HEADER METAL BINDING PROTEIN 16-FEB-19 6QQ0 TITLE CRYSTAL STRUCTURE OF NITRITE BOUND Y323E MUTANT OF HAEM-CU CONTAINING TITLE 2 NITRITE REDUCTASE FROM RALSTONIA PICKETTII 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 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RALSTONIA PICKETTII; SOURCE 3 ORGANISM_TAXID: 329; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_CELL_LINE: BL21 KEYWDS HAEM AND CU CONTAINING NITRITE REDUCTASE, INTER-COPPER ELECTRON KEYWDS 2 TRANSFER, METAL BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.V.ANTONYUK,R.T.SHENOY,T.M.HEDISON,R.R.EADY,S.S.HASNAIN,N.S.SCRUTTON REVDAT 3 20-NOV-24 6QQ0 1 LINK REVDAT 2 26-FEB-20 6QQ0 1 JRNL REVDAT 1 06-NOV-19 6QQ0 0 JRNL AUTH T.M.HEDISON,R.T.SHENOY,A.I.IORGU,D.J.HEYES,K.FISHER, JRNL AUTH 2 G.S.A.WRIGHT,S.HAY,R.R.EADY,S.V.ANTONYUK,S.S.HASNAIN, JRNL AUTH 3 N.S.SCRUTTON JRNL TITL UNEXPECTED ROLES OF A TETHER HARBORING A TYROSINE GATEKEEPER JRNL TITL 2 RESIDUE IN MODULAR NITRITE REDUCTASE CATALYSIS. JRNL REF ACS CATALYSIS V. 9 6087 2019 JRNL REFN ESSN 2155-5435 JRNL PMID 32051772 JRNL DOI 10.1021/ACSCATAL.9B01266 REMARK 2 REMARK 2 RESOLUTION. 1.40 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.63 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 97927 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) : 0.115 REMARK 3 R VALUE (WORKING SET) : 0.113 REMARK 3 FREE R VALUE : 0.146 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 5369 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) : 1.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.44 REMARK 3 REFLECTION IN BIN (WORKING SET) : 7269 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.61 REMARK 3 BIN R VALUE (WORKING SET) : 0.2950 REMARK 3 BIN FREE R VALUE SET COUNT : 369 REMARK 3 BIN FREE R VALUE : 0.3100 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3432 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 54 REMARK 3 SOLVENT ATOMS : 506 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.91 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.41000 REMARK 3 B22 (A**2) : 0.41000 REMARK 3 B33 (A**2) : -1.33000 REMARK 3 B12 (A**2) : 0.20000 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): 0.042 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.043 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.039 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.507 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.988 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.981 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3687 ; 0.012 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 3388 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5039 ; 1.670 ; 1.666 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7899 ; 1.469 ; 1.583 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 487 ; 7.232 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 174 ;33.969 ;23.161 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 582 ;12.416 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;20.588 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 464 ; 0.088 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4223 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 745 ; 0.006 ; 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): 1858 ; 2.040 ; 1.707 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1857 ; 2.032 ; 1.704 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2330 ; 2.631 ; 2.579 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2331 ; 2.630 ; 2.581 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1829 ; 3.317 ; 2.079 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1830 ; 3.317 ; 2.079 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2695 ; 3.817 ; 2.966 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4138 ; 5.023 ;23.191 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4009 ; 4.500 ;22.011 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 7075 ; 2.494 ; 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 : 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 ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 6QQ0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-FEB-19. REMARK 100 THE DEPOSITION ID IS D_1292100692. