HEADER HYDROLASE 25-SEP-14 4WIF TITLE CRYSTAL STRUCTURE OF E47Q MUTANT CYTIDINE DEAMINASE FROM MYCOBACTERIUM TITLE 2 TUBERCULOSIS (MTCDA E47Q) COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTIDINE DEAMINASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: CDD,CYTIDINE AMINOHYDROLASE,CDA; COMPND 5 EC: 3.5.4.5; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 1773; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MTCDA E47Q, CYTIDINE DEAMINASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR D.B.TRIVELLA,A.Z.SANCHEZ-QUITIAN,L.A.BASSO,D.S.SANTOS REVDAT 2 27-DEC-23 4WIF 1 REMARK LINK ATOM REVDAT 1 09-SEP-15 4WIF 0 JRNL AUTH A.Z.SANCHEZ-QUITIAN,V.RODRIGUES-JUNIOR,J.G.REHM,P.EICHLER, JRNL AUTH 2 D.B.B.TRIVELLA,C.V.BIZARRO,L.A.BASSO,D.S.SANTOS JRNL TITL CRYSTAL STRUCTURE OF E47Q MUTANT CYTIDINE DEAMINASE FROM JRNL TITL 2 MYCOBACTERIUM TUBERCULOSIS (MTCDA E47Q) JRNL REF RSC ADV 2015 JRNL REFN ESSN 2046-2069 JRNL DOI 10.1039/C4RA13748E REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.65 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 28844 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) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1321 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1688 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.34 REMARK 3 BIN R VALUE (WORKING SET) : 0.2300 REMARK 3 BIN FREE R VALUE SET COUNT : 83 REMARK 3 BIN FREE R VALUE : 0.2610 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1762 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 280 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.32 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : -0.03000 REMARK 3 B33 (A**2) : 0.02000 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): 0.140 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.133 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.089 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.774 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.938 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.914 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1830 ; 0.007 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1760 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2495 ; 1.222 ; 1.966 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4009 ; 0.765 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 252 ; 5.011 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 70 ;35.968 ;22.857 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 266 ;13.347 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;13.954 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 290 ; 0.076 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2172 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 430 ; 0.001 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 4WIF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-SEP-14. REMARK 100 THE DEPOSITION ID IS D_1000203884. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-MAY-14 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 : LNLS REMARK 200 BEAMLINE : W01B-MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.459 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.20 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29558 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.690 REMARK 200 RESOLUTION RANGE LOW (A) : 111.780 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.9 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06400 REMARK 200 FOR THE DATA SET : 8.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.69 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.78 REMARK 200 COMPLETENESS FOR SHELL (%) : 79.