HEADER OXIDOREDUCTASE 13-DEC-23 8RFQ TITLE LOW PH (5.5) NITRITE-BOUND MSOX MOVIE SERIES DATASET 1 OF THE COPPER TITLE 2 NITRITE REDUCTASE (NIRK) FROM BRADYRHIZOBIUM JAPONICUM USDA110 [5.10 TITLE 3 MGY] - NITRIC OXIDE (NO) INTERMEDIATE 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 NITRITE REDUCTASE, COPPER-CONTAINING NITRITE REDUCTASE, KEYWDS 2 BRJNIR, LOW 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 1 24-JUL-24 8RFQ 0 JRNL AUTH S.L.ROSE,F.MARTIN FERRONI,S.HORRELL,C.DANTE BRONDINO, JRNL AUTH 2 R.R.EADY,S.JAHO,M.A.HOUGH,R.L.OWEN,S.V.ANTONYUK, JRNL AUTH 3 S.SAMAR HASNAIN JRNL TITL SPECTROSCOPICALLY VALIDATED PH-DEPENDENT MSOX MOVIES PROVIDE JRNL TITL 2 DETAILED MECHANISM OF COPPER NITRITE REDUCTASES. JRNL REF J.MOL.BIOL. 68706 2024 JRNL REFN ESSN 1089-8638 JRNL PMID 39002715 JRNL DOI 10.1016/J.JMB.2024.168706 REMARK 2 REMARK 2 RESOLUTION. 1.32 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) : 1.32 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 87986 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) : 0.113 REMARK 3 R VALUE (WORKING SET) : 0.112 REMARK 3 FREE R VALUE : 0.138 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 4844 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) : 1.32 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.35 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6366 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.58 REMARK 3 BIN R VALUE (WORKING SET) : 0.2950 REMARK 3 BIN FREE R VALUE SET COUNT : 388 REMARK 3 BIN FREE R VALUE : 0.3050 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2561 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 63 REMARK 3 SOLVENT ATOMS : 378 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.39 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.08 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.10000 REMARK 3 B22 (A**2) : 0.10000 REMARK 3 B33 (A**2) : -0.33000 REMARK 3 B12 (A**2) : 0.05000 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): 0.035 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.035 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.028 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.691 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): 2860 ; 0.012 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 2694 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3913 ; 1.879 ; 1.846 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6273 ; 0.671 ; 1.770 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 385 ; 7.748 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 9 ;10.898 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 484 ;13.767 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 430 ; 0.103 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3325 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 609 ; 0.003 ; 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): 1400 ; 5.549 ; 1.928 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1399 ; 5.447 ; 1.928 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1765 ; 7.449 ; 3.475 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1766 ; 7.449 ; 3.477 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1460 ; 7.825 ; 2.304 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1432 ; 7.479 ; 2.263 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2089 ;10.560 ; 4.006 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3086 ;14.762 ;28.530 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2955 ;13.244 ;22.430 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 5554 ; 4.178 ; 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 8RFQ 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_1292135191. