HEADER OXIDOREDUCTASE 16-NOV-14 3X1F TITLE H294M MUTANT OF COPPER-CONTAINING NITRITE REDUCTASE FROM GEOBACILLUS TITLE 2 THERMODENITRIFICANS COMPND MOL_ID: 1; COMPND 2 MOLECULE: NITRITE REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACILLUS THERMODENITRIFICANS NG80-2; SOURCE 3 ORGANISM_TAXID: 420246; SOURCE 4 GENE: NIRK; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET22B KEYWDS BETA BARREL, NITRITE REDUCTION, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.FUKUDA,T.INOUE REVDAT 2 08-NOV-23 3X1F 1 REMARK SEQADV LINK REVDAT 1 18-NOV-15 3X1F 0 JRNL AUTH Y.FUKUDA,T.INOUE JRNL TITL STRUCTURAL EVIDENCE OF THE FLEXIBILITY OF THE CUM SITE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 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) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.36 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 88.2 REMARK 3 NUMBER OF REFLECTIONS : 76384 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) : 0.093 REMARK 3 R VALUE (WORKING SET) : 0.092 REMARK 3 FREE R VALUE : 0.115 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4011 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) : 1.35 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.39 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5678 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.54 REMARK 3 BIN R VALUE (WORKING SET) : 0.1210 REMARK 3 BIN FREE R VALUE SET COUNT : 282 REMARK 3 BIN FREE R VALUE : 0.1460 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2295 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 39 REMARK 3 SOLVENT ATOMS : 364 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.25 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01000 REMARK 3 B22 (A**2) : -0.01000 REMARK 3 B33 (A**2) : 0.03000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.032 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.032 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.021 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.140 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.986 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.978 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2615 ; 0.019 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2501 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3589 ; 2.024 ; 1.963 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5794 ; 0.898 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 343 ; 8.165 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 108 ;44.246 ;25.370 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 432 ;11.222 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 5 ;12.018 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 389 ; 0.127 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3070 ; 0.011 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 579 ; 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): 1310 ; 1.566 ; 1.084 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1303 ; 1.286 ; 1.074 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1671 ; 1.647 ; 1.630 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1672 ; 1.653 ; 1.632 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1305 ; 4.411 ; 1.348 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1306 ; 4.418 ; 1.349 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1919 ; 4.247 ; 1.910 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3134 ; 4.348 ;10.837 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3135 ; 4.404 ;10.851 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 5116 ; 5.392 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 120 ;36.990 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 5313 ;10.349 ; 5.000 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 : BABINET MODEL WITH 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 3X1F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-NOV-14. REMARK 100 THE DEPOSITION ID IS D_1000097057. