HEADER LIGASE 17-APR-15 4ZDJ TITLE CRYSTAL STRUCTURE OF THE M. TUBERCULOSIS CTP SYNTHASE PYRG IN COMPLEX TITLE 2 WITH TWO UTP MOLECULES COMPND MOL_ID: 1; COMPND 2 MOLECULE: CTP SYNTHASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CTP SYNTHETASE,UTP--AMMONIA LIGASE; COMPND 5 EC: 6.3.4.2; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS (STRAIN ATCC 25618 / SOURCE 3 H37RV); SOURCE 4 ORGANISM_TAXID: 83332; SOURCE 5 GENE: PYRG, RV1699, MTCI125.21; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET-28A KEYWDS CTP SYNTHASE, PYRG, AMIDOTRANSFERASE, UTP, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR M.BELLINZONI,N.BARILONE,P.M.ALZARI REVDAT 3 10-JAN-24 4ZDJ 1 LINK REVDAT 2 05-AUG-15 4ZDJ 1 JRNL REVDAT 1 01-JUL-15 4ZDJ 0 JRNL AUTH G.MORI,L.R.CHIARELLI,M.ESPOSITO,V.MAKAROV,M.BELLINZONI, JRNL AUTH 2 R.C.HARTKOORN,G.DEGIACOMI,F.BOLDRIN,S.EKINS, JRNL AUTH 3 A.L.DE JESUS LOPES RIBEIRO,L.B.MARINO,I.CENTAROVA, JRNL AUTH 4 Z.SVETLIKOVA,J.BLASKO,E.KAZAKOVA,A.LEPIOSHKIN,N.BARILONE, JRNL AUTH 5 G.ZANONI,A.PORTA,M.FONDI,R.FANI,A.R.BAULARD,K.MIKUSOVA, JRNL AUTH 6 P.M.ALZARI,R.MANGANELLI,L.P.DE CARVALHO,G.RICCARDI,S.T.COLE, JRNL AUTH 7 M.R.PASCA JRNL TITL THIOPHENECARBOXAMIDE DERIVATIVES ACTIVATED BY ETHA KILL JRNL TITL 2 MYCOBACTERIUM TUBERCULOSIS BY INHIBITING THE CTP SYNTHETASE JRNL TITL 3 PYRG. JRNL REF CHEM.BIOL. V. 22 917 2015 JRNL REFN ISSN 1074-5521 JRNL PMID 26097035 JRNL DOI 10.1016/J.CHEMBIOL.2015.05.016 REMARK 2 REMARK 2 RESOLUTION. 1.99 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.1 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 56691 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) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2891 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.99 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.04 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.78 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 3749 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2117 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3529 REMARK 3 BIN R VALUE (WORKING SET) : 0.2106 REMARK 3 BIN FREE R VALUE : 0.2293 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.87 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 220 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4090 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 66 REMARK 3 SOLVENT ATOMS : 226 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 37.03 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.89 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.93870 REMARK 3 B22 (A**2) : -2.43120 REMARK 3 B33 (A**2) : -2.50740 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.222 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.112 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.105 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.111 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.105 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.950 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 4266 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 5823 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 1941 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 