HEADER TRANSFERASE 16-OCT-06 2IRX TITLE CRYSTAL STRUCTURE OF THE POLYMERASE DOMAIN FROM MYCOBACTERIUM TITLE 2 TUBERCULOSIS LIGASE D WITH GTP AND MANGANESE. COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA LIGASE-LIKE PROTEIN RV0938/MT0965; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: LIGD POLYMERASE DOMAIN (RESIDUES 1-300); COMPND 5 EC: 2.7.7.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 83332; SOURCE 4 STRAIN: H37RV; SOURCE 5 GENE: RV0938; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS POLYMERASE, PRIMASE, LIGASE, NHEJ, GTP, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR N.C.BRISSETT,R.S.PITCHER,A.J.DOHERTY REVDAT 5 21-FEB-24 2IRX 1 REMARK SEQADV REVDAT 4 13-JUL-11 2IRX 1 VERSN REVDAT 3 24-FEB-09 2IRX 1 VERSN REVDAT 2 30-OCT-07 2IRX 1 JRNL REVDAT 1 02-JAN-07 2IRX 0 JRNL AUTH R.S.PITCHER,N.C.BRISSETT,A.J.PICHER,P.ANDRADE,R.JUAREZ, JRNL AUTH 2 D.THOMPSON,G.C.FOX,L.BLANCO,A.J.DOHERTY JRNL TITL STRUCTURE AND FUNCTION OF A MYCOBACTERIAL NHEJ DNA REPAIR JRNL TITL 2 POLYMERASE. JRNL REF J.MOL.BIOL. V. 366 391 2007 JRNL REFN ISSN 0022-2836 JRNL PMID 17174332 JRNL DOI 10.1016/J.JMB.2006.10.046 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 34.79 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 25666 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) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1360 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) : 1476 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 78.10 REMARK 3 BIN R VALUE (WORKING SET) : 0.2970 REMARK 3 BIN FREE R VALUE SET COUNT : 86 REMARK 3 BIN FREE R VALUE : 0.3940 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2164 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 33 REMARK 3 SOLVENT ATOMS : 327 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 21.31 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.45 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.39000 REMARK 3 B22 (A**2) : -0.01000 REMARK 3 B33 (A**2) : -0.38000 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): 0.122 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.121 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.075 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.321 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.940 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2248 ; 0.014 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3078 ; 1.429 ; 1.984 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 282 ; 6.007 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 90 ;33.435 ;22.556 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 347 ;14.203 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;21.390 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 353 ; 0.092 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1696 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1115 ; 0.202 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1500 ; 0.299 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 245 ; 0.155 ; 0.200 