION TAG SEQADV 6THE TYR A 319 UNP H0SHH5 EXPRESSION TAG SEQADV 6THE PHE A 320 UNP H0SHH5 EXPRESSION TAG SEQADV 6THE GLN A 321 UNP H0SHH5 EXPRESSION TAG SEQRES 1 A 321 MET PRO GLN THR VAL VAL GLU ALA ASP ILE SER ARG GLU SEQRES 2 A 321 PRO ASP ASP VAL PRO PRO PRO ILE GLY LYS ARG ALA PRO SEQRES 3 A 321 GLN THR VAL ARG VAL ASP LEU LEU SER VAL GLU LEU GLU SEQRES 4 A 321 GLY ARG LEU ALA GLU GLY THR THR PHE GLY TYR TRP THR SEQRES 5 A 321 PHE ASN GLY LYS VAL PRO GLY PRO LEU LEU ARG VAL ARG SEQRES 6 A 321 VAL GLY ASP THR VAL GLU ILE HIS LEU LYS ASN ALA ALA SEQRES 7 A 321 ASP SER ALA MET ILE HIS SER VAL ASP PHE HIS ALA ALA SEQRES 8 A 321 ILE ALA PRO GLY GLY GLY ALA ALA ALA LEU GLN VAL GLU SEQRES 9 A 321 PRO GLY GLY GLU LYS ALA ILE THR TRP LYS ALA LEU VAL SEQRES 10 A 321 PRO GLY LEU PHE VAL TYR HIS CYS ALA THR PRO MET VAL SEQRES 11 A 321 ALA GLU HIS ILE ALA ASN GLY MET TYR GLY MET ILE LEU SEQRES 12 A 321 VAL GLU PRO GLU GLY GLY LEU PRO PRO VAL ASP HIS GLU SEQRES 13 A 321 PHE TYR VAL MET GLN GLY GLU ILE TYR SER ASP ILE PRO SEQRES 14 A 321 TYR GLY GLN HIS GLY SER ALA GLU PHE SER VAL GLU LYS SEQRES 15 A 321 LEU LEU ALA GLU ARG PRO GLU TYR PHE VAL PHE ASN GLY SEQRES 16 A 321 SER VAL GLY ALA LEU SER LYS LEU HIS PRO LEU LYS ALA SEQRES 17 A 321 LYS VAL GLY ASP THR VAL ARG ILE PHE PHE GLY VAL GLY SEQRES 18 A 321 GLY PRO ASN HIS ALA SER SER PHE HIS VAL ILE GLY GLU SEQRES 19 A 321 ILE PHE ASP LYS VAL ASP LEU PHE GLY GLY LEU THR THR SEQRES 20 A 321 PRO PRO LEU ALA GLY ILE GLN THR VAL THR VAL PRO PRO SEQRES 21 A 321 GLY GLY ALA ALA ILE ALA GLU PHE LYS VAL GLU VAL PRO SEQRES 22 A 321 GLY THR TYR THR LEU VAL ASP HIS ALA LEU ALA ARG ALA SEQRES 23 A 321 GLU ARG GLY LEU LEU GLY ILE LEU HIS VAL GLN GLY PRO SEQRES 24 A 321 GLU ASN PRO ASP ILE TYR ASN GLY VAL ALA LEU PRO GLY SEQRES 25 A 321 ALA GLY HIS GLU ASN LEU TYR PHE GLN HET CU A 501 1 HET CU A 502 1 HET YB A 503 1 HET YB A 504 1 HET YB A 505 1 HET ER3 A 506 1 HET ER3 A 507 1 HET ER3 A 508 1 HET ER3 A 509 1 HET TB A 510 1 HET YT3 A 511 1 HET YT3 A 512 1 HET CL A 513 1 HET 9JE A 514 7 HET 9JE A 515 7 HET 9JE A 516 7 HET 9JE A 517 7 HET 9JE A 518 7 HET 9JE A 519 7 HET 9JE A 520 7 HETNAM CU COPPER (II) ION HETNAM YB YTTERBIUM (III) ION HETNAM ER3 ERBIUM (III) ION HETNAM TB TERBIUM(III) ION HETNAM YT3 YTTRIUM (III) ION HETNAM CL CHLORIDE ION HETNAM 9JE PENTANE-1,5-DIOL FORMUL 2 CU 2(CU 2+) FORMUL 4 YB 3(YB 3+) FORMUL 7 ER3 4(ER 3+) FORMUL 11 TB TB 3+ FORMUL 12 YT3 2(Y 3+) FORMUL 14 CL CL 1- FORMUL 15 9JE 7(C5 H12 O2) FORMUL 22 HOH *55(H2 O) HELIX 1 AA1 ALA A 93 LEU A 101 5 9 HELIX 2 AA2 MET A 129 ASN A 136 1 8 HELIX 3 AA3 SER A 179 GLU A 186 1 8 HELIX 4 AA4 ALA A 284 ARG A 288 5 5 SHEET 1 AA1 5 GLU A 108 LYS A 114 0 SHEET 2 AA1 5 THR A 69 ASN A 76 -1 N VAL A 70 O TRP A 113 SHEET 3 AA1 5 THR A 28 ALA A 43 1 N VAL A 29 O GLU A 71 SHEET 4 AA1 5 THR A 46 PHE A 53 -1 O THR A 52 N VAL A 36 SHEET 5 AA1 5 GLY A 174 ALA A 176 1 O ALA A 176 N THR A 47 SHEET 1 AA2 4 LEU A 62 ARG A 65 0 SHEET 2 AA2 4 TYR A 139 GLU A 145 