HEADER OXIDOREDUCTASE 05-SEP-23 8QGF TITLE CRYSTAL STRUCTURE OF AS-ISOLATED M148L MUTANT OF THREE-DOMAIN HEME-CU TITLE 2 NITRITE REDUCTASE FROM RALSTONIA PICKETTII COMPND MOL_ID: 1; COMPND 2 MOLECULE: COPPER-CONTAINING NITRITE REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RALSTONIA PICKETTII; SOURCE 3 ORGANISM_TAXID: 329; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_PLASMID: PET26B-M148L_RPNIR KEYWDS HAEM AND CU CONTAINING NITRITE REDUCTASE, ELECTRON TRANSFER, REDOX KEYWDS 2 REACTIONS, METAL BINDING PROTEIN, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR N.PETCHYAM,S.ANTONYUK,S.S.HASNAIN REVDAT 2 06-NOV-24 8QGF 1 REMARK REVDAT 1 11-SEP-24 8QGF 0 JRNL AUTH N.PETCHYAM,S.ANTONYUK,S.S.HASNAIN JRNL TITL STRUCTURAL STUDIES OF HAEM THREE-DOMAIN COPPER NITRITE JRNL TITL 2 REDUCTASE MUTANTS FROM RALSTONIA PICKETTII JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.32 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 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) : 46.66 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 118239 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) : 0.135 REMARK 3 R VALUE (WORKING SET) : 0.134 REMARK 3 FREE R VALUE : 0.162 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 5839 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL 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) : 8086 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.06 REMARK 3 BIN R VALUE (WORKING SET) : 0.3380 REMARK 3 BIN FREE R VALUE SET COUNT : 416 REMARK 3 BIN FREE R VALUE : 0.3560 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3423 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 45 REMARK 3 SOLVENT ATOMS : 736 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.23 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.99000 REMARK 3 B22 (A**2) : 0.99000 REMARK 3 B33 (A**2) : -3.22000 REMARK 3 B12 (A**2) : 0.50000 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): 0.044 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.043 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.037 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.199 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.982 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.975 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3944 ; 0.012 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 3732 ; 0.008 ; 0.015 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5439 ; 1.683 ; 1.669 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8679 ; 1.430 ; 1.590 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 552 ; 7.054 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 194 ;35.941 ;23.196 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 649 ;11.644 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;19.342 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 505 ; 0.103 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4671 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 905 ; 0.008 ; 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): 1945 ; 1.126 ; 1.534 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1944 ; 1.104 ; 1.532 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2460 ; 1.410 ; 2.311 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2461 ; 1.410 ; 2.313 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1998 ; 1.591 ; 1.700 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1996 ; 1.592 ; 1.700 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2931 ; 1.738 ; 2.487 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4675 ; 3.272 ;20.903 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4415 ; 2.494 ;19.132 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 7675 ; 3.245 ; 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 8QGF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-SEP-23. REMARK 100 THE DEPOSITION ID IS D_1292131728. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-SEP-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.978565 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 124091 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.320 REMARK 200 RESOLUTION RANGE LOW (A) : 46.660 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : 0.13700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.4000 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 (%) : 87.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : 1.88800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 0.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS 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 (%): 54.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PROPANE PH 6.3, 0.1 M REMARK 280 SODIUM CITRATE, 25% PEG3350, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 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+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 63.97600 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 36.93656 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 28.74967 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 63.97600 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 36.93656 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 28.74967 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 63.97600 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 36.93656 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 28.74967 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 73.87312 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 57.49933 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 73.87312 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 57.49933 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 73.87312 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 57.49933 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 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 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 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 A1242 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1262 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1277 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1304 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1307 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1319 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1335 LIES ON A SPECIAL POSITION. 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 HE2 HIS A 99 CU CU A 502 1.12 REMARK 500 HE2 HIS A 368 FE HEC A 503 1.13 REMARK 500 HE2 HIS A 134 CU CU A 502 1.14 REMARK 500 HD1 HIS A 94 CU CU A 501 1.26 REMARK 500 HD1 HIS A 143 CU CU A 501 1.46 REMARK 500 O HOH A 641 O HOH A 1080 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 HE2 HIS A 289 CU CU A 502 3555 1.14 REMARK 500 O HOH A 1094 O HOH A 1094 2555 1.68 REMARK 500 O HOH A 796 O HOH A 865 5454 2.18 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 ARG A 197 73.99 -119.84 REMARK 500 GLU A 252 -125.66 46.01 REMARK 500 GLN A 369 156.03 77.02 REMARK 500 GLN A 369 155.54 77.79 REMARK 500 ASP A 391 83.46 -160.21 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 A1330 DISTANCE = 5.81 ANGSTROMS REMARK 525 HOH A1331 DISTANCE = 5.87 ANGSTROMS REMARK 525 HOH A1332 DISTANCE = 6.02 ANGSTROMS REMARK 525 HOH A1333 DISTANCE = 6.31 ANGSTROMS REMARK 525 HOH A1334 DISTANCE = 6.31 ANGSTROMS REMARK 525 HOH A1335 DISTANCE = 6.56 ANGSTROMS REMARK 525 HOH A1336 DISTANCE = 7.31 ANGSTROMS REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 HOH A 1336 REMARK 615 HOH A 1242 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 94 ND1 REMARK 620 2 CYS A 135 SG 141.9 REMARK 620 3 HIS A 143 ND1 102.2 113.6 REMARK 620 N 1 2 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 99 NE2 REMARK 620 2 HIS A 134 NE2 111.9 REMARK 620 3 HIS A 289 NE2 73.1 100.4 REMARK 620 4 HOH A 636 O 94.4 114.0 145.6 REMARK 620 5 HOH A 874 O 159.1 83.2 119.9 65.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC A 503 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 368 NE2 REMARK 620 2 HEC A 503 NA 93.6 REMARK 620 3 HEC A 503 NB 88.0 89.7 REMARK 620 4 HEC A 503 NC 87.6 178.8 90.4 REMARK 620 5 HEC A 503 ND 92.0 90.0 179.6 90.0 REMARK 620 6 MET A 418 SD 177.8 84.3 92.6 94.5 87.4 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3ZIY RELATED DB: PDB DBREF 8QGF A 5 458 UNP I6NAW4 I6NAW4_RALPI 36 489 SEQADV 8QGF LEU A 148 UNP I6NAW4 MET 179 ENGINEERED MUTATION SEQRES 1 A 454 LEU PRO GLY ASP PHE GLY PRO PRO ARG GLY GLU PRO ILE SEQRES 2 A 454 HIS ALA VAL LEU THR SER PRO PRO LEU VAL PRO PRO PRO SEQRES 3 A 454 VAL ASN ARG THR TYR PRO ALA LYS VAL ILE VAL GLU LEU SEQRES 4 A 454 GLU VAL VAL GLU LYS GLU MET GLN ILE SER GLU GLY VAL SEQRES 5 A 454 SER TYR THR PHE TRP THR PHE GLY GLY THR VAL PRO GLY SEQRES 6 A 454 SER PHE ILE ARG VAL ARG GLN GLY ASP THR VAL GLU PHE SEQRES 7 A 454 HIS LEU LYS ASN HIS PRO SER SER LYS MET PRO HIS ASN SEQRES 8 A 454 ILE ASP LEU HIS GLY VAL THR GLY PRO GLY GLY GLY ALA SEQRES 9 A 454 ALA SER SER PHE THR ALA PRO GLY HIS GLU SER GLN PHE SEQRES 10 A 454 THR PHE LYS ALA LEU ASN GLU GLY ILE TYR VAL TYR HIS SEQRES 11 A 454 CYS ALA THR ALA PRO VAL GLY MET HIS ILE ALA ASN GLY SEQRES 12 A 454 LEU TYR GLY LEU ILE LEU VAL GLU PRO PRO GLU GLY LEU SEQRES 13 A 454 PRO LYS VAL ASP HIS GLU TYR TYR VAL MET GLN GLY ASP SEQRES 14 A 454 PHE TYR THR ALA GLY LYS TYR ARG GLU LYS GLY LEU GLN SEQRES 15 A 454 PRO PHE ASP MET GLU LYS ALA ILE ASP GLU ARG PRO SER SEQRES 16 A 454 TYR VAL LEU PHE ASN GLY ALA GLU GLY ALA LEU THR GLY SEQRES 17 A 454 ASP LYS ALA LEU HIS ALA LYS VAL GLY GLU THR VAL ARG SEQRES 18 A 454 ILE PHE VAL GLY ASN GLY GLY PRO ASN LEU VAL SER SER SEQRES 19 A 454 PHE HIS VAL ILE GLY ALA ILE PHE ASP GLN VAL ARG TYR SEQRES 20 A 454 GLU GLY GLY THR ASN VAL GLN LYS ASN VAL GLN THR THR SEQRES 21 A 454 LEU ILE PRO ALA GLY GLY ALA ALA VAL VAL LYS PHE THR SEQRES 22 A 454 ALA ARG VAL PRO GLY SER TYR VAL LEU VAL ASP HIS SER SEQRES 23 A 454 ILE PHE ARG ALA PHE ASN LYS GLY ALA MET ALA ILE LEU SEQRES 24 A 454 LYS ILE ASP GLY ALA GLU ASN LYS LEU VAL TYR SER GLY SEQRES 25 A 454 LYS GLU LEU ASP SER VAL TYR LEU GLY ASP ARG ALA ALA SEQRES 26 A 454 PRO ASN MET SER ALA VAL THR LYS ALA THR GLN ALA SER SEQRES 27 A 454 VAL SER GLY THR LEU THR VAL GLN ASP GLN VAL GLN ALA SEQRES 28 A 454 GLY ARG ALA LEU PHE ALA GLY THR CYS SER