95 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 648 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 4266 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 1 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 558 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 5227 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 0.97 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.61 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 2.45 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|5 - A|136 } REMARK 3 ORIGIN FOR THE GROUP (A): 12.6485 9.8312 56.0467 REMARK 3 T TENSOR REMARK 3 T11: -0.0460 T22: 0.0038 REMARK 3 T33: -0.0461 T12: 0.0042 REMARK 3 T13: -0.0013 T23: 0.0359 REMARK 3 L TENSOR REMARK 3 L11: 0.6313 L22: 0.5169 REMARK 3 L33: 0.3605 L12: 0.3578 REMARK 3 L13: -0.1601 L23: -0.1810 REMARK 3 S TENSOR REMARK 3 S11: -0.0507 S12: 0.1299 S13: 0.0315 REMARK 3 S21: -0.0339 S22: 0.0301 S23: -0.0536 REMARK 3 S31: 0.0297 S32: 0.0927 S33: 0.0206 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { A|137 - A|162 } REMARK 3 ORIGIN FOR THE GROUP (A): 17.3271 8.8493 60.1005 REMARK 3 T TENSOR REMARK 3 T11: -0.0322 T22: 0.0231 REMARK 3 T33: -0.0148 T12: -0.0088 REMARK 3 T13: 0.0090 T23: 0.0380 REMARK 3 L TENSOR REMARK 3 L11: 4.3218 L22: 1.9664 REMARK 3 L33: 1.3504 L12: -0.2925 REMARK 3 L13: 0.2134 L23: 0.8420 REMARK 3 S TENSOR REMARK 3 S11: -0.0225 S12: 0.2997 S13: -0.0698 REMARK 3 S21: -0.1482 S22: 0.0370 S23: -0.2221 REMARK 3 S31: -0.0346 S32: 0.3388 S33: -0.0145 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: { A|163 - A|181 } REMARK 3 ORIGIN FOR THE GROUP (A): 16.2942 -0.3453 67.0201 REMARK 3 T TENSOR REMARK 3 T11: 0.0106 T22: -0.0071 REMARK 3 T33: -0.0392 T12: 0.0182 REMARK 3 T13: -0.0022 T23: 0.0262 REMARK 3 L TENSOR REMARK 3 L11: 2.7868 L22: 3.5707 REMARK 3 L33: 0.2968 L12: -0.0370 REMARK 3 L13: -1.2620 L23: 0.1005 REMARK 3 S TENSOR REMARK 3 S11: -0.0242 S12: -0.0123 S13: -0.1754 REMARK 3 S21: 0.0686 S22: -0.0345 S23: -0.2299 REMARK 3 S31: 0.1069 S32: 0.1246 S33: 0.0588 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: { A|182 - A|300 } REMARK 3 ORIGIN FOR THE GROUP (A): 16.8019 20.6680 75.5494 REMARK 3 T TENSOR REMARK 3 T11: -0.0427 T22: -0.0307 REMARK 3 T33: -0.0254 T12: -0.0289 REMARK 3 T13: -0.0219 T23: 0.0292 REMARK 3 L TENSOR REMARK 3 L11: 0.5646 L22: 0.5836 REMARK 3 L33: 1.2794 L12: 0.2320 REMARK 3 L13: -0.1219 L23: -0.3346 REMARK 3 S TENSOR REMARK 3 S11: 0.0293 S12: -0.0274 S13: 0.1088 REMARK 3 S21: 0.0957 S22: -0.0562 S23: -0.0933 REMARK 3 S31: -0.1641 S32: 0.1732 S33: 0.0269 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: { A|301 - A|395 } REMARK 3 ORIGIN FOR THE GROUP (A): 5.6119 38.7213 46.5231 REMARK 3 T TENSOR REMARK 3 T11: -0.0670 T22: -0.1087 REMARK 3 T33: 0.0485 T12: 0.0233 REMARK 3 T13: -0.0105 T23: 0.0985 REMARK 3 L TENSOR REMARK 3 L11: 3.2669 L22: 0.8520 REMARK 3 L33: 1.3190 L12: 0.0860 REMARK 3 L13: 0.4672 L23: -0.1741 REMARK 3 S TENSOR REMARK 3 S11: -0.0206 S12: 0.0260 S13: 0.4977 REMARK 3 S21: 0.0888 S22: -0.0183 S23: 0.1516 REMARK 3 S31: -0.2172 S32: -0.1032 S33: 0.0389 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: { A|396 - A|512 } REMARK 3 ORIGIN FOR THE GROUP (A): 11.9336 31.2284 30.0307 REMARK 3 T TENSOR REMARK 3 T11: -0.1182 T22: 0.0617 REMARK 3 T33: -0.0925 T12: -0.0129 REMARK 3 T13: -0.0003 T23: 0.1680 REMARK 3 L TENSOR REMARK 3 L11: 3.2237 L22: 1.3010 REMARK 3 L33: 1.0060 L12: -0.2775 REMARK 3 L13: 0.4546 L23: -0.1154 REMARK 3 S TENSOR REMARK 3 S11: 0.0159 S12: 0.6408 S13: 0.3284 REMARK 3 S21: -0.1927 S22: -0.0320 S23: 0.0439 REMARK 3 S31: -0.0489 S32: 0.0397 S33: 0.0161 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: { A|513 - A|552 } REMARK 3 ORIGIN FOR THE GROUP (A): 17.0444 38.5971 44.6529 REMARK 3 T TENSOR REMARK 3 T11: -0.0412 T22: -0.0318 REMARK 3 T33: 0.0279 T12: -0.0503 REMARK 3 T13: -0.0066 T23: 0.1317 REMARK 3 L TENSOR REMARK 3 L11: 1.8966 L22: 0.9480 REMARK 3 L33: 0.7991 L12: -0.1312 REMARK 3 L13: 0.5854 L23: -0.2126 REMARK 3 S TENSOR REMARK 3 S11: -0.0650 S12: 0.2246 S13: 0.4394 REMARK 3 S21: -0.0013 S22: 0.0167 S23: 0.0843 REMARK 3 S31: -0.2284 S32: 0.1959 S33: 0.0484 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4ZDJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-APR-15. REMARK 100 THE DEPOSITION ID IS D_1000209071. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-MAY-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9801 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 : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 56696 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.990 REMARK 200 RESOLUTION RANGE LOW (A) : 48.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.99 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.04 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.71700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1VCN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 17% PEG20000, 100 MM MGCL2, 100 MM REMARK 280 TRIS-HCL PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 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+1/2 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 0.00000 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 0.00000 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 39.70500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 66.36500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 78.81500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 39.70500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 66.36500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 78.81500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 39.70500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 66.36500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 78.81500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 39.70500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 66.36500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 78.81500 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: 20260 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 71000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -155.0 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 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 157.63000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 157.63000 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 908 