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JUL-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.3 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) : 0.855 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 : 92853 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.320 REMARK 200 RESOLUTION RANGE LOW (A) : 45.160 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.32 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.900 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 (%): 54.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS PH 7.3, 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 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 32.23000 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 32.23000 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 32.23000 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 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 -52.15000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 90.32645 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -104.30000 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 350 APPLY THE FOLLOWING TO CHAINS: C REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 -64.46000 REMARK 350 BIOMT1 5 -0.500000 -0.866025 0.000000 -52.15000 REMARK 350 BIOMT2 5 0.866025 -0.500000 0.000000 90.32645 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 -64.46000 REMARK 350 BIOMT1 6 -0.500000 0.866025 0.000000 -104.30000 REMARK 350 BIOMT2 6 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 -64.46000 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 541 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 728 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 838 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 850 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 859 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 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 CYS A 310 CB SG 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 ASP A 92 CB - CG - OD1 ANGL. DEV. = 6.9 DEGREES REMARK 500 LYS A 316 CD - CE - NZ ANGL. DEV. = -15.2 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 73.99 -105.18 REMARK 500 GLN A 24 -86.57 -80.80 REMARK 500 ALA A 131 70.25 -158.81 REMARK 500 ALA A 131 70.93 -158.81 REMARK 500 LEU A 208 -1.69 81.03 REMARK 500 LEU A 222 45.65 -108.11 REMARK 500 CYS A 310 -1.87 123.11 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 HIS A 301 ASN A 302 142.22 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 0.09 SIDE CHAIN REMARK 500 ARG A 154 0.07 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 854 DISTANCE = 5.82 ANGSTROMS REMARK 525 HOH A 855 DISTANCE = 5.86 ANGSTROMS REMARK 525 HOH A 856 DISTANCE = 5.86 ANGSTROMS REMARK 525 HOH A 857 DISTANCE = 5.93 ANGSTROMS REMARK 525 HOH A 858 DISTANCE = 5.96 ANGSTROMS REMARK 525 HOH A 859 DISTANCE = 6.28 ANGSTROMS REMARK 525 HOH A 860 DISTANCE = 6.31 ANGSTROMS REMARK 525 HOH A 861 DISTANCE = 6.36 ANGSTROMS REMARK 525 HOH A 862 DISTANCE = 6.45 ANGSTROMS REMARK 525 HOH A 863 DISTANCE = 6.47 ANGSTROMS REMARK 525 HOH A 864 DISTANCE = 6.59 ANGSTROMS REMARK 525 HOH A 865 DISTANCE = 7.09 ANGSTROMS REMARK 525 HOH A 866 DISTANCE = 7.32 ANGSTROMS REMARK 525 HOH A 867 DISTANCE = 7.42 ANGSTROMS REMARK 525 HOH A 868 DISTANCE = 7.97 ANGSTROMS REMARK 525 HOH A 869 DISTANCE = 8.13 ANGSTROMS REMARK 525 HOH A 870 DISTANCE = 9.18 ANGSTROMS REMARK 525 HOH A 871 DISTANCE = 10.04 ANGSTROMS REMARK 525 HOH A 872 DISTANCE = 10.82 ANGSTROMS REMARK 525 HOH A 873 DISTANCE = 11.33 ANGSTROMS REMARK 525 HOH A 874 DISTANCE = 12.48 ANGSTROMS REMARK 525 HOH A 875 DISTANCE = 13.74 ANGSTROMS REMARK 525 HOH A 876 DISTANCE = 15.14 ANGSTROMS REMARK 525 HOH A 877 DISTANCE = 15.76 ANGSTROMS REMARK 525 HOH A 878 DISTANCE = 18.45 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 101.1 112.0 REMARK 620 4 MET A 145 SD 84.8 112.5 114.5 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 