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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: ANTIGEN 85-C;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: 85C
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS;
SOURCE 3 ORGANISM_COMMON: BACTERIA
KEYWDS ANTIGEN, 85C, MYCOBACTERIUM TUBERCULOSIS, FIBRONECTIN, DPI
EXPDTA X-RAY DIFFRACTION
AUTHOR D.R.RONNING,T.KLABUNDE,J.C.SACCHETTINI
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 ASTM NSBIEW US ISSN 1072-8368
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 OUTLIER CUTOFF HIGH (RMS(ABS(F))) : NULL
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 91.3
REMARK 3 NUMBER OF REFLECTIONS : 26959
REMARK 3
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
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 TOPOLOGY FILE 1 : NULL
REMARK 3 TOPOLOGY FILE 2 : NULL
REMARK 3 TOPOLOGY FILE 3 : NULL
REMARK 3 TOPOLOGY FILE 4 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1DQY COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-JAN-2000.
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 : HKL2000
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 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 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 (%): NULL
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL
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 1/2+X,1/2+Y,Z
REMARK 290 4555 1/2-X,1/2+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 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 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT
REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR
REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S).
REMARK 350
REMARK 350 GENERATING THE BIOMOLECULE
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 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: COVALENT BOND LENGTHS
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),F6.3)
REMARK 500
REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991
REMARK 500
REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION
REMARK 500 MET A 0 CA MET A 0 N 0.033
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991
REMARK 500
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
REMARK 500 GLN A 12 N - CA - C ANGL. DEV. = -8.3 DEGREES
REMARK 500 ASN A 52 N - CA - C ANGL. DEV. = 9.0 DEGREES
REMARK 500 PHE A 150 N - CA - C ANGL. DEV. = -8.0 DEGREES
REMARK 500 LEU A 151 N - CA - C ANGL. DEV. = 10.0 DEGREES
REMARK 500 ARG A 204 N - CA - C ANGL. DEV. = -8.0 DEGREES
REMARK 500 VAL A 251 N - CA - C ANGL. DEV. = -9.1 DEGREES
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 M RES CSSEQI PSI PHI
REMARK 500 SER A 86 148.39 -47.85
REMARK 500 SER A 124 51.96 -114.17
REMARK 500 SER A 156 42.94 -110.44
REMARK 500 ASP A 220 17.06 -115.59
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1DQZ RELATED DB: PDB
DBREF 1DQY A 0 282 SWS P31953 A85C_MYCTU 46 328
SEQADV 1DQY MET A 0 SWS P31953 ALA 46 CONFLICT
SEQADV 1DQY SER A 156 SWS P31953 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 MPD 402 8
HET MPD 403 8
HETNAM DEP DIETHYLPHOSPHONO GROUP
HETNAM MPD 2-METHYL-2,4-PENTANEDIOL
FORMUL 2 DEP C4 H10 O3 P1
FORMUL 3 MPD 2(C6 H14 O2)
FORMUL 5 HOH *292(H2 O1)
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
CISPEP 1 THR A 213 PRO A 214 0 -0.13
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
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