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- PDB-3hrh: Crystal Structure of Antigen 85C and Glycerol -

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Basic information

Entry
Database: PDB / ID: 3hrh
TitleCrystal Structure of Antigen 85C and Glycerol
ComponentsAntigen 85-C
KeywordsHYDROLASE / alpha/beta hydrolase / Acyltransferase / Secreted
Function / homology
Function and homology information


trehalose O-mycolyltransferase / trehalose O-mycolyltransferase activity / 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 / trehalose O-mycolyltransferase activity / 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
Diacylglycerol acyltransferase/mycolyltransferase Ag85C / Diacylglycerol acyltransferase/mycolyltransferase Ag85C
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsBoucau, J. / Sanki, A.K. / Umesiri, F.E. / Sucheck, S.J. / Ronning, D.R.
CitationJournal: Mol Biosyst / Year: 2009
Title: Design, synthesis and biological evaluation of sugar-derived esters, alpha-ketoesters and alpha-ketoamides as inhibitors for Mycobacterium tuberculosis antigen 85C.
Authors: Sanki, A.K. / Boucau, J. / Umesiri, F.E. / Ronning, D.R. / Sucheck, S.J.
History
DepositionJun 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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: Antigen 85-C
B: Antigen 85-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,32722
Polymers66,4862
Non-polymers1,84220
Water1,856103
1
B: Antigen 85-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,71617
Polymers33,2431
Non-polymers1,47416
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Antigen 85-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6115
Polymers33,2431
Non-polymers3684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6540 Å2
ΔGint-21 kcal/mol
Surface area20240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.777, 80.278, 136.835
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Antigen 85-C / Antigen 85 complex C / Ag85C / 85C / Mycolyl transferase 85C / Fibronectin-binding protein C


Mass: 33242.785 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: fbpC, fbpC2, mpt45, MT0137, MTCI5.03c, Rv0129c / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P0A4V4, UniProt: P9WQN9*PLUS, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.05 Å3/Da / Density % sol: 59.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M Na Acetate and 15% PEG 4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 11, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→48.44 Å / % possible obs: 99.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 18.5 Å2 / Rsym value: 0.138 / Net I/σ(I): 7.6

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1DQY

1dqy


Resolution: 2.3→48.44 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 85706.77 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.221 1634 5 %RANDOM
Rwork0.19 ---
obs0.19 32389 95.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.4426 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 27.3 Å2
Baniso -1Baniso -2Baniso -3
1-3.7 Å20 Å20 Å2
2---6.38 Å20 Å2
3---2.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.3→48.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4304 0 120 103 4527
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.171.5
X-RAY DIFFRACTIONc_mcangle_it1.842
X-RAY DIFFRACTIONc_scbond_it22
X-RAY DIFFRACTIONc_scangle_it2.862.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.275 272 5.4 %
Rwork0.225 4732 -
obs--90 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2gol.pargol.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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