HEADER UNKNOWN FUNCTION 27-MAR-09 3GT2 TITLE CRYSTAL STRUCTURE OF THE P60 DOMAIN FROM M. AVIUM PARATUBERCULOSIS TITLE 2 ANTIGEN MAP1272C COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE UNCHARACTERIZED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM AVIUM SUBSP. PARATUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 1770; SOURCE 4 STRAIN: K-10; SOURCE 5 GENE: MAP1272C, MAP_1272C; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: B834(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PT7HMT KEYWDS P60 DOMAIN, ANTIGEN, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR K.X.RAMYAR,C.K.LINGLE,W.J.MCWHORTER,S.BOUYAIN,J.P.BANNANTINE, AUTHOR 2 B.V.GEISBRECHT REVDAT 2 01-NOV-17 3GT2 1 REMARK REVDAT 1 07-APR-10 3GT2 0 JRNL AUTH K.X.RAMYAR,C.K.LINGLE,W.J.MCWHORTER,S.BOUYAIN, JRNL AUTH 2 J.P.BANNANTINE,B.V.GEISBRECHT JRNL TITL CRYSTAL STRUCTURES OF TWO P60-FAMILY ANTIGENS FROM JRNL TITL 2 MYCOBACTERIUM AVIUM PARATUBERCULOSIS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : MLHL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.68 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.030 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.8 REMARK 3 NUMBER OF REFLECTIONS : 13012 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.201 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.090 REMARK 3 FREE R VALUE TEST SET COUNT : 1313 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 22.6765 - 3.6295 0.97 1378 153 0.1961 0.1802 REMARK 3 2 3.6295 - 2.8827 1.00 1390 155 0.1750 0.1962 REMARK 3 3 2.8827 - 2.5188 0.99 1372 153 0.1747 0.2166 REMARK 3 4 2.5188 - 2.2888 0.99 1386 153 0.1688 0.2216 REMARK 3 5 2.2888 - 2.1248 0.99 1363 148 0.1693 0.2001 REMARK 3 6 2.1248 - 1.9996 0.98 1364 152 0.1686 0.2157 REMARK 3 7 1.9996 - 1.8996 0.94 1292 149 0.1764 0.2093 REMARK 3 8 1.8996 - 1.8169 0.87 1183 137 0.1963 0.1947 REMARK 3 9 1.8169 - 1.7500 0.71 971 113 0.1970 0.2214 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.38 REMARK 3 B_SOL : 74.64 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.760 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.110 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.63 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.53400 REMARK 3 B22 (A**2) : 3.40700 REMARK 3 B33 (A**2) : -7.94100 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 3.88800 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 1037 REMARK 3 ANGLE : 0.971 1407 REMARK 3 CHIRALITY : 0.064 147 REMARK 3 PLANARITY : 0.004 182 REMARK 3 DIHEDRAL : 15.002 365 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -7.3847 30.8294 34.5798 REMARK 3 T TENSOR REMARK 3 T11: 0.1333 T22: 0.1459 REMARK 3 T33: 0.1428 T12: 0.0108 REMARK 3 T13: -0.0012 T23: 0.0100 REMARK 3 L TENSOR REMARK 3 L11: 0.2744 L22: 0.9183 REMARK 3 L33: 0.6832 L12: 0.6927 REMARK 3 L13: 0.0993 L23: 0.0131 REMARK 3 S TENSOR REMARK 3 S11: -0.0414 S12: 0.0097 S13: -0.0842 REMARK 3 S21: 0.0266 S22: 0.0580 S23: 0.0064 REMARK 3 S31: 0.0304 S32: -0.1162 S33: -0.0196 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3GT2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-APR-09. REMARK 100 THE DEPOSITION ID IS D_1000052271. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 97 REMARK 200 PH : 6.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9724 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13278 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 500.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.4460 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 78.