HEADER OXIDOREDUCTASE 13-DEC-23 8RG9 TITLE HIGH PH (8.0) NITRITE-BOUND MSOX MOVIE SERIES DATASET 2 OF THE COPPER TITLE 2 NITRITE REDUCTASE FROM BRADYRHIZOBIUM SP. ORS375 (TWO-DOMAIN) [1.36 TITLE 3 MGY] 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 SP. ORS 375; SOURCE 3 ORGANISM_TAXID: 566679; SOURCE 4 GENE: NIRK; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS COPPER NITRITE REDUCTASE, COPPER-CONTAINING NITRITE REDUCTASE, KEYWDS 2 BR2DNIR, HIGH PH, NITRITE-BOUND, MSOX, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR S.L.ROSE,F.M.FERRONI,S.V.ANTONYUK,R.R.EADY,S.S.HASNAIN REVDAT 2 07-AUG-24 8RG9 1 TITLE JRNL REVDAT 1 24-JUL-24 8RG9 0 JRNL AUTH S.L.ROSE,F.M.FERRONI,S.HORRELL,C.D.BRONDINO,R.R.EADY,S.JAHO, JRNL AUTH 2 M.A.HOUGH,R.L.OWEN,S.V.ANTONYUK,S.S.HASNAIN JRNL TITL SPECTROSCOPICALLY VALIDATED PH-DEPENDENT MSOX MOVIES PROVIDE JRNL TITL 2 DETAILED MECHANISM OF COPPER NITRITE REDUCTASES. JRNL REF J.MOL.BIOL. V. 436 68706 2024 JRNL REFN ESSN 1089-8638 JRNL PMID 39002715 JRNL DOI 10.1016/J.JMB.2024.168706 REMARK 2 REMARK 2 RESOLUTION. 1.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0419 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) : 1.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 107056 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) : 0.114 REMARK 3 R VALUE (WORKING SET) : 0.113 REMARK 3 FREE R VALUE : 0.136 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 5538 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) : 1.25 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.28 REMARK 3 REFLECTION IN BIN (WORKING SET) : 7839 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.99 REMARK 3 BIN R VALUE (WORKING SET) : 0.3000 REMARK 3 BIN FREE R VALUE SET COUNT : 380 REMARK 3 BIN FREE R VALUE : 0.3180 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2596 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 167 REMARK 3 SOLVENT ATOMS : 439 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.72 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.48 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): 0.030 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.031 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.025 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.454 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.988 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.984 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2968 ; 0.012 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 2714 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4076 ; 2.004 ; 1.860 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6317 ; 0.693 ; 1.783 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 381 ; 7.486 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 12 ; 9.540 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 459 ;12.493 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 469 ; 0.100 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3374 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 632 ; 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): 1404 ; 4.794 ; 1.565 