HEADER TRANSFERASE 28-NOV-05 2F67 TITLE CRYSTAL STRUCTURE OF NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASE FROM TITLE 2 TRYPANOSOMA BRUCEI AT 1.6 A RESOLUTION WITH BENZO[CD]INDOL-2(1H)-ONE TITLE 3 BOUND COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 2.4.2.6; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRYPANOSOMA BRUCEI; SOURCE 3 ORGANISM_TAXID: 5691; SOURCE 4 GENE: TB05.30H13.400; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21STAR(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: T7 SYSTEM; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET14B KEYWDS SGPP, STRUCTURAL GENOMICS, PSI, PROTEIN STRUCTURE INITIATIVE NDRT, KEYWDS 2 NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASE, TRYPANOSOMA BRUCEI, STRUCTURAL KEYWDS 3 GENOMICS OF PATHOGENIC PROTOZOA CONSORTIUM, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.BOSCH,M.A.ROBIEN,W.G.J.HOL,STRUCTURAL GENOMICS OF PATHOGENIC AUTHOR 2 PROTOZOA CONSORTIUM (SGPP) REVDAT 7 09-OCT-24 2F67 1 REMARK REVDAT 6 15-NOV-23 2F67 1 REMARK REVDAT 5 23-AUG-23 2F67 1 REMARK SEQADV LINK REVDAT 4 13-JUL-11 2F67 1 VERSN REVDAT 3 24-FEB-09 2F67 1 VERSN REVDAT 2 17-APR-07 2F67 1 JRNL REVDAT 1 06-DEC-05 2F67 0 JRNL AUTH J.BOSCH,M.A.ROBIEN,C.MEHLIN,E.BONI,A.RIECHERS,F.S.BUCKNER, JRNL AUTH 2 W.C.VAN VOORHIS,P.J.MYLER,E.A.WORTHEY,G.DETITTA,J.R.LUFT, JRNL AUTH 3 A.LAURICELLA,S.GULDE,L.A.ANDERSON,O.KALYUZHNIY,H.M.NEELY, JRNL AUTH 4 J.ROSS,T.N.EARNEST,M.SOLTIS,L.SCHOENFELD,F.ZUCKER, JRNL AUTH 5 E.A.MERRITT,E.FAN,C.L.VERLINDE,W.G.J.HOL JRNL TITL USING FRAGMENT COCKTAIL CRYSTALLOGRAPHY TO ASSIST INHIBITOR JRNL TITL 2 DESIGN OF TRYPANOSOMA BRUCEI NUCLEOSIDE JRNL TITL 3 2-DEOXYRIBOSYLTRANSFERASE. JRNL REF J.MED.CHEM. V. 49 5939 2006 JRNL REFN ISSN 0022-2623 JRNL PMID 17004709 JRNL DOI 10.1021/JM060429M REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.9 REMARK 3 NUMBER OF REFLECTIONS : 42601 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) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2251 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.69 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3828 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 55.95 REMARK 3 BIN R VALUE (WORKING SET) : 0.2180 REMARK 3 BIN FREE R VALUE SET COUNT : 207 REMARK 3 BIN FREE R VALUE : 0.2430 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2518 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 53 REMARK 3 SOLVENT ATOMS : 302 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 20.35 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.07 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.07000 REMARK 3 B22 (A**2) : -0.01000 REMARK 3 B33 (A**2) : -0.06000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.02000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.092 