HEADER LIPID TRANSPORT 02-MAY-14 4QA8 TITLE CRYSTAL STRUCTURE OF LPRF FROM MYCOBACTERIUM BOVIS CAVEAT 4QA8 THE C2 CENTER OF PJZ (301 A) HAS A PLANER CONFIGURATION. COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE LIPOPROTEIN LPRF; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 40-261; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM BOVIS; SOURCE 3 ORGANISM_TAXID: 233413; SOURCE 4 STRAIN: ATCC BAA-935 / AF2122/97; SOURCE 5 GENE: LPRF, MB1403; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LIPID TRANSFER, DIACYLATED GLYCOLIPID, LIPID TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR N.C.HA,L.JIAO,J.S.KIM REVDAT 2 20-MAR-24 4QA8 1 REMARK SEQADV REVDAT 1 22-OCT-14 4QA8 0 JRNL AUTH J.S.KIM,L.JIAO,J.I.OH,N.C.HA,Y.H.KIM JRNL TITL CRYSTAL STRUCTURE AND FUNCTIONAL IMPLICATIONS OF LPRF FROM JRNL TITL 2 MYCOBACTERIUM TUBERCULOSIS AND M. BOVIS JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 70 2619 2014 JRNL REFN ISSN 0907-4449 JRNL PMID 25286846 JRNL DOI 10.1107/S1399004714016599 REMARK 2 REMARK 2 RESOLUTION. 1.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.4_1496) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.56 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.250 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.4 REMARK 3 NUMBER OF REFLECTIONS : 61537 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 3455 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 18.5655 - 3.2111 0.92 2649 158 0.1592 0.2006 REMARK 3 2 3.2111 - 2.5508 0.97 2819 158 0.1843 0.2185 REMARK 3 3 2.5508 - 2.2290 0.97 2807 158 0.1760 0.2007 REMARK 3 4 2.2290 - 2.0255 0.96 2773 137 0.1722 0.1849 REMARK 3 5 2.0255 - 1.8805 0.95 2762 143 0.1677 0.1686 REMARK 3 6 1.8805 - 1.7697 0.94 2732 133 0.1717 0.1723 REMARK 3 7 1.7697 - 1.6811 0.95 2714 149 0.1711 0.2025 REMARK 3 8 1.6811 - 1.6080 0.94 2716 154 0.1634 0.1847 REMARK 3 9 1.6080 - 1.5461 0.94 2707 147 0.1578 0.1760 REMARK 3 10 1.5461 - 1.4928 0.92 2686 149 0.1425 0.1625 REMARK 3 11 1.4928 - 1.4461 0.92 2666 146 0.1510 0.1870 REMARK 3 12 1.4461 - 1.4048 0.92 2656 140 0.1431 0.1559 REMARK 3 13 1.4048 - 1.3678 0.91 2600 141 0.1442 0.1663 REMARK 3 14 1.3678 - 1.3345 0.91 2643 146 0.1401 0.1618 REMARK 3 15 1.3345 - 1.3041 0.89 2583 127 0.1437 0.1737 REMARK 3 16 1.3041 - 1.2764 0.90 2595 140 0.1407 0.1774 REMARK 3 17 1.2764 - 1.2509 0.88 2557 122 0.1500 0.1665 REMARK 3 18 1.2509 - 1.2273 0.88 2542 121 0.1431 0.1823 REMARK 3 19 1.2273 - 1.2053 0.87 2468 135 0.1378 0.1537 REMARK 3 20 1.2053 - 1.1849 0.86 2527 133 0.1452 0.1694 REMARK 3 21 1.1849 - 1.1658 0.86 2471 112 0.1448 0.1832 REMARK 3 22 1.1658 - 1.1479 0.84 2457 129 0.1488 0.1349 REMARK 3 23 1.1479 - 1.1310 0.85 2413 161 0.1516 0.1679 REMARK 3 24 1.1310 - 1.1151 0.83 2430 106 0.1665 0.1904 REMARK 3 25 1.1151 - 1.1000 0.81 2340 110 0.1830 0.1854 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.080 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.820 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 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 1682 REMARK 3 ANGLE : 1.159 2306 REMARK 3 CHIRALITY : 0.046 273 REMARK 3 PLANARITY : 0.006 306 REMARK 3 DIHEDRAL : 15.337 648 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 4QA8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-MAY-14. REMARK 100 THE DEPOSITION ID IS D_1000085799. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JUL-12 REMARK 200 TEMPERATURE (KELVIN) : 273 REMARK 200 PH : 7.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 7A (6B, 6C1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9789 REMARK 200 MONOCHROMATOR : DOUBLE MIRRORS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 68768 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.100 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.4 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 82.0 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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS-HCL (PH 7.8), 0.2M MAGNESIUM REMARK 280 CHLORIDE, 28% PEG 4000, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 295.