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1403 ; 4.763 ; 1.564 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1764 ; 6.573 ; 2.813 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1765 ; 6.574 ; 2.816 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1564 ; 7.290 ; 1.961 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1552 ; 7.231 ; 1.941 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2274 ; 9.868 ; 3.445 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3239 ;14.497 ;24.140 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3100 ;12.828 ;20.440 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 5682 ; 4.059 ; 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 ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 8RG9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-DEC-23. REMARK 100 THE DEPOSITION ID IS D_1292135329. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-FEB-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : 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) : 0.775 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 : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 112661 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.250 REMARK 200 RESOLUTION RANGE LOW (A) : 47.890 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 18.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.27 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 14.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05 M HEPES PH 5.5, 1.8 M AMMONIUM REMARK 280 SULPHATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 5555 Z,X,Y REMARK 290 6555 Z+1/2,-X+1/2,-Y REMARK 290 7555 -Z+1/2,-X,Y+1/2 REMARK 290 8555 -Z,X+1/2,-Y+1/2 REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z+1/2,-X+1/2 REMARK 290 11555 Y+1/2,-Z+1/2,-X REMARK 290 12555 -Y+1/2,-Z,X+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 53.54000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.54000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 53.54000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 53.54000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 53.54000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 53.54000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 53.54000 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 53.54000 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 53.54000 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 53.54000 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 53.54000 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 53.54000 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 53.54000 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 53.54000 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 53.54000 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 53.54000 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 53.54000 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 53.54000 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 APPLY THE FOLLOWING TO CHAINS: A, E, F, B, G REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 0.000000 0.000000 1.000000 -53.54000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 53.54000 REMARK 350 BIOMT3 2 0.000000 -1.000000 0.000000 107.08000 REMARK 350 BIOMT1 3 0.000000 -1.000000 0.000000 53.54000 REMARK 350 BIOMT2 3 0.000000 0.000000 -1.000000 107.08000 REMARK 350 BIOMT3 3 1.000000 0.000000 0.000000 53.54000 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 S SO4 A 518 LIES ON A SPECIAL POSITION. REMARK 375 O3 SO4 A 518 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 ASP A 2 REMARK 465 ASN A 341 REMARK 465 GLU A 342 REMARK 465 ASN A 343 REMARK 465 LEU A 344 REMARK 465 TYR A 345 REMARK 465 PHE A 346 REMARK 465 GLN A 347 REMARK 465 GLY A 348 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 5 CG CD CE NZ REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 316 CG CD CE NZ 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 896 O HOH A 926 1.90 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 270 CD GLU A 270 OE1 0.076 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 PHE A 53 CB - CA - C ANGL. DEV. = 12.2 DEGREES REMARK 500 PHE A 53 N - CA - CB ANGL. DEV. = -12.9 DEGREES REMARK 500 ARG A 117 NE - CZ - NH1 ANGL. DEV. = -4.8 DEGREES REMARK 500 ARG A 117 NE - CZ - NH2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG A 154 NE - CZ - NH1 ANGL. DEV. = -4.2 DEGREES REMARK 500 ARG A 169 NE - CZ - NH2 ANGL. DEV. = -6.0 DEGREES REMARK 500 LYS A 289 CD - CE - NZ ANGL. DEV. = -18.3 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 76.29 -106.99 REMARK 500 LYS A 5 76.29 -107.13 REMARK 500 GLN A 24 -85.23 -77.73 REMARK 500 ALA A 131 69.39 -161.03 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 300 147.80 REMARK 500 HIS A 301 ASN A 302 144.15 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 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 A1024 DISTANCE = 5.88 ANGSTROMS REMARK 525 HOH A1026 DISTANCE = 6.06 ANGSTROMS REMARK 525 HOH A1027 DISTANCE = 6.09 ANGSTROMS REMARK 525 HOH A1029 DISTANCE = 6.65 ANGSTROMS REMARK 525 HOH A1030 DISTANCE = 6.87 ANGSTROMS REMARK 525 HOH A1031 DISTANCE = 6.90 ANGSTROMS REMARK 525 HOH A1032 DISTANCE = 6.93 ANGSTROMS REMARK 525 HOH A1033 DISTANCE = 6.95 ANGSTROMS REMARK 525 HOH A1034 DISTANCE = 7.31 ANGSTROMS REMARK 525 HOH A1035 DISTANCE = 8.12 ANGSTROMS REMARK 525 HOH A1036 DISTANCE = 8.83 ANGSTROMS REMARK 525 HOH A1037 DISTANCE = 12.32 ANGSTROMS REMARK 525 HOH A1038 DISTANCE = 13.95 ANGSTROMS REMARK 525 HOH A1039 DISTANCE = 14.57 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 501 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 89 ND1 REMARK 620 2 CYS A 130 SG 130.4 REMARK 620 3 HIS A 140 ND1 99.0 112.1 REMARK 620 4 MET A 145 SD 85.0 114.0 113.6 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 94 NE2 REMARK 620 2 HIS A 129 NE2 107.5 REMARK 620 3 HIS A 301 NE2 68.6 93.0 REMARK 620 4 NO2 A 503 N 124.9 109.9 144.8 REMARK 620 5 NO2 A 503 O1 94.4 107.1 157.1 36.4 REMARK 620 6 NO2 A 503 O2 159.2 90.5 122.1 35.7 69.8 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8RG8 RELATED DB: PDB REMARK 900 8RG8 IS DATASET 1 OF THIS SERIAL MOVIE REMARK 900 RELATED ID: 8RFL RELATED DB: PDB REMARK 900 SAME CITATION REMARK 900 RELATED ID: 