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): 36 ; 0.177 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 18 ; 0.176 ; 0.200 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): 1455 ; 0.795 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2281 ; 1.216 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 927 ; 1.996 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 797 ; 3.017 ; 4.500 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 : 9 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 10 A 19 REMARK 3 ORIGIN FOR THE GROUP (A): 16.6163 15.3522 -5.4902 REMARK 3 T TENSOR REMARK 3 T11: 0.0268 T22: 0.0740 REMARK 3 T33: 0.0749 T12: -0.0266 REMARK 3 T13: -0.0176 T23: -0.0400 REMARK 3 L TENSOR REMARK 3 L11: 3.7196 L22: 8.1576 REMARK 3 L33: 12.7579 L12: 0.8714 REMARK 3 L13: -1.7429 L23: -7.1104 REMARK 3 S TENSOR REMARK 3 S11: -0.1221 S12: 0.3110 S13: -0.0320 REMARK 3 S21: -0.5941 S22: 0.2582 S23: 0.2143 REMARK 3 S31: 0.2601 S32: -0.1568 S33: -0.1361 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 20 A 80 REMARK 3 ORIGIN FOR THE GROUP (A): 20.3611 25.5495 -0.2749 REMARK 3 T TENSOR REMARK 3 T11: 0.0324 T22: 0.0726 REMARK 3 T33: 0.0557 T12: -0.0010 REMARK 3 T13: -0.0081 T23: -0.0093 REMARK 3 L TENSOR REMARK 3 L11: 0.7237 L22: 0.9206 REMARK 3 L33: 0.8030 L12: 0.2819 REMARK 3 L13: -0.3183 L23: 0.0088 REMARK 3 S TENSOR REMARK 3 S11: -0.0347 S12: 0.0846 S13: -0.0478 REMARK 3 S21: -0.0923 S22: 0.0384 S23: -0.0046 REMARK 3 S31: -0.0101 S32: 0.0044 S33: -0.0036 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 81 A 90 REMARK 3 ORIGIN FOR THE GROUP (A): 33.8658 37.9889 -10.6655 REMARK 3 T TENSOR REMARK 3 T11: -0.0154 T22: 0.1210 REMARK 3 T33: 0.1059 T12: -0.0871 REMARK 3 T13: -0.0027 T23: 0.0180 REMARK 3 L TENSOR REMARK 3 L11: 17.0026 L22: 16.3843 REMARK 3 L33: 8.1551 L12: 0.9563 REMARK 3 L13: 1.2982 L23: 1.5752 REMARK 3 S TENSOR REMARK 3 S11: -0.8370 S12: -0.2532 S13: 1.2743 REMARK 3 S21: -0.0540 S22: 0.3870 S23: -1.7506 REMARK 3 S31: -0.7821 S32: 1.2091 S33: 0.4501 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 91 A 120 REMARK 3 ORIGIN FOR THE GROUP (A): 21.0047 31.7227 -5.0174 REMARK 3 T TENSOR REMARK 3 T11: 0.0447 T22: 0.0775 REMARK 3 T33: 0.0468 T12: -0.0066 REMARK 3 T13: -0.0007 T23: 0.0025 REMARK 3 L TENSOR REMARK 3 L11: 0.2668 L22: 1.5219 REMARK 3 L33: 0.7739 L12: 0.5369 REMARK 3 L13: -0.2127 L23: 0.0887 REMARK 3 S TENSOR REMARK 3 S11: -0.0334 S12: 0.1600 S13: 0.0161 REMARK 3 S21: -0.1401 S22: 0.0385 S23: 0.0462 REMARK 3 S31: -0.1351 S32: -0.0083 S33: -0.0051 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 121 A 162 REMARK 3 ORIGIN FOR THE GROUP (A): 20.7998 46.0639 6.7834 REMARK 3 T TENSOR REMARK 3 T11: 0.1471 T22: 0.0442 REMARK 3 T33: 0.1142 T12: 0.0021 REMARK 3 T13: 0.0086 T23: -0.0130 REMARK 3 L TENSOR REMARK 3 L11: 1.6879 L22: 2.0604 REMARK 3 L33: 2.8572 L12: 0.2032 REMARK 3 L13: -0.2058 L23: 0.7747 REMARK 3 S TENSOR REMARK 3 S11: 0.1042 S12: -0.0101 S13: 0.1782 REMARK 3 S21: -0.2016 S22: 0.0091 S23: 0.0386 REMARK 3 S31: -0.2703 S32: 