HEADER OXIDOREDUCTASE 04-AUG-17 5ONY TITLE AS-ISOLATED RESTING STATE COPPER NITRITE REDUCTASE FROM ACHROMOBACTER TITLE 2 XYLOSOXIDANS COMPND MOL_ID: 1; COMPND 2 MOLECULE: COPPER-CONTAINING NITRITE REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE,NITRITE COMPND 5 REDUCTASE (NIR); COMPND 6 EC: 1.7.2.1; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ALCALIGENES XYLOSOXYDANS XYLOSOXYDANS; SOURCE 3 ORGANISM_TAXID: 85698; SOURCE 4 GENE: NIR, NIRK, ERS451415_02178; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS COPPER ION BINDING, OXIDOREDUCTASE ACTIVITY, METAL ION BINDING, KEYWDS 2 NITRITE REDUCTASE ACTIVITY, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR T.P.HALSTED,K.YAMASHITA,K.HIRATA,H.AGO,G.UENO,T.TOSHA,R.R.EADY, AUTHOR 2 S.V.ANTONYUK,M.YAMAMOTO,S.S.HASNAIN REVDAT 4 17-JAN-24 5ONY 1 LINK REVDAT 3 03-OCT-18 5ONY 1 REMARK REVDAT 2 31-JAN-18 5ONY 1 JRNL REVDAT 1 29-NOV-17 5ONY 0 JRNL AUTH T.P.HALSTED,K.YAMASHITA,K.HIRATA,H.AGO,G.UENO,T.TOSHA, JRNL AUTH 2 R.R.EADY,S.V.ANTONYUK,M.YAMAMOTO,S.S.HASNAIN JRNL TITL AN UNPRECEDENTED DIOXYGEN SPECIES REVEALED BY SERIAL JRNL TITL 2 FEMTOSECOND ROTATION CRYSTALLOGRAPHY IN COPPER NITRITE JRNL TITL 3 REDUCTASE. JRNL REF IUCRJ V. 5 22 2018 JRNL REFN ESSN 2052-2525 JRNL PMID 29354268 JRNL DOI 10.1107/S2052252517016128 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.86 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 53635 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) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2884 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4028 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.45 REMARK 3 BIN R VALUE (WORKING SET) : 0.3050 REMARK 3 BIN FREE R VALUE SET COUNT : 177 REMARK 3 BIN FREE R VALUE : 0.2710 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2567 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 40 REMARK 3 SOLVENT ATOMS : 378 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.14 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.59000 REMARK 3 B22 (A**2) : 0.59000 REMARK 3 B33 (A**2) : -1.93000 REMARK 3 B12 (A**2) : 0.30000 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): 0.083 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.087 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.083 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.486 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.944 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2686 ; 0.017 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2476 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3651 ; 1.897 ; 1.964 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5772 ; 1.036 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 336 ; 7.643 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 111 ;35.361 ;24.234 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 419 ;14.231 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;17.035 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 398 ; 0.116 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2965 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 514 ; 0.002 ; 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): 1344 ; 2.209 ; 2.600 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1343 ; 2.183 ; 2.595 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1680 ; 2.924 ; 3.888 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1681 ; 2.929 ; 3.893 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1342 ; 2.858 ; 2.859 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1342 ; 2.857 ; 2.859 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1972 ; 3.992 ; 4.185 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2893 ; 5.313 ;31.716 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2809 ; 5.134 ;30.906 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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 5ONY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-AUG-17. REMARK 100 THE DEPOSITION ID IS D_1200006106. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-NOV-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 56521 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 47.860 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 1OE1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% W/V PEG 550 MME, 10 MM ZNSO4, 100 REMARK 280 MM MES BUFFER, PH 6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293.15K 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 -0.865992 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866059 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.865992 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866059 -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 44.98426 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 25.97268 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 47.85147 REMARK 290 SMTRY1 5 -0.500000 -0.865992 0.000000 44.98426 REMARK 290 SMTRY2 5 0.866059 -0.500000 0.000000 25.97268 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 47.85147 REMARK 290 SMTRY1 6 -0.500000 0.865992 0.000000 44.98426 REMARK 290 SMTRY2 6 -0.866059 -0.500000 0.000000 25.97268 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 47.85147 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 51.94535 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 95.70294 REMARK 290 SMTRY1 8 -0.500000 -0.865992 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866059 -0.500000 0.000000 51.94535 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 95.70294 REMARK 290 SMTRY1 9 -0.500000 0.865992 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866059 -0.500000 0.000000 51.94535 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 95.70294 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: 16860 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 34110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -122.0 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 -0.865992 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866059 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.865992 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866059 -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 965 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 O HOH A 609 O HOH A 627 2.04 REMARK 500 O HOH A 883 O HOH A 951 2.13 REMARK 500 O HOH A 788 O HOH A 932 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 O HOH A 652 O HOH A 851 3555 2.15 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 MET A 135 CG - SD - CE ANGL. DEV. = 11.2 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 GLN A 24 -103.66 -88.02 REMARK 500 ASN A 90 -168.00 -162.99 REMARK 500 ALA A 131 58.91 -153.43 REMARK 500 LEU A 207 13.55 59.46 REMARK 500 VAL A 231 138.21 -39.21 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 300 ASN A 301 146.46 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 967 DISTANCE = 5.84 ANGSTROMS REMARK 525 HOH A 968 DISTANCE = 5.88 ANGSTROMS REMARK 525 HOH A 969 DISTANCE = 5.96 ANGSTROMS REMARK 525 HOH A 970 DISTANCE = 6.03 ANGSTROMS REMARK 525 HOH A 971 DISTANCE = 6.17 ANGSTROMS REMARK 525 HOH A 972 DISTANCE = 6.40 ANGSTROMS REMARK 525 HOH A 973 DISTANCE = 6.54 ANGSTROMS REMARK 525 HOH A 974 DISTANCE = 6.80 ANGSTROMS REMARK 525 HOH A 975 DISTANCE = 6.94 ANGSTROMS REMARK 525 HOH A 976 DISTANCE = 7.88 ANGSTROMS REMARK 525 HOH A 977 DISTANCE = 8.45 ANGSTROMS REMARK 525 HOH A 978 DISTANCE = 10.29 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 125.6 REMARK 620 3 HIS A 139 ND1 103.6 122.4 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 94 NE2 REMARK 620 2 HIS A 129 NE2 108.2 REMARK 620 3 HIS A 300 NE2 72.2 96.4 REMARK 620 4 HOH A 660 O 108.4 109.7 151.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 503 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 165 NE2 REMARK 620 2 ASP A 167 OD1 101.4 REMARK 620 3 ASP A 167 OD2 126.1 55.1 REMARK 620 4 GLU A 195 OE2 93.3 59.4 33.0 REMARK 620 5 HOH A 698 O 92.6 57.5 33.5 2.2 REMARK 620 N 1 2 3 4 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 ZN A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MES A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MES A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PG4 A 506 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5ONX RELATED DB: PDB REMARK 900 5ONX CONTAINS THE SAME PROTEIN COLLECTED USING A SYNCHROTRON X-RAY REMARK 900 SOURCE. DBREF 5ONY A 2 336 UNP O68601 O68601_ALCXX 26 360 SEQRES 1 A 335 ASP ALA ASP LYS LEU PRO HIS THR LYS VAL THR LEU VAL SEQRES 2 A 335 ALA PRO PRO GLN VAL HIS PRO HIS GLU GLN ALA THR LYS SEQRES 3 A 335 SER GLY PRO LYS VAL VAL GLU PHE THR MET THR ILE GLU SEQRES 4 A 335 GLU LYS LYS MET