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 925 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 GLY A 0 REMARK 465 MET A 1 REMARK 465 ARG A 2 REMARK 465 LYS A 3 REMARK 465 HIS A 4 REMARK 465 PRO A 430 REMARK 465 ASP A 431 REMARK 465 GLN A 432 REMARK 465 GLU A 433 REMARK 465 GLU A 434 REMARK 465 ILE A 435 REMARK 465 VAL A 436 REMARK 465 ALA A 437 REMARK 465 GLY A 438 REMARK 465 GLU A 439 REMARK 465 ALA A 440 REMARK 465 ASP A 441 REMARK 465 LEU A 442 REMARK 465 LEU A 553 REMARK 465 LEU A 554 REMARK 465 PRO A 555 REMARK 465 VAL A 556 REMARK 465 GLU A 557 REMARK 465 ILE A 558 REMARK 465 PRO A 559 REMARK 465 GLU A 560 REMARK 465 ILE A 561 REMARK 465 PRO A 562 REMARK 465 GLU A 563 REMARK 465 HIS A 564 REMARK 465 THR A 565 REMARK 465 PRO A 566 REMARK 465 ASN A 567 REMARK 465 GLY A 568 REMARK 465 SER A 569 REMARK 465 SER A 570 REMARK 465 HIS A 571 REMARK 465 ARG A 572 REMARK 465 ASP A 573 REMARK 465 GLY A 574 REMARK 465 VAL A 575 REMARK 465 GLY A 576 REMARK 465 GLN A 577 REMARK 465 PRO A 578 REMARK 465 LEU A 579 REMARK 465 PRO A 580 REMARK 465 GLU A 581 REMARK 465 PRO A 582 REMARK 465 ALA A 583 REMARK 465 SER A 584 REMARK 465 ARG A 585 REMARK 465 GLY A 586 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASP A 357 CG OD1 OD2 REMARK 470 ARG A 514 CG CD NE CZ NH1 NH2 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 18 -61.41 73.06 REMARK 500 CYS A 393 -94.28 57.42 REMARK 500 ARG A 475 73.04 -154.87 REMARK 500 HIS A 524 78.12 -118.45 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 MG A 603 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 UTP A 601 O1A REMARK 620 2 UTP A 601 O2B 95.0 REMARK 620 3 UTP A 601 O2G 97.7 96.1 REMARK 620 4 HOH A 801 O 86.0 177.1 86.4 REMARK 620 5 HOH A 850 O 90.1 89.7 169.8 87.6 REMARK 620 6 HOH A 884 O 166.3 95.9 89.3 82.7 81.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 604 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 UTP A 602 O2B REMARK 620 2 UTP A 602 O2G 88.0 REMARK 620 3 HOH A 701 O 83.6 87.8 REMARK 620 4 HOH A 702 O 167.7 86.3 85.3 REMARK 620 5 HOH A 722 O 84.7 172.7 90.7 100.7 REMARK 620 6 HOH A 901 O 92.5 93.9 175.7 98.8 87.1 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 UTP A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue UTP A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 605 DBREF 4ZDJ A 1 586 UNP P9WHK7 PYRG_MYCTU 1 586 SEQADV 4ZDJ GLY A 0 UNP P9WHK7 EXPRESSION TAG SEQRES 1 A 587 GLY MET ARG LYS HIS PRO GLN THR ALA THR LYS HIS LEU SEQRES 2 A 587 PHE VAL SER GLY GLY VAL ALA SER SER LEU GLY LYS GLY SEQRES 3 A 587 LEU THR ALA SER SER LEU GLY GLN LEU LEU THR ALA ARG SEQRES 4 A 587 GLY LEU HIS VAL THR MET GLN LYS LEU ASP PRO TYR LEU SEQRES 5 A 587 ASN VAL ASP PRO GLY THR MET ASN PRO PHE GLN HIS GLY SEQRES 6 A 587 GLU VAL PHE VAL THR GLU ASP GLY ALA GLU THR ASP LEU SEQRES 7 A 587 ASP VAL GLY HIS TYR GLU ARG PHE LEU ASP ARG ASN LEU SEQRES 8 A 587 PRO GLY SER ALA ASN VAL THR THR GLY GLN VAL TYR SER SEQRES 9 A 587 THR VAL ILE ALA LYS GLU ARG ARG GLY GLU TYR LEU GLY SEQRES 10 A 587 ASP THR VAL GLN VAL ILE PRO HIS ILE THR ASP GLU ILE SEQRES 11 A 587 LYS ARG ARG ILE LEU ALA MET ALA GLN PRO ASP ALA ASP SEQRES 12 A 587 GLY ASN ARG PRO ASP VAL VAL ILE THR GLU ILE GLY GLY