0.0898 S33: -0.1132 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 163 A 192 REMARK 3 ORIGIN FOR THE GROUP (A): 16.6967 48.0968 6.9439 REMARK 3 T TENSOR REMARK 3 T11: 0.1430 T22: 0.0142 REMARK 3 T33: 0.0714 T12: 0.0334 REMARK 3 T13: 0.0056 T23: -0.0047 REMARK 3 L TENSOR REMARK 3 L11: 2.3321 L22: 1.5144 REMARK 3 L33: 1.8296 L12: 1.0275 REMARK 3 L13: -0.7171 L23: 0.7983 REMARK 3 S TENSOR REMARK 3 S11: 0.1173 S12: 0.1331 S13: 0.3719 REMARK 3 S21: -0.2016 S22: -0.0001 S23: 0.2835 REMARK 3 S31: -0.5610 S32: -0.0646 S33: -0.1171 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 193 A 227 REMARK 3 ORIGIN FOR THE GROUP (A): 28.7185 51.2897 15.9367 REMARK 3 T TENSOR REMARK 3 T11: 0.0523 T22: 0.0462 REMARK 3 T33: 0.0701 T12: -0.0295 REMARK 3 T13: 0.0201 T23: -0.0328 REMARK 3 L TENSOR REMARK 3 L11: 0.7343 L22: 2.9191 REMARK 3 L33: 9.8329 L12: 0.9637 REMARK 3 L13: 0.8598 L23: 0.5047 REMARK 3 S TENSOR REMARK 3 S11: -0.0154 S12: -0.0526 S13: 0.0540 REMARK 3 S21: -0.2308 S22: 0.0809 S23: -0.3250 REMARK 3 S31: 0.0701 S32: 0.5863 S33: -0.0655 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 228 A 268 REMARK 3 ORIGIN FOR THE GROUP (A): 18.3961 38.1440 11.2135 REMARK 3 T TENSOR REMARK 3 T11: 0.0569 T22: 0.0617 REMARK 3 T33: 0.0420 T12: 0.0012 REMARK 3 T13: 0.0084 T23: -0.0097 REMARK 3 L TENSOR REMARK 3 L11: 0.7653 L22: 1.6990 REMARK 3 L33: 0.7904 L12: 0.3325 REMARK 3 L13: -0.0048 L23: 0.3821 REMARK 3 S TENSOR REMARK 3 S11: 0.0373 S12: -0.1518 S13: 0.0598 REMARK 3 S21: 0.1011 S22: -0.0380 S23: 0.0772 REMARK 3 S31: -0.1247 S32: 0.0311 S33: 0.0007 REMARK 3 REMARK 3 TLS GROUP : 9 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 269 A 292 REMARK 3 ORIGIN FOR THE GROUP (A): 7.0192 34.8422 8.3037 REMARK 3 T TENSOR REMARK 3 T11: 0.0226 T22: 0.0814 REMARK 3 T33: 0.0806 T12: 0.0266 REMARK 3 T13: 0.0041 T23: -0.0383 REMARK 3 L TENSOR REMARK 3 L11: 3.2820 L22: 1.9387 REMARK 3 L33: 1.8386 L12: 0.7145 REMARK 3 L13: -0.4728 L23: 0.1163 REMARK 3 S TENSOR REMARK 3 S11: -0.0273 S12: -0.0435 S13: 0.1956 REMARK 3 S21: -0.0146 S22: -0.0348 S23: 0.3134 REMARK 3 S31: -0.1546 S32: -0.3869 S33: 0.0621 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2IRX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-NOV-06. REMARK 100 THE DEPOSITION ID IS D_1000039940. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-AUG-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54180 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27079 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 34.790 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.700 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 9.000 REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : 0.06700 REMARK 200 FOR THE DATA SET : 26.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.1 REMARK 200 DATA REDUNDANCY IN SHELL : 5.30 REMARK 200 R MERGE FOR SHELL (I) : 0.40800 REMARK 200 R SYM FOR SHELL (I) : 0.47800 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M NA HEPES, 0.01M MNCL2, 10%(V/V) REMARK 280 ISO-PROPANOL, 20% PEG 4000, 0.01M GTP, PH 7.