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 GLY A 33 REMARK 465 ALA A 34 REMARK 465 MET A 35 REMARK 465 ASP A 36 REMARK 465 PRO A 37 REMARK 465 GLU A 38 REMARK 465 PHE A 39 REMARK 465 GLY A 40 REMARK 465 LYS A 41 REMARK 465 LYS A 42 REMARK 465 PRO A 43 REMARK 465 THR A 44 REMARK 465 THR A 45 REMARK 465 ALA A 46 REMARK 465 SER A 47 REMARK 465 SER A 48 REMARK 465 PRO A 49 REMARK 465 SER A 50 REMARK 465 PRO A 51 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 ASN A 103 101.55 -170.30 REMARK 500 GLN A 203 -23.48 72.23 REMARK 500 ASP A 239 -121.94 50.93 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 PJZ A 301 DBREF 4QA8 A 40 261 UNP P65315 LPRF_MYCBO 40 261 SEQADV 4QA8 GLY A 33 UNP P65315 EXPRESSION TAG SEQADV 4QA8 ALA A 34 UNP P65315 EXPRESSION TAG SEQADV 4QA8 MET A 35 UNP P65315 EXPRESSION TAG SEQADV 4QA8 ASP A 36 UNP P65315 EXPRESSION TAG SEQADV 4QA8 PRO A 37 UNP P65315 EXPRESSION TAG SEQADV 4QA8 GLU A 38 UNP P65315 EXPRESSION TAG SEQADV 4QA8 PHE A 39 UNP P65315 EXPRESSION TAG SEQRES 1 A 229 GLY ALA MET ASP PRO GLU PHE GLY LYS LYS PRO THR THR SEQRES 2 A 229 ALA SER SER PRO SER PRO GLY SER PRO SER PRO GLU ALA SEQRES 3 A 229 GLN GLN ILE LEU GLN ASP SER SER LYS ALA THR LYS GLY SEQRES 4 A 229 LEU HIS SER VAL HIS VAL VAL VAL THR VAL ASN ASN LEU SEQRES 5 A 229 SER THR LEU PRO PHE GLU SER VAL ASP ALA ASP VAL THR SEQRES 6 A 229 ASN GLN PRO GLN GLY ASN GLY GLN ALA VAL GLY ASN ALA SEQRES 7 A 229 LYS VAL ARG MET LYS PRO ASN THR PRO VAL VAL ALA THR SEQRES 8 A 229 GLU PHE LEU VAL THR ASN LYS THR MET TYR THR LYS ARG SEQRES 9 A 229 GLY GLY ASP TYR VAL SER VAL GLY PRO ALA GLU LYS ILE SEQRES 10 A 229 TYR ASP PRO GLY ILE ILE LEU ASP LYS ASP ARG GLY LEU SEQRES 11 A 229 GLY ALA VAL VAL GLY GLN VAL GLN ASN PRO THR ILE GLN SEQRES 12 A 229 GLY ARG ASP ALA ILE ASP GLY LEU ALA THR VAL LYS VAL SEQRES 13 A 229 SER GLY THR ILE ASP ALA ALA VAL ILE ASP PRO ILE VAL SEQRES 14 A 229 PRO GLN LEU GLY LYS GLY GLY GLY ARG LEU PRO ILE THR SEQRES 15 A 229 LEU TRP ILE VAL ASP THR ASN ALA SER THR PRO ALA PRO SEQRES 16 A 229 ALA ALA ASN LEU VAL ARG MET VAL ILE ASP LYS ASP GLN SEQRES 17 A 229 GLY ASN VAL ASP ILE THR LEU SER ASN TRP GLY ALA PRO SEQRES 18 A 229 VAL THR ILE PRO ASN PRO ALA GLY HET PJZ A 301 34 HETNAM PJZ (2R)-2-(DODECANOYLOXY)PROPYL (4E,6E,8E,10E,12E)- HETNAM 2 PJZ PENTADECA-4,6,8,10,12-PENTAENOATE FORMUL 2 PJZ C30 H48 O4 FORMUL 3 HOH *156(H2 O) HELIX 1 1 SER A 55 GLY A 71 1 17 HELIX 2 2 GLU A 147 ILE A 149 5 3 HELIX 3 3 ASP A 151 ILE A 155 5 5 HELIX 4 4 GLY A 161 GLN A 168 1 8 HELIX 5 5 ALA A 194 ASP A 198 1 5 SHEET 1 A11 ASP A 139 PRO A 145 0 SHEET 2 A11 THR A 131 ARG A 136 -1 N ARG A 136 O ASP A 139 SHEET 3 A11 VAL A 121 THR A 128 -1 N LEU A 126 O TYR A 133 SHEET 4 A11 GLY A 104 VAL A 112 -1 N ALA A 106 O VAL A 127 SHEET 5 A11 PHE A 89 ASN A 98 -1 N ASP A 95 O VAL A 107 SHEET 6 A11 SER A 74 ASN A 82 -1 N VAL A 77 O ALA A 94 SHEET 7 A11 GLY A 241 SER A 248 -1 O ASN A 242 N ASN A 82 SHEET 8 A11 LEU A 231 LYS A 238 -1 N MET A 234 O ILE A 245 SHEET 9 A11 ARG A 210 VAL A 218 -1 N TRP A 216 O VAL A 232 SHEET 10 A11 ALA A 184 ASP A 193 -1 N VAL A 188 O LEU A 215 SHEET 11 A11 GLN A 170 ALA A 179 -1 N GLN A 170 O THR A 191 CISPEP 1 GLN A 99 PRO A 100 0 -4.66 CISPEP 2 THR A 224 PRO A 225 0 -0.42 SITE 1 AC1 11 VAL A 96 ALA A 106 ARG A 113 MET A 114 SITE 2 AC1 11 THR A 123 PHE A 125 MET A 132 TYR A 150 SITE 3 AC1 11 PRO A 152 ILE A 155 PRO A 202 CRYST1 31.514 32.381 51.717 76.40 80.79 71.23 P 1 1 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 0.031732 -0.010781 -0.003086 0.00000 SCALE2 0.000000 0.032616 -0.006535 0.00000 SCALE3 0.000000 0.000000 0.019978 0.00000