1 O GLU A 145 N VAL A 64 SHEET 3 AA2 4 GLY A 119 HIS A 124 -1 N TYR A 123 O GLY A 140 SHEET 4 AA2 4 ASP A 87 PHE A 88 -1 N ASP A 87 O HIS A 124 SHEET 1 AA3 6 TYR A 190 PHE A 193 0 SHEET 2 AA3 6 HIS A 155 ILE A 164 -1 N ILE A 164 O TYR A 190 SHEET 3 AA3 6 THR A 213 GLY A 222 1 O PHE A 217 N PHE A 157 SHEET 4 AA3 6 ALA A 263 LYS A 269 -1 O PHE A 268 N VAL A 214 SHEET 5 AA3 6 PHE A 236 LEU A 241 -1 N LYS A 238 O GLU A 267 SHEET 6 AA3 6 LEU A 250 ILE A 253 -1 O LEU A 250 N VAL A 239 SHEET 1 AA4 5 LEU A 206 LYS A 209 0 SHEET 2 AA4 5 GLY A 292 GLN A 297 1 O HIS A 295 N LEU A 206 SHEET 3 AA4 5 GLY A 274 ASP A 280 -1 N TYR A 276 O LEU A 294 SHEET 4 AA4 5 SER A 227 ILE A 232 -1 N ILE A 232 O THR A 277 SHEET 5 AA4 5 VAL A 256 VAL A 258 -1 O VAL A 258 N SER A 227 LINK OE2 GLU A 13 YB YB A 503 1555 19555 2.82 LINK O GLY A 49 ER ER3 A 508 1555 1555 3.44 LINK N ARG A 63 YB YB A 505 1555 1555 3.46 LINK ND1 HIS A 84 CU CU A 501 1555 1555 2.28 LINK NE2 HIS A 89 CU CU A 502 1555 1555 2.11 LINK NE2 HIS A 124 CU CU A 502 1555 1555 2.03 LINK SG CYS A 125 CU CU A 501 1555 1555 2.25 LINK ND1 HIS A 133 CU CU A 501 1555 1555 2.15 LINK SD MET A 138 CU CU A 501 1555 1555 2.49 LINK OD2 ASP A 154 TB TB A 510 1555 1555 2.28 LINK OD2 ASP A 167 ER ER3 A 507 1555 22545 2.56 LINK OE1 GLU A 177 ER ER3 A 507 1555 22545 3.05 LINK OE1 GLU A 177 TB TB A 510 1555 22545 2.57 LINK OE2 GLU A 177 TB TB A 510 1555 22545 3.23 LINK NE2 HIS A 281 CU CU A 502 1555 12555 2.19 LINK CU CU A 502 O HOH A 610 1555 1555 2.01 LINK YB YB A 503 O01 9JE A 519 1555 22545 3.08 LINK YB YB A 503 O07 9JE A 519 1555 22545 2.47 LINK YB YB A 505 O HOH A 650 1555 1555 2.80 LINK ER ER3 A 507 O07 9JE A 520 1555 19555 2.95 LINK TB TB A 510 O07 9JE A 520 1555 19555 2.77 LINK TB TB A 510 O01 9JE A 520 1555 19555 2.34 LINK Y YT3 A 511 O07 9JE A 520 1555 19555 3.10 CISPEP 1 VAL A 57 PRO A 58 0 -1.49 CISPEP 2 PRO A 128 MET A 129 0 -4.39 CISPEP 3 GLY A 222 PRO A 223 0 6.44 SITE 1 AC1 4 HIS A 84 CYS A 125 HIS A 133 MET A 138 SITE 1 AC2 5 ASP A 87 HIS A 89 HIS A 124 HIS A 281 SITE 2 AC2 5 HOH A 610 SITE 1 AC3 2 GLU A 13 9JE A 519 SITE 1 AC4 2 ARG A 63 HOH A 650 SITE 1 AC5 1 ARG A 30 SITE 1 AC6 4 ASP A 167 GLU A 177 TB A 510 9JE A 520 SITE 1 AC7 1 GLY A 49 SITE 1 AC8 5 ASP A 154 GLU A 177 ER3 A 507 YT3 A 511 SITE 2 AC8 5 9JE A 520 SITE 1 AC9 4 ASP A 167 GLU A 177 TB A 510 9JE A 520 SITE 1 AD1 1 VAL A 17 SITE 1 AD2 1 ASN A 54 SITE 1 AD3 2 ASP A 79 HOH A 604 SITE 1 AD4 3 THR A 28 ARG A 30 GLU A 71 SITE 1 AD5 1 PRO A 128 SITE 1 AD6 3 PRO A 18 ASP A 32 LEU A 61 SITE 1 AD7 2 ARG A 30 GLU A 108 SITE 1 AD8 5 ASP A 15 ALA A 81 GLU A 104 PRO A 205 SITE 2 AD8 5 YB A 503 SITE 1 AD9 8 ASP A 154 GLU A 177 VAL A 210 GLY A 211 SITE 2 AD9 8 ASP A 212 ER3 A 507 TB A 510 YT3 A 511 CRYST1 125.141 125.141 125.141 90.00 90.00 90.00 I 2 3 24 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 0.007991 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007991 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007991 0.00000