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 0.41100 REMARK 200 R SYM FOR SHELL (I) : 0.41100 REMARK 200 FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL 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 (%): 51.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES PH7.5; 4.3 M SODIUM REMARK 280 CHLORIDE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.81000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 55.81000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 32.79500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 38.92000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 32.79500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 38.92000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 55.81000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 32.79500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 38.92000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 55.81000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 32.79500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 38.92000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8800 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17210 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -231.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 -77.84000 REMARK 350 BIOMT3 2 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 302 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 314 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 304 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 347 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 PRO A 2 REMARK 465 LEU A 125 REMARK 465 ASP A 126 REMARK 465 ASP A 127 REMARK 465 LEU A 128 REMARK 465 PRO A 129 REMARK 465 ARG A 130 REMARK 465 GLU A 131 REMARK 465 ARG A 132 REMARK 465 ARG A 133 REMARK 465 MET B 1 REMARK 465 PRO B 2 REMARK 465 ASP B 3 REMARK 465 LEU B 125 REMARK 465 ASP B 126 REMARK 465 ASP B 127 REMARK 465 LEU B 128 REMARK 465 PRO B 129 REMARK 465 ARG B 130 REMARK 465 GLU B 131 REMARK 465 ARG B 132 REMARK 465 ARG B 133 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ARG A 26 NE REMARK 480 ARG B 26 NE CZ REMARK 480 ARG B 111 NE 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 350 O HOH A 353 1.87 REMARK 500 O HOH B 335 O HOH B 341 1.93 REMARK 500 O HOH A 307 O HOH A 339 2.01 REMARK 500 O HOH A 321 O HOH A 322 2.06 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 346 O HOH A 346 3555 0.50 REMARK 500 O HOH B 337 O HOH B 337 3554 1.62 REMARK 500 O HOH B 315 O HOH B 348 4545 2.04 REMARK 500 O HOH B 344 O HOH B 344 3554 2.15 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 ARG A 26 CD ARG A 26 NE 0.290 REMARK 500 ARG A 26 NE ARG A 26 CZ 0.176 REMARK 500 ARG B 26 CD ARG B 26 NE 0.216 REMARK 500 ARG B 26 CZ ARG B 26 NH1 0.683 REMARK 500 ARG B 26 CZ ARG B 26 NH2 0.080 REMARK 500 ARG B 111 CD ARG B 111 NE 0.151 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 ARG A 26 CG - CD - NE ANGL. DEV. = -28.0 DEGREES REMARK 500 ARG A 26 CD - NE - CZ ANGL. DEV. = 18.6 DEGREES REMARK 500 ARG A 26 NE - CZ - NH1 ANGL. DEV. = -6.7 DEGREES REMARK 500 ARG A 26 NE - CZ - NH2 ANGL. DEV. = 5.3 DEGREES REMARK 500 ARG B 26 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 ARG B 26 NE - CZ - NH2 ANGL. DEV. = -9.6 DEGREES REMARK 500 ARG B 111 CD - NE - CZ ANGL. DEV. = 21.7 DEGREES REMARK 500 ARG B 111 NE - CZ - NH1 ANGL. DEV. = -9.7 DEGREES REMARK 500 ARG B 111 NE - CZ - NH2 ANGL. DEV. = 8.1 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 B 110 -71.95 -77.58 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 26 0.08 SIDE CHAIN REMARK 500 ARG B 26 0.08 SIDE CHAIN REMARK 500 ARG B 111 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 427 DISTANCE = 6.46 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 ZN A 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 56 SG REMARK 620 2 CYS A 89 SG 117.7 REMARK 620 3 CYS A 92 SG 99.9 113.3 REMARK 620 4 HOH A 307 O 112.3 104.5 109.