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 285K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 21.27850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.75900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.76600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.75900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.27850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.76600 REMARK 290 SMTRY3 4 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: MONOMERIC 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 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 1 REMARK 465 SER A 2 REMARK 465 HIS A 3 REMARK 465 MET A 4 REMARK 465 GLY A 5 REMARK 465 SER A 6 REMARK 465 ALA A 7 REMARK 465 SER A 8 REMARK 465 GLU A 9 REMARK 465 ASP A 293 REMARK 465 ALA A 294 REMARK 465 PRO A 295 REMARK 465 VAL A 296 REMARK 465 ALA A 297 REMARK 465 ASP A 298 REMARK 465 ARG A 299 REMARK 465 LEU A 300 REMARK 465 THR A 301 REMARK 465 ARG A 302 REMARK 465 TYR A 303 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 LYS A 69 -63.25 -103.69 REMARK 500 ASP A 97 18.22 -143.86 REMARK 500 SER A 177 -97.24 -118.10 REMARK 500 THR A 219 119.43 -39.26 REMARK 500 TYR A 244 -9.20 78.83 REMARK 500 ALA A 255 86.50 -69.88 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 MN A 304 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 140 OD1 REMARK 620 2 ASP A 142 OD1 92.9 REMARK 620 3 GTP A 305 O1B 89.3 177.0 REMARK 620 4 GTP A 305 O2G 166.8 89.2 88.2 REMARK 620 5 HOH A 583 O 102.2 86.1 95.4 90.9 REMARK 620 6 HOH A 584 O 77.4 87.4 91.1 89.8 173.5 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 MN A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GTP A 305 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2IRU RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE POLYMERASE DOMAIN FROM MYCOBACTERIUM REMARK 900 TUBERCULOSIS LIGASE D REMARK 900 RELATED ID: 2IRY RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH DGTP DBREF 2IRX A 4 303 UNP P71571 Y938_MYCTU 1 300 SEQADV 2IRX GLY A 1 UNP P71571 EXPRESSION TAG SEQADV 2IRX SER A 2 UNP P71571 EXPRESSION TAG SEQADV 2IRX HIS A 3 UNP P71571 EXPRESSION TAG SEQRES 1 A 303 GLY SER HIS MET GLY SER ALA SER GLU GLN ARG VAL THR SEQRES 2 A 303 LEU THR ASN ALA ASP LYS VAL LEU TYR PRO ALA THR GLY SEQRES 3 A 303 THR THR LYS SER ASP ILE PHE ASP TYR TYR ALA GLY VAL SEQRES 4 A 303 ALA GLU VAL MET LEU GLY HIS ILE ALA GLY ARG PRO ALA SEQRES 5 A 303 THR ARG LYS ARG TRP PRO ASN GLY VAL ASP GLN PRO ALA SEQRES 6 A 303 PHE PHE GLU LYS GLN LEU ALA LEU SER ALA PRO PRO TRP SEQRES 7 A 303 LEU SER ARG ALA THR VAL ALA HIS ARG SER GLY THR THR SEQRES 8 A 303 THR TYR PRO ILE ILE ASP SER ALA THR GLY LEU ALA TRP SEQRES 9 A 303 ILE ALA GLN GLN ALA ALA LEU GLU VAL HIS VAL PRO GLN SEQRES 10 A 303 TRP ARG PHE VAL ALA GLU PRO GLY SER GLY GLU LEU ASN SEQRES 11 A 303 PRO GLY PRO ALA THR ARG LEU VAL PHE ASP LEU ASP PRO SEQRES 12 A 303 GLY GLU GLY VAL MET MET ALA GLN LEU ALA GLU VAL ALA SEQRES 13 A 303 ARG ALA VAL ARG ASP LEU LEU