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.20 REMARK 200 R MERGE FOR SHELL (I) : 0.21600 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: SAD REMARK 200 SOFTWARE USED: PHASES, RESOLVE 2.13, PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BISTRIS-HCL, 1.6 M AMMONIUM REMARK 280 SULFATE, 4% (V/V) PEG 400, PH 6.3, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 273K 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 26.60600 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 ALA A 64 REMARK 465 THR A 65 REMARK 465 ALA A 66 REMARK 465 ASP A 67 REMARK 465 PRO A 68 REMARK 465 GLY A 204 REMARK 465 THR A 205 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 SER A 137 131.83 89.98 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 SO4 A 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 207 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 208 DBREF 3GT2 A 64 205 UNP Q740S0 Q740S0_MYCPA 64 205 SEQRES 1 A 142 ALA THR ALA ASP PRO GLY VAL ARG ALA MSE ASP TYR GLN SEQRES 2 A 142 GLN ALA THR ASP VAL VAL ILE ALA ARG GLY LEU SER GLN SEQRES 3 A 142 ARG GLY VAL PRO PHE SER TRP ALA GLY GLY GLY ILE ASN SEQRES 4 A 142 GLY PRO THR ARG GLY THR GLY THR GLY ALA ASN THR VAL SEQRES 5 A 142 GLY PHE ASP ALA SER GLY LEU MSE GLN TYR ALA TYR ALA SEQRES 6 A 142 GLY ALA GLY ILE LYS LEU PRO ARG SER SER GLY ALA MSE SEQRES 7 A 142 TYR ARG VAL GLY GLN LYS ILE LEU PRO GLN GLN ALA ARG SEQRES 8 A 142 LYS GLY ASP LEU ILE PHE TYR GLY PRO GLU GLY THR GLN SEQRES 9 A 142 SER VAL ALA MSE TYR LEU GLY ASN ASN GLN MSE LEU GLU SEQRES 10 A 142 VAL GLY ASP VAL VAL GLN VAL SER PRO VAL ARG THR ALA SEQRES 11 A 142 GLY MSE ALA PRO TYR MSE VAL ARG VAL LEU GLY THR MODRES 3GT2 MSE A 73 MET SELENOMETHIONINE MODRES 3GT2 MSE A 123 MET SELENOMETHIONINE MODRES 3GT2 MSE A 141 MET SELENOMETHIONINE MODRES 3GT2 MSE A 171 MET SELENOMETHIONINE MODRES 3GT2 MSE A 178 MET SELENOMETHIONINE MODRES 3GT2 MSE A 195 MET SELENOMETHIONINE MODRES 3GT2 MSE A 199 MET SELENOMETHIONINE HET MSE A 73 8 HET MSE A 123 8 HET MSE A 141 8 HET MSE A 171 8 HET MSE A 178 8 HET MSE A 195 8 HET MSE A 199 8 HET SO4 A 206 5 HET SO4 A 207 5 HET EDO A 208 10 HET EDO A 209 10 HETNAM MSE SELENOMETHIONINE HETNAM SO4 SULFATE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 1 MSE 7(C5 H11 N O2 SE) FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 EDO 2(C2 H6 O2) FORMUL 6 HOH *100(H2 O) HELIX 1 1 GLY A 69 SER A 88 1 20 HELIX 2 2 THR A 108 ALA A 112 5 5 HELIX 3 3 ASP A 118 GLY A 129 1 12 HELIX 4 4 SER A 137 TYR A 142 1 6 HELIX 5 5 LEU A 149 ALA A 153 5 5 HELIX 6 6 GLY A 162 THR A 166 5 5 SHEET 1 A 2 THR A 105 ARG A 106 0 SHEET 2 A 2 VAL A 115 GLY A 116 -1 O GLY A 116 N THR A 105 SHEET 1 B 2 GLN A 146 ILE A 148 0 SHEET 2 B 2 MSE A 199 ARG A 201 -1 O MSE A 199 N ILE A 148 SHEET 1 C 4 LEU A 158 TYR A 161 0 SHEET 2 C 4 SER A 168 GLY A 174 -1 O ALA A 170 N ILE A 159 SHEET 3 C 4 GLN A 177 VAL A 181 -1 O GLN A 177 N LEU A 173 SHEET 4 C 4 VAL A 185 PRO A 189 -1 O SER A 188 N MSE A 178 LINK C ALA A 72 N MSE A 73 1555 1555 1.33 LINK C MSE A 73 N ASP A 74 1555 1555 1.33 LINK C LEU A 122 N MSE A 123 1555 1555 1.33 LINK C MSE A 123 N GLN A 124 1555 1555 1.33 LINK C ALA A 140 N MSE A 141 1555 1555 1.33 LINK C MSE A 141 N TYR A 142 1555 1555 1.33 LINK C ALA A 170 N MSE A 171 1555 1555 1.33 LINK C MSE A 171 N TYR A 172 1555 1555 1.33 LINK C GLN A 177 N MSE A 178 1555 1555 1.33 LINK C MSE A 178 N LEU A 179 1555 1555 1.33 LINK C GLY A 194 N MSE A 195 1555 1555 1.33 LINK C MSE A 195 N ALA A 196 1555 1555 1.33 LINK C TYR A 198 N MSE A 199 1555 1555 1.33 LINK C MSE A 199 N VAL A 200 1555 1555 1.33 SITE 1 AC1 3 THR A 105 ARG A 106 TYR A 198 SITE 1 AC2 4 TYR A 172 GLY A 174 ASN A 175 HOH A 262 SITE 1 AC3 3 LYS A 133 HOH A 291 HOH A 294 CRYST1 34.715 53.212 38.325 90.00 102.95 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 0.028806 0.000000 0.006624 0.00000 SCALE2 0.000000 0.018793 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026774 0.00000