109.2 REMARK 620 3 HIS A 301 NE2 70.8 94.3 REMARK 620 4 NO A 405 N 101.0 108.2 157.5 REMARK 620 5 NO A 405 O 134.9 101.0 140.0 36.3 REMARK 620 N 1 2 3 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8RFL RELATED DB: PDB REMARK 900 8RFL IS DATASET 1 OF THIS SERIAL MOVIE SERIES REMARK 900 RELATED ID: 8RFO RELATED DB: PDB REMARK 900 8RFO IS DATASET 2 OF THIS SERIAL MOVIE SERIES REMARK 900 RELATED ID: 8RFP RELATED DB: PDB REMARK 900 8RFP IS DATASET 3 OF THIS SERIAL MOVIE SERIES DBREF 8RFQ A 2 340 UNP Q89EJ6 Q89EJ6_BRADU 29 367 SEQADV 8RFQ MET A 1 UNP Q89EJ6 INITIATING METHIONINE SEQADV 8RFQ CYS A 310 UNP Q89EJ6 GLY 337 CONFLICT SEQRES 1 A 340 MET ASP ASP LEU LYS LEU PRO ARG GLN LYS VAL GLU LEU SEQRES 2 A 340 VAL ALA PRO PRO PHE VAL HIS ALA HIS GLU GLN ALA THR SEQRES 3 A 340 LYS GLN GLY PRO LYS ILE VAL GLU PHE LYS LEU THR ILE SEQRES 4 A 340 GLU GLU LYS LYS VAL VAL ILE ASP GLU LYS GLY THR THR SEQRES 5 A 340 PHE GLN ALA MET THR PHE ASN GLY SER MET PRO GLY PRO SEQRES 6 A 340 LEU MET VAL VAL HIS GLU GLY ASP TYR VAL GLU THR THR SEQRES 7 A 340 LEU VAL ASN PRO ALA THR ASN THR MET PRO HIS ASN ILE SEQRES 8 A 340 ASP PHE HIS SER ALA THR GLY ALA LEU GLY GLY GLY ALA SEQRES 9 A 340 LEU THR LEU ILE ASN PRO GLY GLU GLN VAL VAL LEU ARG SEQRES 10 A 340 TRP LYS ALA THR LYS THR GLY VAL PHE VAL TYR HIS CYS SEQRES 11 A 340 ALA PRO GLY GLY PRO MET ILE PRO TRP HIS VAL VAL SER SEQRES 12 A 340 GLY MET ASN GLY ALA VAL MET VAL LEU PRO ARG ASP GLY SEQRES 13 A 340 LEU ASN ASP GLY LYS GLY HIS ALA LEU LYS TYR ASP LYS SEQRES 14 A 340 VAL TYR TYR VAL GLY GLU GLN ASP MET TYR VAL PRO ARG SEQRES 15 A 340 ASP GLU LYS GLY ASN PHE LYS SER TYR ASP SER PRO GLY SEQRES 16 A 340 GLU ALA PHE THR ASP THR GLU GLU MET MET LYS LYS LEU SEQRES 17 A 340 ILE PRO SER HIS VAL VAL PHE ASN GLY LYS VAL GLY ALA SEQRES 18 A 340 LEU THR GLY LYS ASN ALA LEU THR ALA ASN VAL GLY GLU SEQRES 19 A 340 ASN VAL LEU ILE VAL HIS SER GLN ALA ASN ARG ASP SER SEQRES 20 A 340 ARG PRO HIS LEU ILE GLY GLY HIS GLY ASP TYR VAL TRP SEQRES 21 A 340 GLU THR GLY LYS PHE GLY ASN ALA PRO GLU VAL GLY LEU SEQRES 22 A 340 GLU THR TRP PHE ILE ARG GLY GLY SER ALA GLY ALA ALA SEQRES 23 A 340 MET TYR LYS PHE MET GLN PRO GLY ILE TYR ALA TYR VAL SEQRES 24 A 340 THR HIS ASN LEU ILE GLU ALA ALA ASP LEU CYS ALA THR SEQRES 25 A 340 ALA HIS PHE LYS VAL GLU GLY LYS TRP ASN ASP ASP LEU SEQRES 26 A 340 MET THR GLN VAL LYS ALA PRO ALA GLU ILE PRO ALA ASN SEQRES 27 A 340 THR ASN HET GLC C 1 11 HET FRU C 2 12 HET CU A 401 1 HET CU A 402 1 HET NO2 A 403 3 HET NO2 A 404 3 HET NO A 405 2 HET SO4 A 406 5 HET SO4 A 407 5 HET SO4 A 408 5 HET SO4 A 409 5 HET SO4 A 410 5 HET SO4 A 411 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 SO4 SULFATE ION HETSYN GLC ALPHA-D-GLUCOSE; D-GLUCOSE; GLUCOSE HETSYN FRU BETA-D-FRUCTOSE; D-FRUCTOSE; FRUCTOSE HETSYN NO NITROGEN MONOXIDE FORMUL 2 GLC C6 H12 O6 FORMUL 2 FRU C6 H12 O6 FORMUL 3 CU 2(CU 2+) FORMUL 5 NO2 2(N O2 1-) FORMUL 7 NO N O FORMUL 8 SO4 6(O4 S 2-) FORMUL 14 HOH *378(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 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 C1 GLC C 1 O2 FRU C 2 1555 1555 1.45 LINK ND1 HIS A 89 CU CU A 401 1555 1555 2.06 LINK NE2 HIS A 94 CU CU A 402 1555 1555 2.04 LINK NE2 HIS A 129 CU CU A 402 1555 1555 2.04 LINK SG CYS A 130 CU CU A 401 1555 1555 2.22 LINK ND1 HIS A 140 CU CU A 401 1555 1555 2.05 LINK SD MET A 145 CU CU A 401 1555 1555 2.49 LINK NE2 HIS A 301 CU CU A 402 1555 3455 2.01 LINK CU CU A 402 N NO A 405 1555 1555 2.00 LINK CU CU A 402 O NO A 405 1555 1555 2.07 CISPEP 1 PRO A 16 PRO A 17 0 7.93 CISPEP 2 PRO A 16 PRO A 17 0 7.14 CISPEP 3 MET A 62 PRO A 63 0 -8.05 CRYST1 104.300 104.300 64.460 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 0.009588 0.005535 0.000000 0.00000 SCALE2 0.000000 0.011071 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015513 0.00000