VAL CYS HIS SEQRES 29 A 454 GLN GLY ASN GLY ALA GLY LEU PRO GLY VAL PHE PRO PRO SEQRES 30 A 454 LEU ALA LYS SER ASP PHE LEU ALA ALA ASP PRO LYS ARG SEQRES 31 A 454 ALA MET ASN ILE VAL LEU HIS GLY LEU ASN GLY LYS ILE SEQRES 32 A 454 LYS VAL ASN GLY GLN GLU TYR ASP SER VAL MET PRO PRO SEQRES 33 A 454 MET THR GLN LEU ASN ASP ASP GLU VAL ALA ASN ILE LEU SEQRES 34 A 454 THR TYR VAL LEU ASN SER TRP ASP ASN PRO GLY GLY ARG SEQRES 35 A 454 VAL SER ALA GLU ASP VAL LYS LYS VAL ARG ALA GLN HET CU A 501 1 HET CU A 502 1 HET HEC A 503 75 HETNAM CU COPPER (II) ION HETNAM HEC HEME C FORMUL 2 CU 2(CU 2+) FORMUL 4 HEC C34 H34 FE N4 O4 FORMUL 5 HOH *736(H2 O) HELIX 1 AA1 GLY A 103 PHE A 112 5 10 HELIX 2 AA2 PRO A 139 ASN A 146 1 8 HELIX 3 AA3 ASP A 189 ASP A 195 1 7 HELIX 4 AA4 THR A 211 ALA A 215 5 5 HELIX 5 AA5 SER A 290 LYS A 297 1 8 HELIX 6 AA6 ASP A 320 GLY A 325 1 6 HELIX 7 AA7 ASP A 326 ALA A 328 5 3 HELIX 8 AA8 MET A 332 GLY A 345 1 14 HELIX 9 AA9 THR A 348 ALA A 361 1 14 HELIX 10 AB1 CYS A 364 GLN A 369 1 6 HELIX 11 AB2 SER A 385 ASP A 391 1 7 HELIX 12 AB3 ASP A 391 GLY A 402 1 12 HELIX 13 AB4 ASN A 425 ASN A 438 1 14 HELIX 14 AB5 SER A 448 GLN A 458 1 11 SHEET 1 AA1 4 ILE A 17 HIS A 18 0 SHEET 2 AA1 4 LYS A 38 SER A 53 1 O ILE A 40 N ILE A 17 SHEET 3 AA1 4 THR A 79 ASN A 86 1 O HIS A 83 N VAL A 41 SHEET 4 AA1 4 GLU A 118 LYS A 124 -1 O PHE A 123 N VAL A 80 SHEET 1 AA2 4 ILE A 17 HIS A 18 0 SHEET 2 AA2 4 LYS A 38 SER A 53 1 O ILE A 40 N ILE A 17 SHEET 3 AA2 4 VAL A 56 PHE A 63 -1 O PHE A 60 N LYS A 48 SHEET 4 AA2 4 GLY A 184 LEU A 185 1 O GLY A 184 N SER A 57 SHEET 1 AA3 4 ILE A 72 ARG A 75 0 SHEET 2 AA3 4 TYR A 149 GLU A 155 1 O LEU A 153 N ILE A 72 SHEET 3 AA3 4 GLY A 129 HIS A 134 -1 N GLY A 129 O VAL A 154 SHEET 4 AA3 4 ASP A 97 LEU A 98 -1 N ASP A 97 O HIS A 134 SHEET 1 AA4 6 TYR A 200 PHE A 203 0 SHEET 2 AA4 6 HIS A 165 PHE A 174 -1 N PHE A 174 O TYR A 200 SHEET 3 AA4 6 THR A 223 GLY A 232 1 O PHE A 227 N TYR A 167 SHEET 4 AA4 6 ALA A 271 THR A 277 -1 O ALA A 272 N VAL A 228 SHEET 5 AA4 6 PHE A 246 TYR A 251 -1 N ARG A 250 O VAL A 273 SHEET 6 AA4 6 GLN A 258 VAL A 261 -1 O VAL A 261 N PHE A 246 SHEET 1 AA5 5 LEU A 216 LYS A 219 0 SHEET 2 AA5 5 MET A 300 ASP A 306 1 O LYS A 304 N LEU A 216 SHEET 3 AA5 5 GLY A 282 ASP A 288 -1 N GLY A 282 O ILE A 305 SHEET 4 AA5 5 SER A 237 ILE A 242 -1 N ILE A 242 O VAL A 285 SHEET 5 AA5 5 THR A 263 ILE A 266 -1 O THR A 264 N PHE A 239 SHEET 1 AA6 2 LEU A 403 VAL A 409 0 SHEET 2 AA6 2 GLN A 412 MET A 418 -1 O MET A 418 N LEU A 403 LINK SG CYS A 364 CAB HEC A 503 1555 1555 1.78 LINK SG CYS A 367 CAC HEC A 503 1555 1555 1.80 LINK ND1 HIS A 94 CU CU A 501 1555 1555 2.02 LINK NE2 HIS A 99 CU CU A 502 1555 1555 1.99 LINK NE2 HIS A 134 CU CU A 502 1555 1555 2.00 LINK SG CYS A 135 CU CU A 501 1555 1555 2.16 LINK ND1 HIS A 143 CU CU A 501 1555 1555 2.03 LINK NE2 HIS A 289 CU CU A 502 1555 3555 2.01 LINK NE2 HIS A 368 FE HEC A 503 1555 1555 1.99 LINK SD MET A 418 FE HEC A 503 1555 1555 2.33 LINK CU CU A 502 O HOH A 636 1555 1555 2.01 LINK CU CU A 502 O AHOH A 874 1555 1555 2.19 CISPEP 1 PRO A 24 PRO A 25 0 2.71 CISPEP 2 VAL A 67 PRO A 68 0 -2.91 CISPEP 3 ALA A 138 PRO A 139 0 -11.12 CISPEP 4 GLY A 232 PRO A 233 0 16.25 CRYST1 127.952 127.952 86.249 90.00 90.00 120.00 H 3 9 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 0.007815 0.004512 0.000000 0.00000 SCALE2 0.000000 0.009024 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011594 0.00000