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.092 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.047 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.525 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.939 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2682 ; 0.008 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3631 ; 1.026 ; 1.969 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 330 ; 4.937 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 136 ;31.053 ;23.750 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 449 ;11.059 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;16.353 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 372 ; 0.068 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2092 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1262 ; 0.192 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1817 ; 0.306 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 260 ; 0.310 ; 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): 50 ; 0.126 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 18 ; 0.087 ; 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): 1652 ; 1.717 ; 4.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2576 ; 1.949 ; 6.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1173 ; 2.652 ; 6.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1047 ; 3.763 ;10.000 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 : 8 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 3 A 9 REMARK 3 ORIGIN FOR THE GROUP (A): 0.3769 13.6280 6.6554 REMARK 3 T TENSOR REMARK 3 T11: 0.0017 T22: -0.0556 REMARK 3 T33: -0.0757 T12: 0.0406 REMARK 3 T13: -0.0077 T23: -0.0462 REMARK 3 L TENSOR REMARK 3 L11: 10.4678 L22: 10.0258 REMARK 3 L33: 1.0689 L12: -5.8716 REMARK 3 L13: -0.9114 L23: -1.2037 REMARK 3 S TENSOR REMARK 3 S11: 0.2949 S12: 0.4633 S13: -0.6401 REMARK 3 S21: -0.4804 S22: -0.0687 S23: 0.4704 REMARK 3 S31: -0.0475 S32: 0.1612 S33: -0.2262 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 10 A 47 REMARK 3 ORIGIN FOR THE GROUP (A): 23.4826 9.9121 12.4927 REMARK 3 T TENSOR REMARK 3 T11: 0.0030 T22: -0.0482 REMARK 3 T33: -0.0143 T12: 0.0192 REMARK 3 T13: 0.0168 T23: 0.0029 REMARK 3 L TENSOR REMARK 3 L11: 3.4249 L22: 0.6259 REMARK 3 L33: 2.1481 L12: -0.5180 REMARK 3 L13: 1.7115 L23: -0.3578 REMARK 3 S TENSOR REMARK 3 S11: 0.0323 S12: 0.0447 S13: 0.2790 REMARK 3 S21: -0.0431 S22: -0.0903 S23: -0.1289 REMARK 3 S31: -0.3119 S32: 0.0369 S33: 0.0580 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 48 A 69 REMARK 3 ORIGIN FOR THE GROUP (A): 17.0370 5.8850 25.1315 REMARK 3 T TENSOR REMARK 3 T11: 0.0113 T22: 0.0257 REMARK 3 T33: 0.0018 T12: 0.0150 REMARK 3 T13: 0.0090 T23: -0.0010 REMARK 3 L TENSOR REMARK 3 L11: 1.2730 L22: 0.7351 REMARK 3 L33: 1.3382 L12: 0.2762 REMARK 3 L13: 1.1777 L23: 0.6653 REMARK 3 S