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 56 SG REMARK 620 2 CYS B 89 SG 115.3 REMARK 620 3 CYS B 92 SG 101.8 114.8 REMARK 620 4 HOH B 316 O 112.5 105.8 106.6 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4WIG RELATED DB: PDB DBREF 4WIF A 1 133 UNP P9WPH2 CDD_MYCTO 1 133 DBREF 4WIF B 1 133 UNP P9WPH2 CDD_MYCTO 1 133 SEQADV 4WIF GLN A 47 UNP P9WPH2 GLU 47 ENGINEERED MUTATION SEQADV 4WIF GLN B 47 UNP P9WPH2 GLU 47 ENGINEERED MUTATION SEQRES 1 A 133 MET PRO ASP VAL ASP TRP ASN MET LEU ARG GLY ASN ALA SEQRES 2 A 133 THR GLN ALA ALA ALA GLY ALA TYR VAL PRO TYR SER ARG SEQRES 3 A 133 PHE ALA VAL GLY ALA ALA ALA LEU VAL ASP ASP GLY ARG SEQRES 4 A 133 VAL VAL THR GLY CYS ASN VAL GLN ASN VAL SER TYR GLY SEQRES 5 A 133 LEU THR LEU CYS ALA GLU CYS ALA VAL VAL CYS ALA LEU SEQRES 6 A 133 HIS SER THR GLY GLY GLY ARG LEU LEU ALA LEU ALA CYS SEQRES 7 A 133 VAL ASP GLY HIS GLY SER VAL LEU MET PRO CYS GLY ARG SEQRES 8 A 133 CYS ARG GLN VAL LEU LEU GLU HIS GLY GLY SER GLU LEU SEQRES 9 A 133 LEU ILE ASP HIS PRO VAL ARG PRO ARG ARG LEU GLY ASP SEQRES 10 A 133 LEU LEU PRO ASP ALA PHE GLY LEU ASP ASP LEU PRO ARG SEQRES 11 A 133 GLU ARG ARG SEQRES 1 B 133 MET PRO ASP VAL ASP TRP ASN MET LEU ARG GLY ASN ALA SEQRES 2 B 133 THR GLN ALA ALA ALA GLY ALA TYR VAL PRO TYR SER ARG SEQRES 3 B 133 PHE ALA VAL GLY ALA ALA ALA LEU VAL ASP ASP GLY ARG SEQRES 4 B 133 VAL VAL THR GLY CYS ASN VAL GLN ASN VAL SER TYR GLY SEQRES 5 B 133 LEU THR LEU CYS ALA GLU CYS ALA VAL VAL CYS ALA LEU SEQRES 6 B 133 HIS SER THR GLY GLY GLY ARG LEU LEU ALA LEU ALA CYS SEQRES 7 B 133 VAL ASP GLY HIS GLY SER VAL LEU MET PRO CYS GLY ARG SEQRES 8 B 133 CYS ARG GLN VAL LEU LEU GLU HIS GLY GLY SER GLU LEU SEQRES 9 B 133 LEU ILE ASP HIS PRO VAL ARG PRO ARG ARG LEU GLY ASP SEQRES 10 B 133 LEU LEU PRO ASP ALA PHE GLY LEU ASP ASP LEU PRO ARG SEQRES 11 B 133 GLU ARG ARG HET ZN A 201 1 HET ZN B 201 1 HETNAM ZN ZINC ION FORMUL 3 ZN 2(ZN 2+) FORMUL 5 HOH *280(H2 O) HELIX 1 AA1 ASP A 5 ALA A 17 1 13 HELIX 2 AA2 ALA A 18 ALA A 20 5 3 HELIX 3 AA3 SER A 50 THR A 54 5 5 HELIX 4 AA4 CYS A 56 THR A 68 1 13 HELIX 5 AA5 CYS A 89 GLY A 101 1 13 HELIX 6 AA6 LEU A 115 LEU A 119 1 5 HELIX 7 AA7 ASP B 5 ALA B 18 1 14 HELIX 8 AA8 SER B 50 THR B 54 5 5 HELIX 9 AA9 CYS B 56 THR B 68 1 13 HELIX 10 AB1 CYS B 89 GLY B 101 1 13 HELIX 11 AB2 LEU B 115 LEU B 119 1 5 SHEET 1 AA1 5 VAL A 40 CYS A 44 0 SHEET 2 AA1 5 VAL A 29 VAL A 35 -1 N ALA A 33 O VAL A 41 SHEET 3 AA1 5 LEU A 73 ASP A 80 -1 O LEU A 74 N LEU A 34 SHEET 4 AA1 5 LEU A 105 ILE A 106 1 O LEU A 105 N LEU A 76 SHEET 5 AA1 5 ARG A 113 ARG A 114 -1 O ARG A 113 N ILE A 106 SHEET 1 AA2 5 VAL B 40 CYS B 44 0 SHEET 2 AA2 5 VAL B 29 VAL B 35 -1 N ALA B 33 O VAL B 41 SHEET 3 AA2 5 LEU B 73 ASP B 80 -1 O LEU B 74 N LEU B 34 SHEET 4 AA2 5 LEU B 105 ILE B 106 1 O LEU B 105 N LEU B 76 SHEET 5 AA2 5 ARG B 113 ARG B 114 -1 O ARG B 113 N ILE B 106 LINK SG CYS A 56 ZN ZN A 201 1555 1555 2.35 LINK SG CYS A 89 ZN ZN A 201 1555 1555 2.28 LINK SG CYS A 92 ZN ZN A 201 1555 1555 2.29 LINK ZN ZN A 201 O HOH A 307 1555 1555 2.12 LINK SG CYS B 56 ZN ZN B 201 1555 1555 2.30 LINK SG CYS B 89 ZN ZN B 201 1555 1555 2.32 LINK SG CYS B 92 ZN ZN B 201 1555 1555 2.32 LINK ZN ZN B 201 O HOH B 316 1555 1555 1.89 SITE 1 AC1 5 CYS A 56 CYS A 89 CYS A 92 HOH A 307 SITE 2 AC1 5 HOH A 339 SITE 1 AC2 4 CYS B 56 CYS B 89 CYS B 92 HOH B 316 CRYST1 65.590 77.840 111.620 90.00 90.00 90.00 C 2 2 21 16 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 0.015246 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012847 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008959 0.00000