PDB Short entry for 1DQY HEADER IMMUNE SYSTEM 05-JAN-00 1DQY TITLE CRYSTAL STRUCTURE OF ANTIGEN 85C FROM MYCOBACTERIUM TITLE 2 TUBERCULOSIS WITH DIETHYL PHOSPHATE INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (ANTIGEN 85-C); COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 85C SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 1773 KEYWDS ANTIGEN, 85C, MYCOBACTERIUM TUBERCULOSIS, FIBRONECTIN, DPI, KEYWDS 2 STRUCTURAL GENOMICS, PSI, PROTEIN STRUCTURE INITIATIVE, TB KEYWDS 3 STRUCTURAL GENOMICS CONSORTIUM, TBSGC, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR D.R.RONNING,T.KLABUNDE,J.C.SACCHETTINI,TB STRUCTURAL AUTHOR 2 GENOMICS CONSORTIUM (TBSGC) REVDAT 3 24-FEB-09 1DQY 1 VERSN REVDAT 2 01-FEB-05 1DQY 1 AUTHOR KEYWDS REMARK REVDAT 1 12-JUL-00 1DQY 0 JRNL AUTH D.R.RONNING,T.KLABUNDE,G.S.BESRA,V.D.VISSA, JRNL AUTH 2 J.T.BELISLE,J.C.SACCHETTINI JRNL TITL CRYSTAL STRUCTURE OF THE SECRETED FORM OF ANTIGEN JRNL TITL 2 85C REVEALS POTENTIAL TARGETS FOR MYCOBACTERIAL JRNL TITL 3 DRUGS AND VACCINES. JRNL REF NAT.STRUCT.BIOL. V. 7 141 2000 JRNL REFN ISSN 1072-8368 JRNL PMID 10655617 JRNL DOI 10.1038/72413 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.83 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.83 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 91.3 REMARK 3 NUMBER OF REFLECTIONS : 26959 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2675 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) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2205 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 8 REMARK 3 SOLVENT ATOMS : 308 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) : 0.70800 REMARK 3 B22 (A**2) : 1.55500 REMARK 3 B33 (A**2) : -2.26300 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.54800 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.25 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL 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) : 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 : 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : MPD.PAR REMARK 3 PARAMETER FILE 4 : DEP.PAR REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1DQY COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-JAN-00. REMARK 100 THE RCSB ID CODE IS RCSB010310. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL 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 : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 64.40000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.90400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 64.40000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 33.90400 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 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 2 48.04 -78.56 REMARK 500 PRO A 54 37.48 -92.08 REMARK 500 PHE A 76 19.59 56.68 REMARK 500 SER A 86 -47.85 148.39 REMARK 500 ARG A 101 -62.71 -132.25 REMARK 500 SER A 124 -114.17 51.96 REMARK 500 ASN A 152 53.21 -152.02 REMARK 500 SER A 156 -110.44 42.94 REMARK 500 SER A 215 -169.43 -162.59 REMARK 500 ASP A 220 -115.59 17.06 REMARK 500 ASN A 221 173.44 -51.39 REMARK 500 ARG A 248 12.94 -143.14 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 DEP A 401 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MRD A 402 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MRD A 403 