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-DEC-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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) : 0.96861 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS 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 : 103296 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 61.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 1.16000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES (PH7.5), 20% PEG 3350, 0.2 REMARK 280 M SODIUM CITRATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 284K 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 63.82500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 36.84938 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 28.85333 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 63.82500 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 36.84938 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 28.85333 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 63.82500 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 36.84938 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 28.85333 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 73.69876 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 57.70667 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 73.69876 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 57.70667 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 73.69876 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 57.70667 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: 19550 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 44270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -206.0 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 -0.500000 -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 A 943 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1021 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1099 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1100 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1106 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 ALA A 1 REMARK 465 SER A 2 REMARK 465 ALA A 3 REMARK 465 LYS A 4 REMARK 465 PRO A 461 REMARK 465 ALA A 462 REMARK 465 LYS A 463 REMARK 465 ALA A 464 REMARK 465 VAL A 465 REMARK 465 ALA A 466 REMARK 465 GLU A 467 REMARK 465 HIS A 468 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 O HOH A 881 O HOH A 1031 5444 1.83 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 49 CD GLU A 49 OE2 -0.076 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 72.65 -119.84 REMARK 500 GLU A 252 -122.43 44.96 REMARK 500 ASN A 260 54.20 70.09 REMARK 500 ASP A 320 -159.69 -141.08 REMARK 500 GLN A 369 158.65 76.01 REMARK 500 ASP A 391 88.10 -157.85 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 SER A 290 ILE A 291 -148.39 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 THR A 264 10.03 REMARK 500 REMARK 500 REMARK: NULL 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 139.3 REMARK 620 3 HIS A 143 ND1 101.9 106.3 REMARK 620 4 MET A 148 SD 83.1 111.5 112.4 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 99 NE2 REMARK 620 2 HIS A 134 NE2 109.8 REMARK 620 3 HIS A 289 NE2 73.3 98.7 REMARK 620 4 NO2 A 504 N 131.5 91.6 147.6 REMARK 620 5 NO2 A 504 O1 95.6 115.1 146.2 36.6 REMARK 620 6 HOH A 608 O 93.9 111.7 149.5 37.7 4.7 REMARK 620 N 1 2 3 4 5 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 91.1 REMARK 620 3 HEC A 503 NB 88.2 91.1 REMARK 620 4 HEC A 503 NC 89.5 178.5 87.5 REMARK 620 5 HEC A 503 ND 90.4 89.7 178.4 91.7 REMARK 620 6 MET A 418 SD 176.6 85.6 92.1 93.8 89.3 REMARK 620 N 1 2 3 4 5 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 HEC A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NO2 A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 505 DBREF 6QQ0 A 1 468 UNP I6NAW4 I6NAW4_RALPI 32 499 SEQADV 6QQ0 GLU A 323 UNP I6NAW4 TYR 354 ENGINEERED MUTATION SEQRES 1 A 468 ALA SER ALA LYS LEU PRO GLY ASP PHE GLY PRO PRO ARG SEQRES 2 A 468 GLY GLU PRO ILE HIS ALA VAL LEU THR SER PRO PRO LEU SEQRES 3 A 468 VAL PRO PRO PRO VAL ASN ARG THR TYR PRO ALA LYS VAL SEQRES 4 A 468 ILE VAL GLU LEU GLU VAL VAL GLU LYS GLU MET GLN ILE SEQRES 5 A 468 SER GLU GLY VAL SER TYR THR PHE TRP THR PHE GLY GLY SEQRES 6 A 468 THR VAL PRO GLY SER PHE ILE ARG VAL ARG GLN GLY ASP SEQRES 7 A 468 THR VAL GLU PHE HIS LEU LYS