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-APR-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL38B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.78000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 76384 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : 2.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.10300 REMARK 200 FOR THE DATA SET : 14.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.39 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.31000 REMARK 200 FOR SHELL : 2.900 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: PDB ENTRY 3WKO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M ACETATE BUFFER, 5.0%(W/V) PEG REMARK 280 4000, 75 MM CUSO4, PH 4.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K 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 57.48850 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 33.19100 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 28.04600 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 57.48850 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 33.19100 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 28.04600 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 57.48850 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 33.19100 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 28.04600 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 66.38200 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 56.09200 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 66.38200 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 56.09200 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 66.38200 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 56.09200 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: 12490 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28150 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -223.0 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 CU CU A 407 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 722 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 863 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 -28 REMARK 465 ASN A -27 REMARK 465 ARG A -26 REMARK 465 ASN A -25 REMARK 465 VAL A -24 REMARK 465 TYR A -23 REMARK 465 ALA A -22 REMARK 465 VAL A -21 REMARK 465 LEU A -20 REMARK 465 SER A -19 REMARK 465 THR A -18 REMARK 465 VAL A -17 REMARK 465 LEU A -16 REMARK 465 ALA A -15 REMARK 465 ALA A -14 REMARK 465 SER A -13 REMARK 465 LEU A -12 REMARK 465 LEU A -11 REMARK 465 ALA A -10 REMARK 465 ALA A -9 REMARK 465 CYS A -8 REMARK 465 ASN A -7 REMARK 465 SER A -6 REMARK 465 GLY A -5 REMARK 465 GLY A -4 REMARK 465 GLU A -3 REMARK 465 GLN A -2 REMARK 465 VAL A -1 REMARK 465 LYS A 0 REMARK 465 ALA A 1 REMARK 465 GLU A 2 REMARK 465 SER A 3 REMARK 465 LYS A 4 REMARK 465 ASN A 5 REMARK 465 LYS A 6 REMARK 465 THR A 7 REMARK 465 ALA A 8 REMARK 465 ALA A 9 REMARK 465 THR A 10 REMARK 465 GLN A 11 REMARK 465 GLN A 12 REMARK 465 SER A 13 REMARK 465 GLU A 14 REMARK 465 PRO A 15 REMARK 465 ASN A 16 REMARK 465 VAL A 17 REMARK 465 GLU A 314 REMARK 465 ASP A 315 REMARK 465 ASP A 316 REMARK 465 GLY A 317 REMARK 465 THR A 318 REMARK 465 GLU A 319 REMARK 465 THR A 320 REMARK 465 SER A 321 REMARK 465 GLY A 322 REMARK 465 HIS A 323 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 239 CD GLU A 239 OE1 -0.073 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PHE A 110 CB - CG - CD1 ANGL. DEV. = 4.2 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 VAL A 92 -22.57 -141.35 REMARK 500 SER A 242 78.03 -116.62 REMARK 500 SER A 274 -0.07 79.37 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 VAL A 292 THR A 293 147.36 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 403 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 39 NE2 REMARK 620 2 HOH A 838 O 103.1 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 