HEADER TRANSFERASE 06-AUG-08 2ZQ5 TITLE CRYSTAL STRUCTURE OF SULFOTRANSFERASE STF1 FROM MYCOBACTERIUM TITLE 2 TUBERCULOSIS H37RV (TYPE1 FORM) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE UNCHARACTERIZED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SULFOTRANSFERASE, STF1; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 1773; SOURCE 4 STRAIN: H37RV; SOURCE 5 GENE: MT3632, RV3529C; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX4T3 KEYWDS SULFOTRANSFERASE FOLD, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.TANAKA,M.KIMURA,Y.KAKUTA REVDAT 4 13-MAR-24 2ZQ5 1 REMARK REVDAT 3 11-DEC-19 2ZQ5 1 REMARK REVDAT 2 13-NOV-19 2ZQ5 1 REMARK SEQADV REVDAT 1 29-SEP-09 2ZQ5 0 JRNL AUTH S.TANAKA,M.KIMURA,Y.KAKUTA JRNL TITL CRYSTAL STRUCTURE OF SULFOTRANSFERASE STF1 FROM JRNL TITL 2 MYCOBACTERIUM TUBERCULOSIS H37RV JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.08 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 481773.120 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 23701 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 SET) : 0.176 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1196 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.13 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3741 REMARK 3 BIN R VALUE (WORKING SET) : 0.1700 REMARK 3 BIN FREE R VALUE : 0.1920 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 225 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.013 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2913 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 704 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 5.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.72000 REMARK 3 B22 (A**2) : -0.10000 REMARK 3 B33 (A**2) : -1.62000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.69000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.19 REMARK 3 ESD FROM SIGMAA (A) : 0.04 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.22 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.07 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.004 REMARK 3 BOND ANGLES (DEGREES) : 1.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 20.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.750 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 50.18 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2ZQ5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-AUG-08. REMARK 100 THE DEPOSITION ID IS D_1000028285. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.1 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 56164 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.03400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.12500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 10.00 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, 0.1M BIS-TRIS PH 7.1, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 47.88050 REMARK 290 SMTRY3 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 MET A 1 REMARK 465 THR A 2 REMARK 465 ARG A 3 REMARK 465 ARG A 4 REMARK 465 PRO A 5 REMARK 465 ASP A 6 REMARK 465 VAL A 350 REMARK 465 HIS A 351 REMARK 465 ALA A 352 REMARK 465 GLU A 353 REMARK 465 SER A 354 REMARK 465 GLN A 355 REMARK 465 SER A 356 REMARK 465 GLY A 357 REMARK 465 ALA A 358 REMARK 465 ARG A 359 REMARK 465 ALA A 360 REMARK 465 PRO A 361 REMARK 465 LYS A 362 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 10 -70.11 -81.89 REMARK 500 ALA A 11 169.65 171.46 REMARK 500 GLU A 50 -11.28 -146.21 REMARK 500 ARG A 92 60.33 38.17 REMARK 500 PRO A 158 77.53 -56.01 REMARK 500 TYR A 160 149.04 66.52 REMARK 500 THR A 161 80.04 58.09 REMARK 500 LEU A 163 -175.55 -53.13 REMARK 500 ASN A 232 144.64 -175.88 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2ZQ6 RELATED DB: PDB DBREF 2ZQ5 A 1 384 UNP P71872 P71872_MYCTU 1 384 SEQADV 2ZQ5 ASP A 149 UNP P71872 GLN 149 CONFLICT SEQRES 1 A 384 MET THR ARG ARG PRO ASP ARG LYS ASP VAL ALA THR VAL SEQRES 2 A 384 ASP GLU LEU HIS ALA SER ALA THR LYS LEU VAL GLY LEU SEQRES 3 A 384 ASP ASP PHE GLY THR ASP ASP ASP ASN TYR ARG GLU ALA SEQRES 4 A 384 LEU GLY VAL LEU LEU ASP ALA TYR GLN GLY GLU ALA GLY SEQRES 5 A 384 LEU THR VAL LEU GLY SER LYS MET ASN ARG PHE PHE LEU SEQRES 6 A 384 ARG GLY ALA LEU VAL ALA ARG LEU LEU SER GLN SER ALA SEQRES 7 A 384 TRP LYS GLN TYR PRO GLU HIS VAL ASP VAL ALA ILE LYS SEQRES 8 A 384 ARG PRO ILE PHE VAL THR GLY LEU VAL ARG THR GLY THR SEQRES 9 A 384 THR ALA LEU HIS ARG LEU LEU GLY ALA ASP PRO ALA HIS SEQRES 10 A 384 GLN GLY LEU HIS MET TRP LEU ALA GLU TYR PRO GLN PRO SEQRES 11 A 384 ARG PRO PRO ARG GLU THR TRP GLU SER ASN PRO LEU TYR SEQRES 12 A 384 ARG GLN LEU ASP ALA ASP PHE THR GLN HIS HIS ALA GLU SEQRES 13 A 384 ASN PRO GLY TYR THR GLY LEU HIS PHE MET ALA ALA TYR SEQRES 14 A 384 GLU LEU GLU GLU CYS TRP GLN LEU LEU ARG GLN SER LEU SEQRES 15 A 384 HIS SER VAL SER TYR GLU ALA LEU ALA HIS VAL PRO SER SEQRES 16 A 384 TYR ALA ASP TRP LEU SER ARG GLN ASP TRP THR PRO SER SEQRES 17 A 384 TYR CYS ARG HIS ARG ARG ASN LEU GLN LEU ILE GLY LEU SEQRES 18 A 384 ASN ASP ALA GLU LYS ARG TRP VAL LEU LYS ASN PRO SER SEQRES 19 A 384 HIS LEU PHE ALA LEU ASP ALA LEU MET ALA THR TYR PRO SEQRES 20 A 384 ASP ALA LEU VAL VAL GLN THR HIS ARG PRO VAL GLU THR SEQRES 21 A 384 ILE MET ALA SER MET CYS SER LEU ALA GLN HIS THR THR SEQRES 22 A 384 GLU GLY TRP SER THR LYS PHE VAL GLY ALA GLN ILE GLY SEQRES 23 A 384 ALA ASP ALA MET ASP THR TRP SER ARG GLY LEU GLU ARG SEQRES 24 A 384 PHE ASN ALA ALA ARG ALA LYS TYR ASP SER ALA GLN PHE SEQRES 25 A 384 TYR ASP VAL ASP TYR HIS ASP LEU ILE ALA ASP PRO LEU SEQRES 26 A 384 GLY THR VAL ALA ASP ILE TYR ARG HIS PHE GLY LEU THR SEQRES 27 A 384 LEU SER ASP GLU ALA ARG GLN ALA MET THR THR VAL HIS SEQRES 28 A 384 ALA GLU SER GLN SER GLY ALA ARG ALA PRO LYS HIS SER SEQRES 29 A 384 TYR SER LEU ALA ASP TYR GLY LEU THR VAL GLU MET VAL SEQRES 30 A 384 LYS GLU ARG PHE ALA GLY LEU FORMUL 2 HOH *704(H2 O) HELIX 1 1 THR A 12 GLY A 25 1 14 HELIX 2 2 ASN A 35 ALA A 51 1 17 HELIX 3 3 THR A 54 TYR A 82 1 29 HELIX 4 4 PRO A 83 VAL A 88 5 6 HELIX 5 5 GLY A 103 GLY A 112 1 10 HELIX 6 6 HIS A 121 TYR A 127 1 7 HELIX 7 7 PRO A 133 SER A 139 5 7 HELIX 8 8 ASN A 140 ASN A 157 1 18 HELIX 9 9 CYS A 174 ARG A 179 1 6 HELIX 10 10 GLN A 180 LEU A 182 5 3 HELIX 11 11 SER A 186 LEU A 190 5 5 HELIX 12 12 VAL A 193 ARG A 202 1 10 HELIX 13 13 TRP A 205 GLY A 220 1 16 HELIX 14 14 PRO A 233 ALA A 238 1 6 HELIX 15 15 ALA A 238 TYR A 246 1 9 HELIX 16 16 PRO A 257 THR A 260 5 4 HELIX 17 17 ILE A 261 THR A 273 1 13 HELIX 18 18 VAL A 281 ALA A 305 1 25 HELIX 19 19 LYS A 306 TYR A 307 5 2 HELIX 20 20 ASP A 308 ALA A 310 5 3 HELIX 21 21 TYR A 317 ASP A 323 1 7 HELIX 22 22 ASP A 323 PHE A 335 1 13 HELIX 23 23 SER A 340 THR A 349 1 10 HELIX 24 24 SER A 366 GLY A 371 5 6 HELIX 25 25 THR A 373 PHE A 381 1 9 SHEET 1 A 5 HIS A 117 GLY A 119 0 SHEET 2 A 5 ARG A 227 LYS A 231 1 O ARG A 227 N GLN A 118 SHEET 3 A 5 ILE A 94 THR A 97 1 N ILE A 94 O LEU A 230 SHEET 4 A 5 LEU A 250 HIS A 255 1 O VAL A 252 N PHE A 95 SHEET 5 A 5 PHE A 312 ASP A 316 1 O VAL A 315 N GLN A 253 CRYST1 40.864 95.761 48.038 90.00 106.43 90.00 P 1 21 1 2 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 0.024471 0.000000 0.007216 0.00000 SCALE2 0.000000 0.010443 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021703 0.00000