TENSOR REMARK 3 S11: -0.0216 S12: 0.0007 S13: 0.0828 REMARK 3 S21: 0.0046 S22: 0.0116 S23: 0.0867 REMARK 3 S31: -0.1943 S32: -0.0690 S33: 0.0099 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 70 A 160 REMARK 3 ORIGIN FOR THE GROUP (A): 27.1736 -7.3534 11.2667 REMARK 3 T TENSOR REMARK 3 T11: -0.0355 T22: -0.0046 REMARK 3 T33: -0.0297 T12: 0.0120 REMARK 3 T13: 0.0067 T23: -0.0053 REMARK 3 L TENSOR REMARK 3 L11: 0.5056 L22: 0.8336 REMARK 3 L33: 0.7076 L12: -0.1648 REMARK 3 L13: 0.1362 L23: -0.0798 REMARK 3 S TENSOR REMARK 3 S11: 0.0501 S12: 0.0386 S13: -0.0099 REMARK 3 S21: -0.0644 S22: -0.0279 S23: -0.0331 REMARK 3 S31: 0.0112 S32: 0.0087 S33: -0.0222 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 : B 3 B 7 REMARK 3 ORIGIN FOR THE GROUP (A): -2.1032 -29.9041 37.3580 REMARK 3 T TENSOR REMARK 3 T11: -0.0541 T22: -0.0884 REMARK 3 T33: -0.1056 T12: -0.0196 REMARK 3 T13: 0.0212 T23: -0.0672 REMARK 3 L TENSOR REMARK 3 L11: 18.2299 L22: 23.6976 REMARK 3 L33: 11.7820 L12: 6.6838 REMARK 3 L13: -0.5806 L23: -5.2285 REMARK 3 S TENSOR REMARK 3 S11: 0.2163 S12: -0.4912 S13: 0.6700 REMARK 3 S21: 0.8561 S22: 0.0938 S23: 0.6763 REMARK 3 S31: -0.1077 S32: -0.0733 S33: -0.3101 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 : B 8 B 47 REMARK 3 ORIGIN FOR THE GROUP (A): 22.5805 -24.8618 30.8659 REMARK 3 T TENSOR REMARK 3 T11: 0.0035 T22: -0.0309 REMARK 3 T33: -0.0061 T12: -0.0140 REMARK 3 T13: -0.0140 T23: 0.0047 REMARK 3 L TENSOR REMARK 3 L11: 3.3995 L22: 0.6976 REMARK 3 L33: 1.1044 L12: 0.6251 REMARK 3 L13: -1.4421 L23: -0.2075 REMARK 3 S TENSOR REMARK 3 S11: 0.0197 S12: -0.0153 S13: -0.3076 REMARK 3 S21: 0.0160 S22: -0.0916 S23: -0.0671 REMARK 3 S31: 0.2352 S32: 0.0092 S33: 0.0719 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 : B 48 B 61 REMARK 3 ORIGIN FOR THE GROUP (A): 19.5857 -22.5769 14.5736 REMARK 3 T TENSOR REMARK 3 T11: -0.0507 T22: -0.0265 REMARK 3 T33: -0.0407 T12: -0.0290 REMARK 3 T13: -0.0076 T23: -0.0156 REMARK 3 L TENSOR REMARK 3 L11: 2.0531 L22: 5.7171 REMARK 3 L33: 3.9641 L12: -1.3068 REMARK 3 L13: 0.0397 L23: -1.5709 REMARK 3 S TENSOR REMARK 3 S11: 0.0539 S12: 0.0243 S13: -0.1797 REMARK 3 S21: -0.0911 S22: -0.0606 S23: 0.1751 REMARK 3 S31: 0.1461 S32: -0.1342 S33: 0.0067 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 : B 62 B 160 REMARK 3 ORIGIN FOR THE GROUP (A): 25.9663 -8.4343 31.2540 REMARK 3 T TENSOR REMARK 3 T11: -0.0320 T22: -0.0010 REMARK 3 T33: -0.0304 T12: -0.0120 REMARK 3 T13: -0.0050 T23: -0.0008 REMARK 3 L TENSOR REMARK 3 L11: 0.5065 L22: 0.7821 REMARK 3 L33: 0.6546 L12: 0.1639 REMARK 3 L13: -0.0637 L23: 0.0325 REMARK 3 S TENSOR REMARK 3 S11: 0.0369 S12: -0.0380 S13: 0.0023 REMARK 3 S21: 0.0564 S22: -0.0182 S23: -0.0326 REMARK 3 S31: 0.0022 S32: -0.0050 S33: -0.0187 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: NULL REMARK 4 REMARK 4 2F67 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-NOV-05. REMARK 100 THE DEPOSITION ID IS D_1000035500. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-APR-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 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 : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42601 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.9 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09400 REMARK 200 FOR THE DATA SET : 7.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 56.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.28200 REMARK 200 FOR SHELL : 2.500 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 2A0K REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30 % PEG MME 2000, 0.2 AMMONIUM REMARK 280 SULFATE, 0.1 SODIUM ACETATE TRIHYDRATE PH 4.6, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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+1/2,Y+1/2,Z 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 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 29.46400 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.75650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 29.46400 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 37.75650 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14680 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -85.0 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 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 494 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 480 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 MSE A 1 REMARK 465 ALA A 2 REMARK 465 LYS A 161 REMARK 465 MSE B 1 REMARK 465 ALA B 2 REMARK 465 LYS B 161 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 371 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 381 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 361 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 12B B 372 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 12B A 382 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 372 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 382 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2A0K RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASE FROM REMARK 900 TRYPANOSOMA BRUCEI AT 1.8 A RESOLUTION REMARK 900 RELATED ID: 2F2T RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASE FROM REMARK 900 TRYPANOSOMA BRUCEI AT 1.7 A RESOLUTION WITH 5-AMINOISOQUINOLINE REMARK 900 BOUND REMARK 900 RELATED ID: 2F62 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASE FROM REMARK 900 TRYPANOSOMA BRUCEI AT 1.5 A RESOLUTION WITH (2-ETHYLPHENYL)METHANOL REMARK 900 BOUND REMARK 900 RELATED ID: 2F64 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASE FROM REMARK 900 TRYPANOSOMA BRUCEI AT 1.6 A RESOLUTION WITH 