ALA ASP ILE GLY LEU VAL SEQRES 14 A 303 THR PHE PRO VAL THR SER GLY SER LYS GLY LEU HIS LEU SEQRES 15 A 303 TYR THR PRO LEU ASP GLU PRO VAL SER SER ARG GLY ALA SEQRES 16 A 303 THR VAL LEU ALA LYS ARG VAL ALA GLN ARG LEU GLU GLN SEQRES 17 A 303 ALA MET PRO ALA LEU VAL THR SER THR MET THR LYS SER SEQRES 18 A 303 LEU ARG ALA GLY LYS VAL PHE VAL ASP TRP SER GLN ASN SEQRES 19 A 303 SER GLY SER LYS THR THR ILE ALA PRO TYR SER LEU ARG SEQRES 20 A 303 GLY ARG THR HIS PRO THR VAL ALA ALA PRO ARG THR TRP SEQRES 21 A 303 ALA GLU LEU ASP ASP PRO ALA LEU ARG GLN LEU SER TYR SEQRES 22 A 303 ASP GLU VAL LEU THR ARG ILE ALA ARG ASP GLY ASP LEU SEQRES 23 A 303 LEU GLU ARG LEU ASP ALA ASP ALA PRO VAL ALA ASP ARG SEQRES 24 A 303 LEU THR ARG TYR HET MN A 304 1 HET GTP A 305 32 HETNAM MN MANGANESE (II) ION HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE FORMUL 2 MN MN 2+ FORMUL 3 GTP C10 H16 N5 O14 P3 FORMUL 4 HOH *327(H2 O) HELIX 1 1 THR A 28 ALA A 48 1 21 HELIX 2 2 SER A 98 GLN A 108 1 11 HELIX 3 3 MET A 148 ASP A 165 1 18 HELIX 4 4 SER A 191 MET A 210 1 20 HELIX 5 5 THR A 219 ARG A 223 5 5 HELIX 6 6 TRP A 231 SER A 235 5 5 HELIX 7 7 ALA A 261 ASP A 265 5 5 HELIX 8 8 TYR A 273 GLY A 284 1 12 SHEET 1 A 4 PHE A 66 GLU A 68 0 SHEET 2 A 4 THR A 53 ARG A 56 -1 N ARG A 54 O GLU A 68 SHEET 3 A 4 GLU A 112 VAL A 115 -1 O HIS A 114 N THR A 53 SHEET 4 A 4 THR A 240 ILE A 241 -1 O THR A 240 N VAL A 115 SHEET 1 B 2 SER A 80 ALA A 85 0 SHEET 2 B 2 THR A 90 ILE A 95 -1 O THR A 91 N VAL A 84 SHEET 1 C 4 TRP A 118 ALA A 122 0 SHEET 2 C 4 LEU A 129 PRO A 143 -1 O ASN A 130 N VAL A 121 SHEET 3 C 4 VAL A 227 ASP A 230 -1 O ASP A 230 N ASP A 140 SHEET 4 C 4 VAL A 214 THR A 215 1 N THR A 215 O VAL A 229 SHEET 1 D 5 TRP A 118 ALA A 122 0 SHEET 2 D 5 LEU A 129 PRO A 143 -1 O ASN A 130 N VAL A 121 SHEET 3 D 5 LEU A 180 VAL A 190 -1 O VAL A 190 N ALA A 134 SHEET 4 D 5 PHE A 171 THR A 174 -1 N VAL A 173 O HIS A 181 SHEET 5 D 5 ALA A 256 PRO A 257 -1 O ALA A 256 N THR A 174 SHEET 1 E 2 THR A 253 VAL A 254 0 SHEET 2 E 2 LEU A 271 SER A 272 -1 O LEU A 271 N VAL A 254 LINK OD1 ASP A 140 MN MN A 304 1555 1555 2.20 LINK OD1 ASP A 142 MN MN A 304 1555 1555 2.16 LINK MN MN A 304 O1B GTP A 305 1555 1555 2.26 LINK MN MN A 304 O2G GTP A 305 1555 1555 2.20 LINK MN MN A 304 O HOH A 583 1555 1555 2.17 LINK MN MN A 304 O HOH A 584 1555 1555 2.51 SITE 1 AC1 5 ASP A 140 ASP A 142 GTP A 305 HOH A 583 SITE 2 AC1 5 HOH A 584 SITE 1 AC2 28 LYS A 55 PHE A 67 HIS A 114 ASP A 140 SITE 2 AC2 28 ASP A 142 SER A 175 SER A 177 LYS A 178 SITE 3 AC2 28 GLY A 179 HIS A 181 GLN A 233 THR A 239 SITE 4 AC2 28 ARG A 247 ARG A 249 MN A 304 HOH A 431 SITE 5 AC2 28 HOH A 475 HOH A 481 HOH A 580 HOH A 581 SITE 6 AC2 28 HOH A 582 HOH A 584 HOH A 585 HOH A 586 SITE 7 AC2 28 HOH A 591 HOH A 593 HOH A 597 HOH A 617 CRYST1 42.557 75.532 89.518 90.00 90.00 90.00 P 21 21 21 4 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 0.023498 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013239 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011171 0.00000