404 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 42 NE2 REMARK 620 2 HIS A 83 ND1 98.2 REMARK 620 3 HOH A 559 O 93.3 102.8 REMARK 620 4 HOH A 620 O 173.3 88.2 87.2 REMARK 620 N 1 2 3 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 95 ND1 REMARK 620 2 CYS A 135 SG 138.9 REMARK 620 3 HIS A 143 ND1 100.0 105.3 REMARK 620 4 MET A 148 SD 81.5 113.6 116.9 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 100 NE2 REMARK 620 2 HIS A 134 NE2 111.1 REMARK 620 3 HOH A 861 O 105.3 96.7 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 406 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 167 OD2 REMARK 620 2 ACY A 412 OXT 89.7 REMARK 620 3 HOH A 502 O 92.0 177.8 REMARK 620 4 HOH A 730 O 94.5 91.0 90.3 REMARK 620 5 HOH A 830 O 168.9 87.4 90.7 96.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 406 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 167 OD1 REMARK 620 2 HOH A 502 O 95.2 REMARK 620 3 HOH A 856 O 92.7 97.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 405 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 239 OE2 REMARK 620 2 HOH A 845 O 84.6 REMARK 620 3 HOH A 849 O 105.7 140.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 407 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 MET A 270 SD REMARK 620 2 HOH A 863 O 103.9 REMARK 620 N 1 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 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 411 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY A 412 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY A 413 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3X1E RELATED DB: PDB REMARK 900 RELATED ID: 3X1G RELATED DB: PDB DBREF 3X1F A -28 323 UNP A4IL26 A4IL26_GEOTN 1 352 SEQADV 3X1F MET A 294 UNP A4IL26 HIS 323 ENGINEERED MUTATION SEQRES 1 A 352 MET ASN ARG ASN VAL TYR ALA VAL LEU SER THR VAL LEU SEQRES 2 A 352 ALA ALA SER LEU LEU ALA ALA CYS ASN SER GLY GLY GLU SEQRES 3 A 352 GLN VAL LYS ALA GLU SER LYS ASN LYS THR ALA ALA THR SEQRES 4 A 352 GLN GLN SER GLU PRO ASN VAL ILE ALA ALA HIS LYS GLY SEQRES 5 A 352 VAL ASN GLN ALA PRO VAL PRO LEU LYS MET GLU ARG VAL SEQRES 6 A 352 GLY PRO HIS ASP VAL HIS ILE GLU MET THR ALA GLN ILE SEQRES 7 A 352 THR ASP ILE GLU ILE ASP LYS GLY LYS ILE TYR LYS ALA SEQRES 8 A 352 TRP THR PHE ASN GLY GLN ALA PRO GLY PRO LEU VAL VAL SEQRES 9 A 352 VAL ASN GLU GLY ASP THR ILE HIS PHE THR LEU LYS ASN SEQRES 10 A 352 MET ASP PRO VAL VAL PRO HIS SER MET ASP PHE HIS ALA SEQRES 11 A 352 VAL HIS ALA SER PRO SER LYS ASP PHE ILE ASP VAL MET SEQRES 12 A 352 PRO ASN LYS SER GLY THR PHE THR TYR PRO ALA ASN LYS SEQRES 13 A 352 PRO GLY VAL PHE MET TYR HIS CYS GLY THR LYS PRO VAL SEQRES 14 A 352 LEU GLN HIS ILE ALA ASN GLY MET HIS GLY VAL ILE ILE SEQRES 15 A 352 VAL LYS PRO LYS ASN GLY TYR PRO THR ASP LYS GLU VAL SEQRES 16 A 352 ASP ARG GLU TYR VAL LEU ILE GLN ASN GLU TRP TYR LYS SEQRES 17 A 352 TYR ASN ASP MET ASN ASP PHE GLN ASN GLY VAL PRO SER SEQRES 18 A 352 TYR VAL VAL PHE SER SER LYS ALA LEU LYS PRO GLY ASP SEQRES 19 A 352 PRO ASN THR ASN GLY ASP THR PHE THR LEU LYS GLU LYS SEQRES 20 A 352 PRO LEU LEU ALA LYS VAL GLY GLU LYS ILE ARG LEU TYR SEQRES 21 A 352 ILE ASN ASN VAL GLY PRO ASN GLU VAL SER SER PHE HIS SEQRES 22 A 352 VAL VAL GLY THR VAL PHE ASP ASP VAL TYR LEU ASP GLY SEQRES 23 A 352 ASN PRO ASN ASN HIS LEU GLN GLY MET GLN THR VAL MET SEQRES 24 A 352 LEU PRO ALA SER GLY GLY ALA VAL VAL GLU PHE THR VAL SEQRES 25 A 352 THR ARG PRO GLY THR TYR PRO ILE VAL THR MET GLN PHE SEQRES 26 A 352 ASN HIS ALA GLN LYS GLY ALA VAL ALA MET LEU LYS VAL SEQRES 27 A 352 THR GLU THR GLY GLU ASP ASP GLY THR GLU THR SER GLY SEQRES 28 A 352 HIS HET CU A 401 1 HET CU A 402 1 HET CU A 403 1 HET CU A 404 1 HET CU A 405 2 HET CU A 406 2 HET CU A 407 1 HET ACY A 408 4 HET ACY A 409 4 HET MPD A 410 16 HET MPD A 411 8 HET ACY A 412 4 HET ACY A 413 4 HETNAM CU COPPER (II) ION HETNAM ACY ACETIC ACID HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL FORMUL 2 CU 7(CU 2+) FORMUL 9 ACY 4(C2 H4 O2) FORMUL 11 MPD 2(C6 H14 O2) FORMUL 15 HOH *364(H2 O) HELIX 1 1 ILE A 18 LYS A 22 5 5 HELIX 2 2 SER A 105 PHE A 110 1 6 HELIX 3 3 PRO A 139 ASN A 146 1 8 HELIX 4 4 THR A 162 VAL A 166 5 5 HELIX 5 5 ASP A 182 GLY A 189 1 8 HELIX 6 6 PHE A 213 LYS A 218 1 6 HELIX 7 7 GLN A 295 LYS A 301 1 7 SHEET 1 A 3 LYS A 32 GLY A 37 0 SHEET 2 A 3 ASP A 40 ASP A 55 -1 O HIS A 42 N GLU A 34 SHEET 3 A 3 LYS A 58 PHE A 65 -1 O TYR A 60 N ILE A 52 SHEET 1 B 4 LYS A 32 GLY A 37 0 SHEET 2 B 4 ASP A 40 ASP A 55 -1 O HIS A 42 N GLU A 34 SHEET 3 B 4 ASP A 80 ASN A 88 1 O THR A 85 N ILE A 43 SHEET 4 B 4 SER A 118 ALA A 125 -1 O PHE A 121 N PHE A 84 SHEET 1 C 4 VAL A 74 ASN A 77 0 SHEET 2 C 4 HIS A 149 LYS A 155 1 O LYS A 155 N VAL A 76 SHEET 3 C 4 GLY A 129 HIS A 134 -1 N PHE A 131 O ILE A 152 SHEET 4 C 4 ASP A 98 PHE A 99 -1 N ASP A 98 O HIS A 134 SHEET 1 D 6 TYR A 193 LYS A 199 0 SHEET 2 D 6 ARG A 168 TRP A 177 -1 N ASN A 175 O VAL A 195 SHEET 3 D 6 LYS A 227 GLY A 236 1 O ARG A 229 N ARG A 168 SHEET 4 D 6 GLY A 276 THR A 282 -1 O PHE A 281 N ILE A 228 SHEET 5 D 6 PHE A 250 LEU A 255 -1 N TYR A 254 O VAL A 278 SHEET 6 D 6 HIS A 262 MET A 266 -1 O LEU A 263 N VAL A 253 SHEET 1 E 5 LEU A 220 LYS A 223 0 SHEET 2 E 5 VAL A 304 THR A 310 1 O LYS A 308 N LEU A 220 SHEET 3 E 5 GLY A 287 THR A 293 -1 N GLY A 287 O VAL A 309 SHEET 4 E 5 SER A 241 VAL A 245 -1 N HIS A 244 O VAL A 292 SHEET 5 E 5 VAL A 269 LEU A 271 -1 O LEU A 271 N SER A 241 LINK NE2 HIS A 39 CU CU A 403 1555 1555 2.04 LINK NE2 HIS A 42 CU CU A 404 1555 1555 2.08 LINK ND1 HIS A 83 CU CU A 404 1555 1555 1.99 LINK ND1 HIS A 95 CU CU A 401 1555 1555 2.04 LINK NE2 HIS A 100 CU CU A 402 1555 1555 2.04 LINK NE2 HIS A 134 CU CU A 402 1555 1555 2.08 LINK SG CYS A 135 CU CU A 401 1555 1555 2.19 LINK ND1 HIS A 143 CU CU A 401 1555 1555 1.99 LINK SD MET A 148 CU CU A 401 1555 1555 2.58 LINK OD2 ASP A 167 CU A CU A 406 1555 1555 2.08 LINK OD1 ASP A 167 CU B CU A 406 1555 1555 2.11 LINK OE2 GLU A 239 CU B CU A 405 1555 1555 2.23 LINK SD MET A 270 CU CU A 407 1555 1555 2.40 LINK NE2 HIS A 298 CU A CU A 405 1555 1555 2.16 LINK CU CU A 402 O HOH A 861 1555 1555 2.18 LINK CU CU A 403 O HOH A 838 1555 1555 2.69 LINK CU CU A 404 O HOH A 559 1555 1555 2.26 LINK CU CU A 404 O HOH A 620 1555 1555 2.07 LINK CU B CU A 405 O BHOH A 845 1555 1555 2.38 LINK CU B CU A 405 O BHOH A 849 1555 1555 1.97 LINK CU A CU A 406 OXT ACY A 412 1555 1555 2.06 LINK CU A CU A 406 O HOH A 502 1555 1555 1.90 LINK CU B CU A 406 O HOH A 502 1555 1555 2.49 LINK CU A CU A 406 O HOH A 730 1555 1555 2.40 LINK CU A CU A 406 O HOH A 830 1555 1555 1.99 LINK CU B CU A 406 O HOH A 856 1555 1555 2.26 LINK CU CU A 407 O HOH A 863 1555 1555 2.25 CISPEP 1 ALA A 69 PRO A 70 0 -13.08 CISPEP 2 LYS A 138 PRO A 139 0 -9.94 CISPEP 3 GLY A 236 PRO A 237 0 20.79 SITE 1 AC1 4 HIS A 95 CYS A 135 HIS A 143 MET A 148 SITE 1 AC2 4 HIS A 100 HIS A 134 MET A 294 HOH A 861 SITE 1 AC3 2 HIS A 39 HOH A 838 SITE 1 AC4 5 HIS A 42 GLU A 53 HIS A 83 HOH A 559 SITE 2 AC4 5 HOH A 620 SITE 1 AC5 6 PRO A 191 GLU A 239 HIS A 298 HOH A 530 SITE 2 AC5 6 HOH A 845 HOH A 849 SITE 1 AC6 6 ASP A 167 ACY A 412 HOH A 502 HOH A 730 SITE 2 AC6 6 HOH A 830 HOH A 856 SITE 1 AC7 2 MET A 270 HOH A 863 SITE 1 AC8 5 ASP A 98 HIS A 134 VAL A 246 HOH A 733 SITE 2 AC8 5 HOH A 861 SITE 1 AC9 2 HOH A 507 HOH A 741 SITE 1 BC1 8 ASP A 163 VAL A 166 ASP A 167 ARG A 168 SITE 2 BC1 8 GLU A 169 ARG A 229 HOH A 669 HOH A 829 SITE 1 BC2 4 ASP A 55 SER A 192 GLN A 300 HOH A 595 SITE 1 BC3 6 ASP A 167 VAL A 224 GLY A 225 CU A 406 SITE 2 BC3 6 HOH A 501 HOH A 830 SITE 1 BC4 8 PRO A 128 ASN A 258 ASN A 260 HOH A 567 SITE 2 BC4 8 HOH A 661 HOH A 705 HOH A 707 HOH A 752 CRYST1 114.977 114.977 84.138 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 0.008697 0.005021 0.000000 0.00000 SCALE2 0.000000 0.010043 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011885 0.00000