1-METHYLQUINOLIN-2(1H)- REMARK 900 ONE BOUND REMARK 900 RELATED ID: TBRU015777AAA RELATED DB: TARGETDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 AUTHORS STATE THAT THERE ARE TWO INDEPENDENT SEQUENCE REMARK 999 CONFIRMATIONS OF TWO DIFFERENT CLONES WHICH CLEARLY REMARK 999 SHOW THE SEQUENCE AS GIVEN. AUTHORS ALSO HAVE EXPRESSED REMARK 999 MULTIPLE CLONES AT DIFFERENT TIMES AND ALL OF THESE REMARK 999 BATCHES SHOW THE SAME ELECTRON DENSITY FOR THESE RESIDUES. DBREF 2F67 A 9 161 UNP Q57VC7 Q57VC7_9TRYP 1 153 DBREF 2F67 B 9 161 UNP Q57VC7 Q57VC7_9TRYP 1 153 SEQADV 2F67 MSE A 1 UNP Q57VC7 CLONING ARTIFACT SEQADV 2F67 ALA A 2 UNP Q57VC7 CLONING ARTIFACT SEQADV 2F67 HIS A 3 UNP Q57VC7 EXPRESSION TAG SEQADV 2F67 HIS A 4 UNP Q57VC7 EXPRESSION TAG SEQADV 2F67 HIS A 5 UNP Q57VC7 EXPRESSION TAG SEQADV 2F67 HIS A 6 UNP Q57VC7 EXPRESSION TAG SEQADV 2F67 HIS A 7 UNP Q57VC7 EXPRESSION TAG SEQADV 2F67 HIS A 8 UNP Q57VC7 EXPRESSION TAG SEQADV 2F67 MSE A 9 UNP Q57VC7 MET 1 MODIFIED RESIDUE SEQADV 2F67 MSE A 24 UNP Q57VC7 MET 16 MODIFIED RESIDUE SEQADV 2F67 MSE A 42 UNP Q57VC7 MET 34 MODIFIED RESIDUE SEQADV 2F67 GLU A 53 UNP Q57VC7 GLY 45 SEE REMARK 999 SEQADV 2F67 MSE A 64 UNP Q57VC7 MET 56 MODIFIED RESIDUE SEQADV 2F67 CYS A 93 UNP Q57VC7 TYR 85 SEE REMARK 999 SEQADV 2F67 MSE A 100 UNP Q57VC7 MET 92 MODIFIED RESIDUE SEQADV 2F67 MSE A 111 UNP Q57VC7 MET 103 MODIFIED RESIDUE SEQADV 2F67 GLY A 118 UNP Q57VC7 GLU 110 SEE REMARK 999 SEQADV 2F67 MSE A 136 UNP Q57VC7 MET 128 MODIFIED RESIDUE SEQADV 2F67 MSE B 1 UNP Q57VC7 CLONING ARTIFACT SEQADV 2F67 ALA B 2 UNP Q57VC7 CLONING ARTIFACT SEQADV 2F67 HIS B 3 UNP Q57VC7 EXPRESSION TAG SEQADV 2F67 HIS B 4 UNP Q57VC7 EXPRESSION TAG SEQADV 2F67 HIS B 5 UNP Q57VC7 EXPRESSION TAG SEQADV 2F67 HIS B 6 UNP Q57VC7 EXPRESSION TAG SEQADV 2F67 HIS B 7 UNP Q57VC7 EXPRESSION TAG SEQADV 2F67 HIS B 8 UNP Q57VC7 EXPRESSION TAG SEQADV 2F67 MSE B 9 UNP Q57VC7 MET 1 MODIFIED RESIDUE SEQADV 2F67 MSE B 24 UNP Q57VC7 MET 16 MODIFIED RESIDUE SEQADV 2F67 MSE B 42 UNP Q57VC7 MET 34 MODIFIED RESIDUE SEQADV 2F67 GLU B 53 UNP Q57VC7 GLY 45 SEE REMARK 999 SEQADV 2F67 MSE B 64 UNP Q57VC7 MET 56 MODIFIED RESIDUE SEQADV 2F67 CYS B 93 UNP Q57VC7 TYR 85 SEE REMARK 999 SEQADV 2F67 MSE B 100 UNP Q57VC7 MET 92 MODIFIED RESIDUE SEQADV 2F67 MSE B 111 UNP Q57VC7 MET 103 MODIFIED RESIDUE SEQADV 2F67 GLY B 118 UNP Q57VC7 GLU 110 SEE REMARK 999 SEQADV 2F67 MSE B 136 UNP Q57VC7 MET 128 MODIFIED RESIDUE SEQRES 1 A 161 MSE ALA HIS HIS HIS HIS HIS HIS MSE ARG LYS ILE TYR SEQRES 2 A 161 ILE ALA GLY PRO ALA VAL PHE ASN PRO ASP MSE GLY ALA SEQRES 3 A 161 SER TYR TYR ASN LYS VAL ARG GLU LEU LEU LYS LYS GLU SEQRES 4 A 161 ASN VAL MSE PRO LEU ILE PRO THR ASP ASN GLU ALA THR SEQRES 5 A 161 GLU ALA LEU ASP ILE ARG GLN LYS ASN ILE GLN MSE ILE SEQRES 6 A 161 LYS ASP CYS ASP ALA VAL ILE ALA ASP LEU