8RFO RELATED DB: PDB REMARK 900 SAME CITATION REMARK 900 RELATED ID: 8RFP RELATED DB: PDB REMARK 900 SAME CITATION REMARK 900 RELATED ID: 8RFQ RELATED DB: PDB REMARK 900 SAME CITATION REMARK 900 RELATED ID: 8RFR RELATED DB: PDB REMARK 900 SAME CITATION REMARK 900 RELATED ID: 8RFS RELATED DB: PDB REMARK 900 SAME CITATION REMARK 900 RELATED ID: 8RFT RELATED DB: PDB REMARK 900 SAME CITATION REMARK 900 RELATED ID: 8RFU RELATED DB: PDB REMARK 900 SAME CITATION REMARK 900 RELATED ID: 8RFV RELATED DB: PDB REMARK 900 SAME CITATION REMARK 900 RELATED ID: 8RFW RELATED DB: PDB REMARK 900 SAME CITATION REMARK 900 RELATED ID: 8RFX RELATED DB: PDB REMARK 900 SAME CITATION REMARK 900 RELATED ID: 8RFY RELATED DB: PDB REMARK 900 SAME CITATION DBREF 8RG9 A 2 341 UNP H0SLX7 H0SLX7_BRAS3 25 364 SEQADV 8RG9 MET A 1 UNP H0SLX7 INITIATING METHIONINE SEQADV 8RG9 GLU A 342 UNP H0SLX7 EXPRESSION TAG SEQADV 8RG9 ASN A 343 UNP H0SLX7 EXPRESSION TAG SEQADV 8RG9 LEU A 344 UNP H0SLX7 EXPRESSION TAG SEQADV 8RG9 TYR A 345 UNP H0SLX7 EXPRESSION TAG SEQADV 8RG9 PHE A 346 UNP H0SLX7 EXPRESSION TAG SEQADV 8RG9 GLN A 347 UNP H0SLX7 EXPRESSION TAG SEQADV 8RG9 GLY A 348 UNP H0SLX7 EXPRESSION TAG SEQRES 1 A 348 MET ASP ASP LEU LYS LEU PRO ARG GLN ARG VAL ASP LEU SEQRES 2 A 348 VAL ALA PRO PRO PHE VAL HIS VAL HIS GLU GLN ALA THR SEQRES 3 A 348 LYS GLN GLY PRO LYS ILE MET GLU PHE LYS LEU VAL VAL SEQRES 4 A 348 GLN GLU LYS LYS MET VAL ILE ASP GLU LYS GLY THR THR SEQRES 5 A 348 PHE GLN ALA MET THR PHE ASN GLY SER MET PRO GLY PRO SEQRES 6 A 348 LEU MET VAL VAL HIS GLU GLY ASP TYR VAL GLU VAL THR SEQRES 7 A 348 LEU VAL ASN PRO ALA THR ASN THR MET PRO HIS ASN ILE SEQRES 8 A 348 ASP PHE HIS SER ALA THR GLY ALA LEU GLY GLY GLY ALA SEQRES 9 A 348 LEU THR LEU ILE ASN PRO GLY GLU GLN VAL VAL LEU ARG SEQRES 10 A 348 TRP LYS ALA THR ARG THR GLY VAL PHE VAL TYR HIS CYS SEQRES 11 A 348 ALA PRO GLY GLY PRO MET ILE PRO TRP HIS VAL VAL SER SEQRES 12 A 348 GLY MET ASN GLY ALA VAL MET VAL LEU PRO ARG ASP GLY SEQRES 13 A 348 LEU ASN ASP GLY HIS GLY HIS SER LEU ARG TYR ASP ARG SEQRES 14 A 348 ILE TYR TYR ILE GLY GLU GLN ASP LEU TYR VAL PRO ARG SEQRES 15 A 348 ASP GLU LYS GLY ASN PHE LYS SER TYR ASP SER PRO GLY SEQRES 16 A 348 GLU ALA TYR SER ASP THR GLU GLU VAL MET ARG LYS LEU SEQRES 17 A 348 THR PRO THR HIS VAL VAL PHE ASN GLY LYS ALA GLY ALA SEQRES 18 A 348 LEU THR GLY LYS ASN ALA LEU ASN ALA ASN VAL GLY GLU SEQRES 19 A 348 ASN VAL LEU ILE VAL HIS SER GLN ALA ASN ARG ASP SER SEQRES 20 A 348 ARG PRO HIS LEU ILE GLY GLY HIS GLY ASP TYR VAL TRP SEQRES 21 A 348 GLU THR GLY LYS PHE SER ASN ALA PRO GLU THR GLY LEU SEQRES 22 A 348 GLU THR TRP PHE ILE ARG GLY GLY SER ALA GLY ALA ALA SEQRES 23 A 348 LEU TYR LYS PHE LEU GLN PRO GLY ILE TYR ALA TYR VAL SEQRES 24 A 348 THR HIS ASN LEU ILE GLU ALA ALA ASN LEU GLY ALA THR SEQRES 25 A 348 ALA HIS PHE LYS VAL GLU GLY LYS TRP ASN ASP ASP LEU SEQRES 26 A 348 MET THR GLN VAL LYS ALA PRO ALA ASP ILE PRO THR GLY SEQRES 27 A 348 SER THR ASN GLU ASN LEU TYR PHE GLN GLY HET GLC E 1 11 HET FRU E 2 12 HET GLC F 1 11 HET FRU F 2 12 HET GLC B 1 11 HET FRU B 2 12 HET GLC G 1 11 HET FRU G 2 12 HET CU A 501 1 HET CU A 502 1 HET