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- PDB-1dqy: CRYSTAL STRUCTURE OF ANTIGEN 85C FROM MYCOBACTERIUM TUBERCULOSIS ... -

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Basic information

Entry
Database: PDB / ID: 1dqy
TitleCRYSTAL STRUCTURE OF ANTIGEN 85C FROM MYCOBACTERIUM TUBERCULOSIS WITH DIETHYL PHOSPHATE INHIBITOR
ComponentsPROTEIN (ANTIGEN 85-C)
KeywordsIMMUNE SYSTEM / ANTIGEN / 85C / MYCOBACTERIUM TUBERCULOSIS / FIBRONECTIN / DPI / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


trehalose O-mycolyltransferase activity / trehalose O-mycolyltransferase / diacylglycerol O-acyltransferase / diacylglycerol O-acyltransferase activity / mycolate cell wall layer assembly / glycolipid biosynthetic process / zymogen binding / lipid transport / acyltransferase activity, transferring groups other than amino-acyl groups / peptidoglycan-based cell wall ...trehalose O-mycolyltransferase activity / trehalose O-mycolyltransferase / diacylglycerol O-acyltransferase / diacylglycerol O-acyltransferase activity / mycolate cell wall layer assembly / glycolipid biosynthetic process / zymogen binding / lipid transport / acyltransferase activity, transferring groups other than amino-acyl groups / peptidoglycan-based cell wall / response to antibiotic / extracellular region
Similarity search - Function
: / Esterase-like / Putative esterase / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DIETHYL PHOSPHONATE / Diacylglycerol acyltransferase/mycolyltransferase Ag85C / Diacylglycerol acyltransferase/mycolyltransferase Ag85C
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.83 Å
AuthorsRonning, D.R. / Klabunde, T. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: Crystal structure of the secreted form of antigen 85C reveals potential targets for mycobacterial drugs and vaccines.
Authors: Ronning, D.R. / Klabunde, T. / Besra, G.S. / Vissa, V.D. / Belisle, J.T. / Sacchettini, J.C.
History
DepositionJan 5, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (ANTIGEN 85-C)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5894
Polymers31,2151
Non-polymers3743
Water5,260292
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.800, 67.808, 39.765
Angle α, β, γ (deg.)90.00, 102.73, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PROTEIN (ANTIGEN 85-C) / 85C


Mass: 31214.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: P0A4V4, UniProt: P9WQN9*PLUS
#2: Chemical ChemComp-DEP / DIETHYL PHOSPHONATE


Mass: 138.102 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H11O3P
#3: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.63 %
Crystal
*PLUS
Density % sol: 53 %
Crystal grow
*PLUS
pH: 5.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1100 mMsodium citrate1reservoir
20.7 M1reservoirNH4H2PO4
31 mMpHMPS1drop

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.83 Å / Lowest resolution: 30 Å / Num. obs: 128115 / % possible obs: 94.4 % / Num. measured all: 27884 / Rmerge(I) obs: 0.052
Reflection shell
*PLUS
% possible obs: 80.3 % / Rmerge(I) obs: 0.226

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Processing

Software
NameClassification
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 1.83→30 Å / σ(F): 1
RfactorNum. reflection% reflection
Rfree0.1887 2675 9.1 %
Rwork0.1684 --
all0.186 --
obs0.1654 26959 91.3 %
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.708 Å20 Å20.548 Å2
2--1.555 Å20 Å2
3----2.263 Å2
Refinement stepCycle: LAST / Resolution: 1.83→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2205 0 8 308 2521
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004975
X-RAY DIFFRACTIONc_angle_deg1.24843
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3mpd.par
X-RAY DIFFRACTION4dep.par
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.165 / Rfactor Rfree: 0.188 / Rfactor Rwork: 0.168
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 21.02 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.05
X-RAY DIFFRACTIONc_angle_deg1.25

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