HEADER TRANSFERASE 16-JUN-04 1TPY TITLE STRUCTURE OF THE CYCLOPROPANE SYNTHASE MMAA2 FROM MYCOBACTERIUM TITLE 2 TUBERCULOSIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHOXY MYCOLIC ACID SYNTHASE 2; COMPND 3 CHAIN: A; COMPND 4 EC: 2.1.1.79; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 1773; SOURCE 4 GENE: MMAA2; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET30B-MMAA2 KEYWDS METHYLTRANSFERASE, CYCLOPROPANE SYNTHASE, MYCOLIC ACIDS, KEYWDS 2 TUBERCULOSIS, SAM-DEPENDENT, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR C.V.SMITH,J.C.SACCHETTINI REVDAT 3 23-AUG-23 1TPY 1 REMARK SEQADV REVDAT 2 24-FEB-09 1TPY 1 VERSN REVDAT 1 19-OCT-04 1TPY 0 JRNL AUTH C.V.SMITH,J.C.SACCHETTINI JRNL TITL STRUCTURE OF THE CYCLOPROPANE SYNTHASE MMAA2 FROM JRNL TITL 2 MYCOBACTERIUM TUBERCULOSIS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 3.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.6 REMARK 3 NUMBER OF REFLECTIONS : 16498 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) : 0.194 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1654 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 : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.34 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 82.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2050 REMARK 3 BIN FREE R VALUE : 0.2430 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 227 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.016 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2292 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 50 REMARK 3 SOLVENT ATOMS : 192 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.24 REMARK 3 ESD FROM SIGMAA (A) : 0.13 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) : 0.29 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.22 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.780 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.220 ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.840 ; 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 : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1TPY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-JUL-04. REMARK 100 THE DEPOSITION ID IS D_1000022819. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-NOV-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.3 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 : SINGLE CRYSTAL, CYLINDRICALLY REMARK 200 BENT, SI(220) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17358 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.05820 REMARK 200 R SYM (I) : 0.03600 REMARK 200 FOR THE DATA SET : 10.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.19 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PCAA ENTRY 1LIE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 6000, MES BUFFER, CETYL TRIMETHYL REMARK 280 AMMONIUM BROMIDE, S-ADENOSYL-L-HOMOCYSTEINE, PH 6.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 292K 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 21.29350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 66.84150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.21000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 66.84150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.29350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.21000 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 MET A 1 REMARK 465 VAL A 2 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 ASP A 4 -169.15 53.87 REMARK 500 HIS A 15 -61.48 -101.34 REMARK 500 SER A 19 123.54 169.96 REMARK 500 ASP A 111 62.23 -110.47 REMARK 500 ARG A 224 137.98 -178.42 REMARK 500 GLN A 254 -95.56 -125.10 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO3 