SER PRO PHE SEQRES 7 A 161 ARG GLY HIS GLU PRO ASP CYS GLY THR ALA PHE GLU VAL SEQRES 8 A 161 GLY CYS ALA ALA ALA LEU ASN LYS MSE VAL LEU THR PHE SEQRES 9 A 161 THR SER ASP ARG ARG ASN MSE ARG GLU LYS TYR GLY SER SEQRES 10 A 161 GLY VAL ASP LYS ASP ASN LEU ARG VAL GLU GLY PHE GLY SEQRES 11 A 161 LEU PRO PHE ASN LEU MSE LEU TYR ASP GLY VAL GLU VAL SEQRES 12 A 161 PHE ASP SER PHE GLU SER ALA PHE LYS TYR PHE LEU ALA SEQRES 13 A 161 ASN PHE PRO SER LYS SEQRES 1 B 161 MSE ALA HIS HIS HIS HIS HIS HIS MSE ARG LYS ILE TYR SEQRES 2 B 161 ILE ALA GLY PRO ALA VAL PHE ASN PRO ASP MSE GLY ALA SEQRES 3 B 161 SER TYR TYR ASN LYS VAL ARG GLU LEU LEU LYS LYS GLU SEQRES 4 B 161 ASN VAL MSE PRO LEU ILE PRO THR ASP ASN GLU ALA THR SEQRES 5 B 161 GLU ALA LEU ASP ILE ARG GLN LYS ASN ILE GLN MSE ILE SEQRES 6 B 161 LYS ASP CYS ASP ALA VAL ILE ALA ASP LEU SER PRO PHE SEQRES 7 B 161 ARG GLY HIS GLU PRO ASP CYS GLY THR ALA PHE GLU VAL SEQRES 8 B 161 GLY CYS ALA ALA ALA LEU ASN LYS MSE VAL LEU THR PHE SEQRES 9 B 161 THR SER ASP ARG ARG ASN MSE ARG GLU LYS TYR GLY SER SEQRES 10 B 161 GLY VAL ASP LYS ASP ASN LEU ARG VAL GLU GLY PHE GLY SEQRES 11 B 161 LEU PRO PHE ASN LEU MSE LEU TYR ASP GLY VAL GLU VAL SEQRES 12 B 161 PHE ASP SER PHE GLU SER ALA PHE LYS TYR PHE LEU ALA SEQRES 13 B 161 ASN PHE PRO SER LYS MODRES 2F67 MSE A 9 MET SELENOMETHIONINE MODRES 2F67 MSE A 24 MET SELENOMETHIONINE MODRES 2F67 MSE A 42 MET SELENOMETHIONINE MODRES 2F67 MSE A 64 MET SELENOMETHIONINE MODRES 2F67 MSE A 100 MET SELENOMETHIONINE MODRES 2F67 MSE A 111 MET SELENOMETHIONINE MODRES 2F67 MSE A 136 MET SELENOMETHIONINE MODRES 2F67 MSE B 9 MET SELENOMETHIONINE MODRES 2F67 MSE B 24 MET SELENOMETHIONINE MODRES 2F67 MSE B 42 MET SELENOMETHIONINE MODRES 2F67 MSE B 64 MET SELENOMETHIONINE MODRES 2F67 MSE B 100 MET SELENOMETHIONINE MODRES 2F67 MSE B 111 MET SELENOMETHIONINE MODRES 2F67 MSE B 136 MET SELENOMETHIONINE HET MSE A 9 8 HET MSE A 24 8 HET MSE A 42 8 HET MSE A 64 8 HET MSE A 100 8 HET MSE A 111 8 HET MSE A 136 8 HET MSE B 9 8 HET MSE B 24 8 HET MSE B 42 8 HET MSE B 64 8 HET MSE B 100 8 HET MSE B 111 8 HET MSE B 136 8 HET SO4 A 381 5 HET SO4 A 361 5 HET 12B A 382 13 HET GOL A 372 6 HET SO4 B 371 5 HET 12B B 372 13 HET GOL B 382 6 HETNAM MSE SELENOMETHIONINE HETNAM SO4 SULFATE ION HETNAM 12B BENZO[CD]INDOL-2(1H)-ONE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 MSE 14(C5 H11 N O2 SE) FORMUL 3 SO4 3(O4 S 2-) FORMUL 5 12B 2(C11 H7 N O) FORMUL 6 GOL 2(C3 H8 O3) FORMUL 10 HOH *302(H2 O) HELIX 1 1 GLY A 16 ASN A 21 5 6 HELIX 2 2 GLY A 25 LYS A 38 1 14 HELIX 3 3 GLU A 53 CYS A 68 1 16 HELIX 4 4 ASP A 84 LEU A 97 1 14 HELIX 5 5 ASN A 110 GLY A 116 1 7 HELIX 6 6 ASN A 134 TYR A 138 5 5 HELIX 7 7 SER A 146 PHE A 158 1 13 HELIX 8 8 GLY B 16 ASN B 21 5 6 HELIX 9 9 GLY B 25 LYS B 38 1 14 HELIX 10 10 GLU B 53 CYS B 68 1 16 HELIX 