NO2 A 503 3 HET NO2 A 504 3 HET NO2 A 505 3 HET NO A 506 2 HET GOL A 507 6 HET GOL A 508 6 HET SO4 A 509 5 HET SO4 A 510 5 HET SO4 A 511 5 HET SO4 A 512 5 HET SO4 A 513 5 HET SO4 A 514 5 HET SO4 A 515 5 HET SO4 A 516 5 HET SO4 A 517 5 HET SO4 A 518 5 HETNAM GLC ALPHA-D-GLUCOPYRANOSE HETNAM FRU BETA-D-FRUCTOFURANOSE HETNAM CU COPPER (II) ION HETNAM NO2 NITRITE ION HETNAM NO NITRIC OXIDE HETNAM GOL GLYCEROL HETNAM SO4 SULFATE ION HETSYN GLC ALPHA-D-GLUCOSE; D-GLUCOSE; GLUCOSE HETSYN FRU BETA-D-FRUCTOSE; D-FRUCTOSE; FRUCTOSE HETSYN NO NITROGEN MONOXIDE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GLC 4(C6 H12 O6) FORMUL 2 FRU 4(C6 H12 O6) FORMUL 6 CU 2(CU 2+) FORMUL 8 NO2 3(N O2 1-) FORMUL 11 NO N O FORMUL 12 GOL 2(C3 H8 O3) FORMUL 14 SO4 10(O4 S 2-) FORMUL 24 HOH *439(H2 O) HELIX 1 AA1 GLY A 98 THR A 106 5 9 HELIX 2 AA2 PRO A 135 SER A 143 1 9 HELIX 3 AA3 SER A 193 LYS A 207 1 15 HELIX 4 AA4 THR A 223 ALA A 227 5 5 HELIX 5 AA5 ASN A 302 LEU A 309 1 8 SHEET 1 AA1 3 ARG A 8 ARG A 10 0 SHEET 2 AA1 3 ILE A 32 VAL A 45 1 O GLU A 34 N GLN A 9 SHEET 3 AA1 3 THR A 52 PHE A 58 -1 O THR A 57 N GLN A 40 SHEET 1 AA2 4 ARG A 8 ARG A 10 0 SHEET 2 AA2 4 ILE A 32 VAL A 45 1 O GLU A 34 N GLN A 9 SHEET 3 AA2 4 TYR A 74 ASN A 81 1 O TYR A 74 N MET A 33 SHEET 4 AA2 4 GLU A 112 LYS A 119 -1 O TRP A 118 N VAL A 75 SHEET 1 AA3 4 LEU A 66 HIS A 70 0 SHEET 2 AA3 4 ASN A 146 LEU A 152 1 O MET A 150 N MET A 67 SHEET 3 AA3 4 GLY A 124 HIS A 129 -1 N GLY A 124 O VAL A 151 SHEET 4 AA3 4 ASP A 92 PHE A 93 -1 N ASP A 92 O HIS A 129 SHEET 1 AA4 2 LEU A 157 ASN A 158 0 SHEET 2 AA4 2 SER A 164 LEU A 165 -1 O LEU A 165 N LEU A 157 SHEET 1 AA5 6 HIS A 212 PHE A 215 0 SHEET 2 AA5 6 ARG A 169 LEU A 178 -1 N GLN A 176 O VAL A 214 SHEET 3 AA5 6 ASN A 235 GLN A 242 1 O VAL A 239 N ILE A 173 SHEET 4 AA5 6 SER A 282 LYS A 289 -1 O ALA A 286 N ILE A 238 SHEET 5 AA5 6 GLY A 256 TRP A 260 -1 N TYR A 258 O LEU A 287 SHEET 6 AA5 6 GLU A 270 LEU A 273 -1 O GLU A 270 N VAL A 259 SHEET 1 AA6 4 LEU A 228 ASN A 231 0 SHEET 2 AA6 4 THR A 312 GLU A 318 1 O HIS A 314 N LEU A 228 SHEET 3 AA6 4 GLY A 294 THR A 300 -1 N TYR A 298 O ALA A 313 SHEET 4 AA6 4 PRO A 249 ILE A 252 -1 N ILE A 252 O ALA A 297 LINK C1 AGLC E 1 O2 AFRU E 2 1555 1555 1.43 LINK C1 AGLC F 1 O2 AFRU F 2 1555 1555 1.44 LINK C1 GLC B 1 O2 FRU B 2 1555 1555 1.40 LINK C1 AGLC G 1 O2 AFRU G 2 1555 1555 1.40 LINK ND1 HIS A 89 CU CU A 501 1555 1555 2.03 LINK NE2 HIS A 94 CU CU A 502 1555 1555 2.00 LINK NE2 HIS A 129 CU CU A 502 1555 1555 2.06 LINK SG CYS A 130 CU CU A 501 1555 1555 2.18 LINK ND1 HIS A 140 CU CU A 501 1555 1555 2.02 LINK SD MET A 145 CU CU A 501 1555 1555 2.49 LINK NE2 HIS A 301 CU CU A 502 1555 12565 2.06 LINK CU CU A 502 N ANO2 A 503 1555 1555 1.99 LINK CU CU A 502 O1 ANO2 A 503 1555 1555 1.97 LINK CU CU A 502 O2 ANO2 A 503 1555 1555 2.11 CISPEP 1 PRO A 16 PRO A 17 0 10.15 CISPEP 2 PRO A 16 PRO A 17 0 9.81 CISPEP 3 MET A 62 PRO A 63 0 -7.54 CRYST1 107.080 107.080 107.080 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 0.009339 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009339 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009339 0.00000