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DQZ RELATED DB: PDB REMARK 900 RELATED ID: RV0129C RELATED DB: TARGETDB DBREF 1DQY A 0 282 UNP P0A4V4 A85C_MYCTU 46 328 SEQADV 1DQY MET A 0 UNP P0A4V4 ALA 46 CONFLICT SEQADV 1DQY SER A 156 UNP P0A4V4 GLY 202 CONFLICT SEQRES 1 A 283 MET PHE SER ARG PRO GLY LEU PRO VAL GLU TYR LEU GLN SEQRES 2 A 283 VAL PRO SER ALA SER MET GLY ARG ASP ILE LYS VAL GLN SEQRES 3 A 283 PHE GLN GLY GLY GLY PRO HIS ALA VAL TYR LEU LEU ASP SEQRES 4 A 283 GLY LEU ARG ALA GLN ASP ASP TYR ASN GLY TRP ASP ILE SEQRES 5 A 283 ASN THR PRO ALA PHE GLU GLU TYR TYR GLN SER GLY LEU SEQRES 6 A 283 SER VAL ILE MET PRO VAL GLY GLY GLN SER SER PHE TYR SEQRES 7 A 283 THR ASP TRP TYR GLN PRO SER GLN SER ASN GLY GLN ASN SEQRES 8 A 283 TYR THR TYR LYS TRP GLU THR PHE LEU THR ARG GLU MET SEQRES 9 A 283 PRO ALA TRP LEU GLN ALA ASN LYS GLY VAL SER PRO THR SEQRES 10 A 283 GLY ASN ALA ALA VAL GLY LEU SER MET SER GLY GLY SER SEQRES 11 A 283 ALA LEU ILE LEU ALA ALA TYR TYR PRO GLN GLN PHE PRO SEQRES 12 A 283 TYR ALA ALA SER LEU SER GLY PHE LEU ASN PRO SER GLU SEQRES 13 A 283 SER TRP TRP PRO THR LEU ILE GLY LEU ALA MET ASN ASP SEQRES 14 A 283 SER GLY GLY TYR ASN ALA ASN SER MET TRP GLY PRO SER SEQRES 15 A 283 SER ASP PRO ALA TRP LYS ARG ASN ASP PRO MET VAL GLN SEQRES 16 A 283 ILE PRO ARG LEU VAL ALA ASN ASN THR ARG ILE TRP VAL SEQRES 17 A 283 TYR CYS GLY ASN GLY THR PRO SER ASP LEU GLY GLY ASP SEQRES 18 A 283 ASN ILE PRO ALA LYS PHE LEU GLU GLY LEU THR LEU ARG SEQRES 19 A 283 THR ASN GLN THR PHE ARG ASP THR TYR ALA ALA ASP GLY SEQRES 20 A 283 GLY ARG ASN GLY VAL PHE ASN PHE PRO PRO ASN GLY THR SEQRES 21 A 283 HIS SER TRP PRO TYR TRP ASN GLU GLN LEU VAL ALA MET SEQRES 22 A 283 LYS ALA ASP ILE GLN HIS VAL LEU ASN GLY HET DEP A 401 8 HET MRD A 402 8 HET MRD A 403 8 HETNAM DEP DIETHYL PHOSPHONATE HETNAM MRD (4R)-2-METHYLPENTANE-2,4-DIOL FORMUL 2 DEP C4 H11 O3 P FORMUL 3 MRD 2(C6 H14 O2) FORMUL 5 HOH *292(H2 O) HELIX 1 1 ASN A 47 THR A 53 1 7 HELIX 2 2 PRO A 54 TYR A 60 1 7 HELIX 3 3 LYS A 94 ARG A 101 1 8 HELIX 4 4 ARG A 101 GLY A 112 1 12 HELIX 5 5 MET A 125 TYR A 137 1 13 HELIX 6 6 TRP A 157 SER A 169 1 13 HELIX 7 7 ASN A 173 GLY A 179 1 7 HELIX 8 8 ASP A 183 ASN A 189 1 7 HELIX 9 9 GLN A 194 ASN A 201 1 8 HELIX 10 10 ASN A 221 ASP A 245 1 25 HELIX 11 11 SER A 261 GLY A 282 1 22 SHEET 1 A 8 VAL A 8 SER A 15 0 SHEET 2 A 8 ARG A 20 GLN A 27 -1 O ARG A 20 N SER A 15 SHEET 3 A 8 SER A 65 PRO A 69 -1 N VAL A 66 O GLN A 27 SHEET 4 A 8 ALA A 33 LEU A 36 1 O VAL A 34 N ILE A 67 SHEET 5 A 8 ALA A 119 LEU A 123 1 O ALA A 119 N TYR A 35 SHEET 6 A 8 TYR A 143 LEU A 147 1 O TYR A 143 N ALA A 120 SHEET 7 A 8 ARG A 204 TYR A 208 1 O ARG A 204 N ALA A 144 SHEET 8 A 8 GLY A 250 ASN A 253 1 O VAL A 251 N VAL A 207 LINK OG SER A 124 P DEP A 401 1555 1555 1.59 CISPEP 1 THR A 213 PRO A 214 0 -0.13 SITE 1 AC1 6 GLY A 39 LEU A 40 SER A 124 MET A 125 SITE 2 AC1 6 ASP A 216 LEU A 217 SITE 1 AC2 10 PHE A 26 GLY A 28 GLY A 29 GLY A 30 SITE 2 AC2 10 PRO A 31 SER A 65 LYS A 111 GLY A 112 SITE 3 AC2 10 HOH A1504 HOH A1542 SITE 1 AC3 6 PRO A 159 LEU A 164 ASN A 175 TRP A 186 SITE 2 AC3 6 HOH A1364 HOH A1575 CRYST1 128.800 67.808 39.765 90.00 102.73 90.00 C 1 2 1 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 0.007764 0.000000 0.001754 0.00000 SCALE2 0.000000 0.014748 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025781 0.00000