11 11 ASP B 84 LEU B 97 1 14 HELIX 12 12 ASN B 110 GLY B 116 1 7 HELIX 13 13 ASN B 134 TYR B 138 5 5 HELIX 14 14 SER B 146 PHE B 158 1 13 SHEET 1 A 4 MSE A 42 LEU A 44 0 SHEET 2 A 4 LYS A 11 ALA A 15 1 N ILE A 12 O LEU A 44 SHEET 3 A 4 ALA A 70 ASP A 74 1 O ASP A 74 N ALA A 15 SHEET 4 A 4 MSE A 100 PHE A 104 1 O LEU A 102 N ALA A 73 SHEET 1 B 5 MSE B 42 LEU B 44 0 SHEET 2 B 5 LYS B 11 ALA B 15 1 N ILE B 12 O LEU B 44 SHEET 3 B 5 ALA B 70 ASP B 74 1 O ASP B 74 N ALA B 15 SHEET 4 B 5 MSE B 100 PHE B 104 1 O LEU B 102 N ALA B 73 SHEET 5 B 5 VAL B 143 PHE B 144 1 O PHE B 144 N THR B 103 LINK C HIS A 8 N MSE A 9 1555 1555 1.33 LINK C MSE A 9 N ARG A 10 1555 1555 1.33 LINK C ASP A 23 N MSE A 24 1555 1555 1.33 LINK C MSE A 24 N GLY A 25 1555 1555 1.33 LINK C VAL A 41 N MSE A 42 1555 1555 1.33 LINK C MSE A 42 N PRO A 43 1555 1555 1.34 LINK C GLN A 63 N MSE A 64 1555 1555 1.33 LINK C MSE A 64 N ILE A 65 1555 1555 1.34 LINK C LYS A 99 N MSE A 100 1555 1555 1.33 LINK C MSE A 100 N VAL A 101 1555 1555 1.33 LINK C ASN A 110 N MSE A 111 1555 1555 1.33 LINK C MSE A 111 N ARG A 112 1555 1555 1.33 LINK C LEU A 135 N MSE A 136 1555 1555 1.34 LINK C MSE A 136 N LEU A 137 1555 1555 1.34 LINK C HIS B 8 N MSE B 9 1555 1555 1.33 LINK C MSE B 9 N ARG B 10 1555 1555 1.33 LINK C ASP B 23 N MSE B 24 1555 1555 1.33 LINK C MSE B 24 N GLY B 25 1555 1555 1.33 LINK C VAL B 41 N MSE B 42 1555 1555 1.33 LINK C MSE B 42 N PRO B 43 1555 1555 1.34 LINK C GLN B 63 N MSE B 64 1555 1555 1.33 LINK C MSE B 64 N ILE B 65 1555 1555 1.33 LINK C LYS B 99 N MSE B 100 1555 1555 1.33 LINK C MSE B 100 N VAL B 101 1555 1555 1.34 LINK C ASN B 110 N MSE B 111 1555 1555 1.33 LINK C MSE B 111 N ARG B 112 1555 1555 1.33 LINK C LEU B 135 N MSE B 136 1555 1555 1.34 LINK C MSE B 136 N LEU B 137 1555 1555 1.34 SITE 1 AC1 9 HIS B 6 HIS B 8 MSE B 9 LYS B 11 SITE 2 AC1 9 ARG B 112 ARG B 125 HOH B 437 HOH B 457 SITE 3 AC1 9 HOH B 518 SITE 1 AC2 8 HIS A 6 HIS A 8 MSE A 9 LYS A 11 SITE 2 AC2 8 ARG A 112 ARG A 125 HOH A 478 HOH A 501 SITE 1 AC3 6 HIS A 7 ARG A 10 GLU A 39 ASN A 40 SITE 2 AC3 6 SER A 160 HOH A 420 SITE 1 AC4 9 PHE A 20 PRO A 46 GLU A 50 ILE A 57 SITE 2 AC4 9 ASN A 61 GOL A 372 GLU B 127 ASN B 134 SITE 3 AC4 9 LEU B 135 SITE 1 AC5 9 GLU A 127 ASN A 134 LEU A 135 PHE B 20 SITE 2 AC5 9 PRO B 46 GLU B 50 ILE B 57 ASN B 61 SITE 3 AC5 9 GOL B 382 SITE 1 AC6 10 ALA A 15 GLY A 16 VAL A 19 PHE A 20 SITE 2 AC6 10 ASP A 84 GLY A 86 THR A 87 GLU A 90 SITE 3 AC6 10 ASN B 134 12B B 372 SITE 1 AC7 9 ASN A 134 12B A 382 ALA B 15 GLY B 16 SITE 2 AC7 9 VAL B 19 PHE B 20 ASP B 84 GLY B 86 SITE 3 AC7 9 GLU B 90 CRYST1 58.928 75.513 86.336 90.00 90.01 90.00 C 1 2 1 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 0.016970 0.000000 0.000002 0.00000 SCALE2 0.000000 0.013243 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011583 0.00000