VAL ILE ASP ASP LYS GLY THR THR LEU SEQRES 5 A 335 GLN ALA MET THR PHE ASN GLY SER MET PRO GLY PRO THR SEQRES 6 A 335 LEU VAL VAL HIS GLU GLY ASP TYR VAL GLN LEU THR LEU SEQRES 7 A 335 VAL ASN PRO ALA THR ASN ALA MET PRO HIS ASN VAL ASP SEQRES 8 A 335 PHE HIS GLY ALA THR GLY ALA LEU GLY GLY ALA LYS LEU SEQRES 9 A 335 THR ASN VAL ASN PRO GLY GLU GLN ALA THR LEU ARG PHE SEQRES 10 A 335 LYS ALA ASP ARG SER GLY THR PHE VAL TYR HIS CYS ALA SEQRES 11 A 335 PRO GLU GLY MET VAL PRO TRP HIS VAL VAL SER GLY MET SEQRES 12 A 335 SER GLY THR LEU MET VAL LEU PRO ARG ASP GLY LEU LYS SEQRES 13 A 335 ASP PRO GLN GLY LYS PRO LEU HIS TYR ASP ARG ALA TYR SEQRES 14 A 335 THR ILE GLY GLU PHE ASP LEU TYR ILE PRO LYS GLY PRO SEQRES 15 A 335 ASP GLY LYS TYR LYS ASP TYR ALA THR LEU ALA GLU SER SEQRES 16 A 335 TYR GLY ASP THR VAL GLN VAL MET ARG THR LEU THR PRO SEQRES 17 A 335 SER HIS ILE VAL PHE ASN GLY LYS VAL GLY ALA LEU THR SEQRES 18 A 335 GLY ALA ASN ALA LEU THR ALA LYS VAL GLY GLU THR VAL SEQRES 19 A 335 LEU LEU ILE HIS SER GLN ALA ASN ARG ASP THR ARG PRO SEQRES 20 A 335 HIS LEU ILE GLY GLY HIS GLY ASP TRP VAL TRP GLU THR SEQRES 21 A 335 GLY LYS PHE ALA ASN PRO PRO GLN ARG ASP LEU GLU THR SEQRES 22 A 335 TRP PHE ILE ARG GLY GLY SER ALA GLY ALA ALA LEU TYR SEQRES 23 A 335 THR PHE LYS GLN PRO GLY VAL TYR ALA TYR LEU ASN HIS SEQRES 24 A 335 ASN LEU ILE GLU ALA PHE GLU LEU GLY ALA ALA GLY HIS SEQRES 25 A 335 ILE LYS VAL GLU GLY LYS TRP ASN ASP ASP LEU MET LYS SEQRES 26 A 335 GLN ILE LYS ALA PRO ALA PRO ILE PRO ARG HET CU A 501 1 HET CU A 502 1 HET ZN A 503 1 HET MES A 504 12 HET MES A 505 12 HET PG4 A 506 13 HETNAM CU COPPER (II) ION HETNAM ZN ZINC ION HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID HETNAM PG4 TETRAETHYLENE GLYCOL FORMUL 2 CU 2(CU 2+) FORMUL 4 ZN ZN 2+ FORMUL 5 MES 2(C6 H13 N O4 S) FORMUL 7 PG4 C8 H18 O5 FORMUL 8 HOH *378(H2 O) HELIX 1 AA1 ASP A 2 LEU A 6 5 5 HELIX 2 AA2 GLY A 98 THR A 106 5 9 HELIX 3 AA3 MET A 135 SER A 142 1 8 HELIX 4 AA4 THR A 192 THR A 206 1 15 HELIX 5 AA5 THR A 222 ALA A 226 5 5 HELIX 6 AA6 ASN A 301 GLU A 307 1 7 SHEET 1 AA1 3 HIS A 8 LYS A 10 0 SHEET 2 AA1 3 VAL A 32 VAL A 45 1 O GLU A 34 N THR A 9 SHEET 3 AA1 3 THR A 52 PHE A 58 -1 O LEU A 53 N MET A 44 SHEET 1 AA2 4 HIS A 8 LYS A 10 0 SHEET 2 AA2 4 VAL A 32 VAL A 45 1 O GLU A 34 N THR 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 PHE A 118 N VAL A 75 SHEET 1 AA3 4 LEU A 67 HIS A 70 0 SHEET 2 AA3 4 SER A 145 LEU A 151 1 O MET A 149 N LEU A 67 SHEET 3 AA3 4 GLY A 124 HIS A 129 -1 N GLY A 124 O VAL A 150 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 211 PHE A 214 0 SHEET 2 AA4 6 ARG A 168 LEU A 177 -1 N LEU A 177 O HIS A 211 SHEET 3 AA4 6 THR A 234 GLN A 241 1 O ILE A 238 N ILE A 172 SHEET 4 AA4 6 SER A 281 THR A 288 -1 O ALA A 285 N LEU A 237 SHEET 5 AA4 6 GLY A 255 TRP A 259 -1 N TRP A 257 O LEU A 286 SHEET 6 AA4 6 GLN A 269 LEU A 272 -1 O GLN A 269 N VAL A 258 SHEET 1 AA5 4 LEU A 227 LYS A 230 0 SHEET 2 AA5 4 ALA A 311 GLU A 317 1 O LYS A 315 N LEU A 227 SHEET 3 AA5 4 GLY A 293 ASN A 299 -1 N GLY A 293 O VAL A 316 SHEET 4 AA5 4 PRO A 248 ILE A 251 -1 N ILE A 251 O ALA A 296 LINK ND1 HIS A 89 CU CU A 501 1555 1555 2.11 LINK NE2 HIS A 94 CU CU A 502 1555 1555 2.04 LINK NE2 HIS A 129 CU CU A 502 1555 1555 2.01 LINK SG CYS A 130 CU CU A 501 1555 1555 2.11 LINK ND1 HIS A 139 CU CU A 501 1555 1555 2.02 LINK NE2 HIS A 165 ZN ZN A 503 1555 9544 1.74 LINK OD1 ASP A 167 ZN ZN A 503 1555 9544 2.55 LINK OD2 ASP A 167 ZN ZN A 503 1555 9544 2.05 LINK OE2 GLU A 195 ZN ZN A 503 1555 1555 2.10 LINK NE2 HIS A 300 CU CU A 502 1555 2555 2.09 LINK CU CU A 502 O HOH A 660 1555 1555 1.72 LINK ZN ZN A 503 O HOH A 698 1555 5445 1.88 CISPEP 1 PRO A 16 PRO A 17 0 9.06 CISPEP 2 MET A 62 PRO A 63 0 -9.86 SITE 1 AC1 4 HIS A 89 CYS A 130 HIS A 139 MET A 144 SITE 1 AC2 6 ASP A 92 HIS A 94 HIS A 129 HIS A 249 SITE 2 AC2 6 HIS A 300 HOH A 660 SITE 1 AC3 4 HIS A 165 ASP A 167 GLU A 195 HOH A 698 SITE 1 AC4 5 ASP A 47 ASP A 48 LYS A 49 PHE A 306 SITE 2 AC4 5 GLU A 307 SITE 1 AC5 6 LEU A 164 HIS A 165 THR A 288 HOH A 685 SITE 2 AC5 6 HOH A 740 HOH A 760 SITE 1 AC6 4 ALA A 296 PHE A 306 ALA A 311 HIS A 313 CRYST1 90.347 90.347 143.580 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 0.011115 0.006417 0.000000 0.00000 SCALE2 0.000000 0.012834 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006966 0.00000