SEQRES 13 A 587 THR VAL GLY ASP ILE GLU SER GLN PRO PHE LEU GLU ALA SEQRES 14 A 587 ALA ARG GLN VAL ARG HIS TYR LEU GLY ARG GLU ASP VAL SEQRES 15 A 587 PHE PHE LEU HIS VAL SER LEU VAL PRO TYR LEU ALA PRO SEQRES 16 A 587 SER GLY GLU LEU LYS THR LYS PRO THR GLN HIS SER VAL SEQRES 17 A 587 ALA ALA LEU ARG SER ILE GLY ILE THR PRO ASP ALA LEU SEQRES 18 A 587 ILE LEU ARG CYS ASP ARG ASP VAL PRO GLU ALA LEU LYS SEQRES 19 A 587 ASN LYS ILE ALA LEU MET CYS ASP VAL ASP ILE ASP GLY SEQRES 20 A 587 VAL ILE SER THR PRO ASP ALA PRO SER ILE TYR ASP ILE SEQRES 21 A 587 PRO LYS VAL LEU HIS ARG GLU GLU LEU ASP ALA PHE VAL SEQRES 22 A 587 VAL ARG ARG LEU ASN LEU PRO PHE ARG ASP VAL ASP TRP SEQRES 23 A 587 THR GLU TRP ASP ASP LEU LEU ARG ARG VAL HIS GLU PRO SEQRES 24 A 587 HIS GLU THR VAL ARG ILE ALA LEU VAL GLY LYS TYR VAL SEQRES 25 A 587 GLU LEU SER ASP ALA TYR LEU SER VAL ALA GLU ALA LEU SEQRES 26 A 587 ARG ALA GLY GLY PHE LYS HIS ARG ALA LYS VAL GLU ILE SEQRES 27 A 587 CYS TRP VAL ALA SER ASP GLY CYS GLU THR THR SER GLY SEQRES 28 A 587 ALA ALA ALA ALA LEU GLY ASP VAL HIS GLY VAL LEU ILE SEQRES 29 A 587 PRO GLY GLY PHE GLY ILE ARG GLY ILE GLU GLY LYS ILE SEQRES 30 A 587 GLY ALA ILE ALA TYR ALA ARG ALA ARG GLY LEU PRO VAL SEQRES 31 A 587 LEU GLY LEU CYS LEU GLY LEU GLN CYS ILE VAL ILE GLU SEQRES 32 A 587 ALA ALA ARG SER VAL GLY LEU THR ASN ALA ASN SER ALA SEQRES 33 A 587 GLU PHE ASP PRO ASP THR PRO ASP PRO VAL ILE ALA THR SEQRES 34 A 587 MET PRO ASP GLN GLU GLU ILE VAL ALA GLY GLU ALA ASP SEQRES 35 A 587 LEU GLY GLY THR MET ARG LEU GLY SER TYR PRO ALA VAL SEQRES 36 A 587 LEU GLU PRO ASP SER VAL VAL ALA GLN ALA TYR GLN THR SEQRES 37 A 587 THR GLN VAL SER GLU ARG HIS ARG HIS ARG TYR GLU VAL SEQRES 38 A 587 ASN ASN ALA TYR ARG ASP LYS ILE ALA GLU SER GLY LEU SEQRES 39 A 587 ARG PHE SER GLY THR SER PRO ASP GLY HIS LEU VAL GLU SEQRES 40 A 587 PHE VAL GLU TYR PRO PRO ASP ARG HIS PRO PHE VAL VAL SEQRES 41 A 587 GLY THR GLN ALA HIS PRO GLU LEU LYS SER ARG PRO THR SEQRES 42 A 587 ARG PRO HIS PRO LEU PHE VAL ALA PHE VAL GLY ALA ALA SEQRES 43 A 587 ILE ASP TYR LYS ALA GLY GLU LEU LEU PRO VAL GLU ILE SEQRES 44 A 587 PRO GLU ILE PRO GLU HIS THR PRO ASN GLY SER SER HIS SEQRES 45 A 587 ARG ASP GLY VAL GLY GLN PRO LEU PRO GLU PRO ALA SER SEQRES 46 A 587 ARG GLY HET UTP A 601 29 HET UTP A 602 29 HET MG A 603 1 HET MG A 604 1 HET GOL A 605 6 HETNAM UTP URIDINE 5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 UTP 2(C9 H15 N2 O15 P3) FORMUL 4 MG 2(MG 2+) FORMUL 6 GOL C3 H8 O3 FORMUL 7 HOH *226(H2 O) HELIX 1 AA1 GLY A 23 ARG A 38 1 16 HELIX 2 AA2 ASP A 54 MET A 58 5 5 HELIX 3 AA3 ASN A 59 GLY A 64 1 6 HELIX 4 AA4 LEU A 77 ASP A 87 1 11 HELIX 5 AA5 PRO A 91 SER A 93 5 3 HELIX 6 AA6 THR A 98 ARG A 111 1 14 HELIX 7 AA7 GLN A 120 MET A 136 1 17 HELIX 8 AA8 SER A 162 GLY A 177 1 16 HELIX 9 AA9 THR A 200 ILE A 213 1 14 HELIX 10 AB1 PRO A 229 ASP A 241 1 13 HELIX 11 AB2 ASP A 243 ASP A 245 5 3 HELIX 12 AB3 SER A 255 TYR A 257 5 3 HELIX 13 AB4 ASP A 258 GLU A 266 1 9 HELIX 14 AB5 GLU A 267 LEU A 276 1 10 HELIX 15 AB6 TRP A 285 GLU A 297 1 13 HELIX 16 AB7 LEU A 313 ALA A 316 5 4 HELIX 17 AB8 TYR A 317 HIS A 331 1 15 HELIX 18 AB9 ASP A 343 GLU A 346 5 4 HELIX 19 AC1 THR A 347 GLY A 356 1 