ASN HIS PRO SER SER LYS SEQRES 8 A 468 MET PRO HIS ASN ILE ASP LEU HIS GLY VAL THR GLY PRO SEQRES 9 A 468 GLY GLY GLY ALA ALA SER SER PHE THR ALA PRO GLY HIS SEQRES 10 A 468 GLU SER GLN PHE THR PHE LYS ALA LEU ASN GLU GLY ILE SEQRES 11 A 468 TYR VAL TYR HIS CYS ALA THR ALA PRO VAL GLY MET HIS SEQRES 12 A 468 ILE ALA ASN GLY MET TYR GLY LEU ILE LEU VAL GLU PRO SEQRES 13 A 468 PRO GLU GLY LEU PRO LYS VAL ASP HIS GLU TYR TYR VAL SEQRES 14 A 468 MET GLN GLY ASP PHE TYR THR ALA GLY LYS TYR ARG GLU SEQRES 15 A 468 LYS GLY LEU GLN PRO PHE ASP MET GLU LYS ALA ILE ASP SEQRES 16 A 468 GLU ARG PRO SER TYR VAL LEU PHE ASN GLY ALA GLU GLY SEQRES 17 A 468 ALA LEU THR GLY ASP LYS ALA LEU HIS ALA LYS VAL GLY SEQRES 18 A 468 GLU THR VAL ARG ILE PHE VAL GLY ASN GLY GLY PRO ASN SEQRES 19 A 468 LEU VAL SER SER PHE HIS VAL ILE GLY ALA ILE PHE ASP SEQRES 20 A 468 GLN VAL ARG TYR GLU GLY GLY THR ASN VAL GLN LYS ASN SEQRES 21 A 468 VAL GLN THR THR LEU ILE PRO ALA GLY GLY ALA ALA VAL SEQRES 22 A 468 VAL LYS PHE THR ALA ARG VAL PRO GLY SER TYR VAL LEU SEQRES 23 A 468 VAL ASP HIS SER ILE PHE ARG ALA PHE ASN LYS GLY ALA SEQRES 24 A 468 MET ALA ILE LEU LYS ILE ASP GLY ALA GLU ASN LYS LEU SEQRES 25 A 468 VAL TYR SER GLY LYS GLU LEU ASP SER VAL GLU LEU GLY SEQRES 26 A 468 ASP ARG ALA ALA PRO ASN MET SER ALA VAL THR LYS ALA SEQRES 27 A 468 THR GLN ALA SER VAL SER GLY THR LEU THR VAL GLN ASP SEQRES 28 A 468 GLN VAL GLN ALA GLY ARG ALA LEU PHE ALA GLY THR CYS SEQRES 29 A 468 SER VAL CYS HIS GLN GLY ASN GLY ALA GLY LEU PRO GLY SEQRES 30 A 468 VAL PHE PRO PRO LEU ALA LYS SER ASP PHE LEU ALA ALA SEQRES 31 A 468 ASP PRO LYS ARG ALA MET ASN ILE VAL LEU HIS GLY LEU SEQRES 32 A 468 ASN GLY LYS ILE LYS VAL ASN GLY GLN GLU TYR ASP SER SEQRES 33 A 468 VAL MET PRO PRO MET THR GLN LEU ASN ASP ASP GLU VAL SEQRES 34 A 468 ALA ASN ILE LEU THR TYR VAL LEU ASN SER TRP ASP ASN SEQRES 35 A 468 PRO GLY GLY ARG VAL SER ALA GLU ASP VAL LYS LYS VAL SEQRES 36 A 468 ARG ALA GLN PRO ALA PRO ALA LYS ALA VAL ALA GLU HIS HET CU A 501 1 HET CU A 502 1 HET HEC A 503 43 HET NO2 A 504 3 HET GOL A 505 6 HETNAM CU COPPER (II) ION HETNAM HEC HEME C HETNAM NO2 NITRITE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 CU 2(CU 2+) FORMUL 4 HEC C34 H34 FE N4 O4 FORMUL 5 NO2 N O2 1- FORMUL 6 GOL C3 H8 O3 FORMUL 7 HOH *506(H2 O) HELIX 1 AA1 GLY A 103 SER A 111 5 9 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 GLU A 155 N VAL A 74 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 5 TYR A 200 PHE A 203 0 SHEET 2 AA4 5 HIS A 165 PHE A 174 -1 N PHE A 174 O TYR A 200 SHEET 3 AA4 5 THR A 223 GLY A 232 1 O PHE A 227 N TYR A 167 SHEET 4 AA4 5 ALA A 271 THR A 277 -1 O PHE A 276 N VAL A 224 SHEET 5 AA4 5 GLN A 248 TYR A 251 -1 N ARG A 250 O VAL A 273 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 1.86 LINK SG CYS A 367 CAC HEC A 503 1555 1555 1.92 LINK ND1 HIS A 94 CU CU A 501 1555 1555 2.00 LINK NE2 HIS A 99 CU CU A 502 1555 1555 2.03 LINK NE2 HIS A 134 CU CU A 502 1555 1555 1.98 LINK SG CYS A 135 CU CU A 501 1555 1555 2.22 LINK ND1 HIS A 143 CU CU A 501 1555 1555 2.09 LINK SD MET A 148 CU CU A 501 1555 1555 2.58 LINK NE2 HIS A 289 CU CU A 502 1555 3555 2.03 LINK NE2 HIS A 368 FE HEC A 503 1555 1555 2.06 LINK SD MET A 418 FE HEC A 503 1555 1555 2.32 LINK CU CU A 502 N ANO2 A 504 1555 1555 2.09 LINK CU CU A 502 O1 ANO2 A 504 1555 1555 1.95 LINK CU CU A 502 O BHOH A 608 1555 1555 2.09 CISPEP 1 PRO A 24 PRO A 25 0 2.96 CISPEP 2 VAL A 67 PRO A 68 0 -0.44 CISPEP 3 ALA A 138 PRO A 139 0 -7.44 CISPEP 4 GLY A 232 PRO A 233 0 15.25 SITE 1 AC1 4 HIS A 94 CYS A 135 HIS A 143 MET A 148 SITE 1 AC2 6 HIS A 99 HIS A 134 HIS A 240 HIS A 289 SITE 2 AC2 6 NO2 A 504 HOH A 608 SITE 1 AC3 16 THR A 363 CYS A 364 CYS A 367 HIS A 368 SITE 2 AC3 16 PRO A 380 PRO A 381 LEU A 382 SER A 385 SITE 3 AC3 16 PHE A 387 LEU A 403 ASN A 404 GLY A 405 SITE 4 AC3 16 TYR A 414 SER A 416 MET A 418 MET A 421 SITE 1 AC4 9 ASP A 97 HIS A 99 HIS A 134 HIS A 240 SITE 2 AC4 9 ILE A 242 HIS A 289 CU A 502 HOH A 608 SITE 3 AC4 9 HOH A 824 SITE 1 AC5 7 GLU A 47 THR A 59 TRP A 61 VAL A 417 SITE 2 AC5 7 HOH A 754 HOH A 863 HOH A1057 CRYST1 127.650 127.650 86.560 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 0.007834 0.004523 0.000000 0.00000 SCALE2 0.000000 0.009046 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011553 0.00000