A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SAH A 1900 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 16A A 1901 DBREF 1TPY A 2 287 UNP Q79FX6 Q79FX6_MYCTU 32 317 SEQADV 1TPY MET A 1 UNP Q79FX6 INITIATING METHIONINE SEQRES 1 A 287 MET VAL ASN ASP LEU THR PRO HIS PHE GLU ASP VAL GLN SEQRES 2 A 287 ALA HIS TYR ASP LEU SER ASP ASP PHE PHE ARG LEU PHE SEQRES 3 A 287 LEU ASP PRO THR GLN THR TYR SER CYS ALA HIS PHE GLU SEQRES 4 A 287 ARG GLU ASP MET THR LEU GLU GLU ALA GLN ILE ALA LYS SEQRES 5 A 287 ILE ASP LEU ALA LEU GLY LYS LEU GLY LEU GLN PRO GLY SEQRES 6 A 287 MET THR LEU LEU ASP ILE GLY CYS GLY TRP GLY ALA THR SEQRES 7 A 287 MET ARG ARG ALA ILE ALA GLN TYR ASP VAL ASN VAL VAL SEQRES 8 A 287 GLY LEU THR LEU SER LYS ASN GLN ALA ALA HIS VAL GLN SEQRES 9 A 287 LYS SER PHE ASP GLU MET ASP THR PRO ARG ASP ARG ARG SEQRES 10 A 287 VAL LEU LEU ALA GLY TRP GLU GLN PHE ASN GLU PRO VAL SEQRES 11 A 287 ASP ARG ILE VAL SER ILE GLY ALA PHE GLU HIS PHE GLY SEQRES 12 A 287 HIS ASP ARG HIS ALA ASP PHE PHE ALA ARG ALA HIS LYS SEQRES 13 A 287 ILE LEU PRO PRO ASP GLY VAL LEU LEU LEU HIS THR ILE SEQRES 14 A 287 THR GLY LEU THR ARG GLN GLN MET VAL ASP HIS GLY LEU SEQRES 15 A 287 PRO LEU THR LEU TRP LEU ALA ARG PHE LEU LYS PHE ILE SEQRES 16 A 287 ALA THR GLU ILE PHE PRO GLY GLY GLN PRO PRO THR ILE SEQRES 17 A 287 GLU MET VAL GLU GLU GLN SER ALA LYS THR GLY PHE THR SEQRES 18 A 287 LEU THR ARG ARG GLN SER LEU GLN PRO HIS TYR ALA ARG SEQRES 19 A 287 THR LEU ASP LEU TRP ALA GLU ALA LEU GLN GLU HIS LYS SEQRES 20 A 287 SER GLU ALA ILE ALA ILE GLN SER GLU GLU VAL TYR GLU SEQRES 21 A 287 ARG TYR MET LYS TYR LEU THR GLY CYS ALA LYS LEU PHE SEQRES 22 A 287 ARG VAL GLY TYR ILE ASP VAL ASN GLN PHE THR LEU ALA SEQRES 23 A 287 LYS HET CO3 A 902 4 HET SAH A1900 26 HET 16A A1901 20 HETNAM CO3 CARBONATE ION HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE HETNAM 16A CETYL-TRIMETHYL-AMMONIUM FORMUL 2 CO3 C O3 2- FORMUL 3 SAH C14 H20 N6 O5 S FORMUL 4 16A C19 H42 N 1+ FORMUL 5 HOH *192(H2 O) HELIX 1 1 HIS A 8 ASP A 17 1 10 HELIX 2 2 SER A 19 LEU A 25 1 7 HELIX 3 3 THR A 44 GLY A 58 1 15 HELIX 4 4 GLY A 76 ASP A 87 1 12 HELIX 5 5 SER A 96 GLU A 109 1 14 HELIX 6 6 GLY A 122 PHE A 126 5 5 HELIX 7 7 ALA A 138 GLY A 143 1 6 HELIX 8 8 ARG A 146 LEU A 158 1 13 HELIX 9 9 THR A 173 HIS A 180 1 8 HELIX 10 10 THR A 185 ILE A 199 1 15 HELIX 11 11 THR A 207 GLY A 219 1 13 HELIX 12 12 LEU A 228 HIS A 246 1 19 HELIX 13 13 HIS A 246 GLN A 254 1 9 HELIX 14 14 SER A 255 GLY A 276 1 22 SHEET 1 A 7 ARG A 116 LEU A 120 0 SHEET 2 A 7 ASN A 89 THR A 94 1 N GLY A 92 O LEU A 119 SHEET 3 A 7 THR A 67 ILE A 71 1 N LEU A 68 O ASN A 89 SHEET 4 A 7 ARG A 132 ILE A 136 1 O VAL A 134 N LEU A 69 SHEET 5 A 7 VAL A 163 GLY A 171 1 O HIS A 167 N SER A 135 SHEET 6 A 7 ILE A 278 ALA A 286 -1 O LEU A 285 N LEU A 164 SHEET 7 A 7 THR A 221 SER A 227 -1 N ARG A 224 O THR A 284 SITE 1 AC1 9 SER A 34 CYS A 35 GLY A 137 GLU A 140 SITE 2 AC1 9 HIS A 167 THR A 168 ILE A 169 TYR A 232 SITE 3 AC1 9 16A A1901 SITE 1 AC2 25 VAL A 12 TYR A 16 THR A 32 TYR A 33 SITE 2 AC2 25 SER A 34 GLY A 72 GLY A 74 THR A 94 SITE 3 AC2 25 LEU A 95 SER A 96 GLN A 99 GLY A 122 SITE 4 AC2 25 TRP A 123 GLU A 124 ILE A 136 GLY A 137 SITE 5 AC2 25 ALA A 138 HIS A 141 PHE A 142 16A A1901 SITE 6 AC2 25 HOH A1902 HOH A1905 HOH A1928 HOH A1932 SITE 7 AC2 25 HOH A1946 SITE 1 AC3 14 TYR A 16 TYR A 33 GLY A 137 GLU A 140 SITE 2 AC3 14 HIS A 141 ILE A 169 ILE A 195 PHE A 200 SITE 3 AC3 14 PRO A 205 TYR A 232 LEU A 236 CYS A 269 SITE 4 AC3 14 CO3 A 902 SAH A1900 CRYST1 42.587 58.420 133.683 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 0.023481 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017117 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007480 0.00000