10 HELIX 20 AC2 ILE A 372 GLY A 386 1 15 HELIX 21 AC3 CYS A 393 VAL A 407 1 15 HELIX 22 AC4 SER A 459 GLN A 466 1 8 HELIX 23 AC5 TYR A 484 ALA A 489 1 6 HELIX 24 AC6 GLU A 490 GLY A 492 5 3 HELIX 25 AC7 HIS A 524 SER A 529 5 6 HELIX 26 AC8 HIS A 535 GLU A 552 1 18 SHEET 1 AA1 7 ASN A 95 THR A 97 0 SHEET 2 AA1 7 VAL A 42 ASP A 48 1 N ASP A 48 O VAL A 96 SHEET 3 AA1 7 VAL A 148 ILE A 153 1 O GLU A 152 N GLN A 45 SHEET 4 AA1 7 LYS A 10 GLY A 16 1 N VAL A 14 O ILE A 153 SHEET 5 AA1 7 VAL A 181 LEU A 188 1 O LEU A 184 N PHE A 13 SHEET 6 AA1 7 ALA A 219 CYS A 224 1 O ILE A 221 N SER A 187 SHEET 7 AA1 7 VAL A 247 PRO A 251 1 O ILE A 248 N LEU A 222 SHEET 1 AA2 2 PHE A 67 VAL A 68 0 SHEET 2 AA2 2 GLU A 74 THR A 75 -1 O THR A 75 N PHE A 67 SHEET 1 AA3 2 TYR A 191 LEU A 192 0 SHEET 2 AA3 2 GLU A 197 LEU A 198 -1 O GLU A 197 N LEU A 192 SHEET 1 AA4 9 ALA A 333 ALA A 341 0 SHEET 2 AA4 9 GLU A 300 GLY A 308 1 N VAL A 302 O GLU A 336 SHEET 3 AA4 9 GLY A 360 ILE A 363 1 O LEU A 362 N ALA A 305 SHEET 4 AA4 9 VAL A 389 LEU A 392 1 O LEU A 392 N ILE A 363 SHEET 5 AA4 9 VAL A 518 THR A 521 1 O VAL A 519 N VAL A 389 SHEET 6 AA4 9 VAL A 505 GLU A 509 -1 N VAL A 508 O GLY A 520 SHEET 7 AA4 9 ARG A 494 THR A 498 -1 N ARG A 494 O GLU A 509 SHEET 8 AA4 9 ARG A 447 LEU A 455 -1 N VAL A 454 O THR A 498 SHEET 9 AA4 9 GLN A 469 HIS A 476 -1 O HIS A 476 N ARG A 447 SHEET 1 AA5 3 ASN A 413 SER A 414 0 SHEET 2 AA5 3 PRO A 424 THR A 428 1 O ILE A 426 N ASN A 413 SHEET 3 AA5 3 TYR A 478 VAL A 480 -1 O GLU A 479 N ALA A 427 LINK O1A UTP A 601 MG MG A 603 1555 1555 2.01 LINK O2B UTP A 601 MG MG A 603 1555 1555 1.95 LINK O2G UTP A 601 MG MG A 603 1555 1555 2.13 LINK O2B UTP A 602 MG MG A 604 1555 1555 2.11 LINK O2G UTP A 602 MG MG A 604 1555 1555 2.09 LINK MG MG A 603 O HOH A 801 1555 1555 2.00 LINK MG MG A 603 O HOH A 850 1555 1555 2.09 LINK MG MG A 603 O HOH A 884 1555 1555 2.13 LINK MG MG A 604 O HOH A 701 1555 1555 1.96 LINK MG MG A 604 O HOH A 702 1555 1555 2.03 LINK MG MG A 604 O HOH A 722 1555 1555 2.09 LINK MG MG A 604 O HOH A 901 1555 1555 2.14 CISPEP 1 ILE A 122 PRO A 123 0 8.92 SITE 1 AC1 21 SER A 20 GLN A 120 VAL A 121 ILE A 122 SITE 2 AC1 21 ASP A 159 ILE A 160 GLU A 161 LYS A 199 SITE 3 AC1 21 THR A 200 LYS A 201 GLN A 204 LYS A 235 SITE 4 AC1 21 MG A 603 HOH A 715 HOH A 737 HOH A 756 SITE 5 AC1 21 HOH A 801 HOH A 812 HOH A 835 HOH A 850 SITE 6 AC1 21 HOH A 884 SITE 1 AC2 25 SER A 21 LEU A 22 GLY A 23 LYS A 24 SITE 2 AC2 25 LEU A 26 THR A 27 PRO A 194 ARG A 223 SITE 3 AC2 25 THR A 250 ASP A 252 ALA A 253 ILE A 256 SITE 4 AC2 25 ILE A 259 MG A 604 HOH A 701 HOH A 702 SITE 5 AC2 25 HOH A 703 HOH A 722 HOH A 732 HOH A 745 SITE 6 AC2 25 HOH A 778 HOH A 781 HOH A 798 HOH A 819 SITE 7 AC2 25 HOH A 901 SITE 1 AC3 4 UTP A 601 HOH A 801 HOH A 850 HOH A 884 SITE 1 AC4 5 UTP A 602 HOH A 701 HOH A 702 HOH A 722 SITE 2 AC4 5 HOH A 901 SITE 1 AC5 8 PRO A 60 PHE A 61 ALA A 316 TYR A 317 SITE 2 AC5 8 GLY A 365 PHE A 367 HOH A 750 HOH A 791 CRYST1 79.410 132.730 157.630 90.00 90.00 90.00 I 2 2 2 8 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 0.012593 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007534 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006344 0.00000