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- PDB-1va5: Antigen 85C with octylthioglucoside in active site -

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Basic information

Entry
Database: PDB / ID: 1va5
TitleAntigen 85C with octylthioglucoside in active site
ComponentsAntigen 85-C
KeywordsTRANSFERASE / alpha-beta hydrolase / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


trehalose O-mycolyltransferase / trehalose O-mycolyltransferase activity / diacylglycerol O-acyltransferase / diacylglycerol O-acyltransferase activity / glycolipid biosynthetic process / mycolate cell wall layer assembly / 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 / glycolipid biosynthetic process / mycolate cell wall layer assembly / 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 / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsRonning, D.R. / Vissa, V. / Besra, G.S. / Belisle, J.T. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Mycobacterium tuberculosis Antigen 85A and 85C Structures Confirm Binding Orientation and Conserved Substrate Specificity
Authors: Ronning, D.R. / Vissa, V. / Besra, G.S. / Belisle, J.T. / Sacchettini, J.C.
History
DepositionFeb 11, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)67,5756
Polymers66,3412
Non-polymers1,2344
Water4,540252
1
A: Antigen 85-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7883
Polymers33,1711
Non-polymers6172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Antigen 85-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7883
Polymers33,1711
Non-polymers6172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)144.818, 68.117, 82.281
Angle α, β, γ (deg.)90.00, 119.60, 90.00
Int Tables number5
Space group name H-MC121
Detailsthe biological assembly is a monomer

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Components

#1: Protein Antigen 85-C


Mass: 33170.723 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: fbpC2 / Plasmid: pET29 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: P0A4V4, UniProt: P9WQN9*PLUS, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Sugar
ChemComp-SOG / octyl 1-thio-beta-D-glucopyranoside / 2-HYDROXYMETHYL-6-OCTYLSULFANYL-TETRAHYDRO-PYRAN-3,4,5-TRIOL / 1-S-OCTYL-BETA-D-THIOGLUCOSIDE / octyl 1-thio-beta-D-glucoside / octyl 1-thio-D-glucoside / octyl 1-thio-glucoside / N-Octyl beta-D-thioglucopyranoside


Type: D-saccharide / Mass: 308.434 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C14H28O5S / Comment: detergent*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.66 Å3/Da / Density % sol: 53.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: octylthioglucoside, Sodium Acetate, Imidazole, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Aug 4, 2000 / Details: mirrors
RadiationMonochromator: Ni MIRROR + Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.02→38.72 Å / Num. all: 121933 / Num. obs: 44080 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 9.4 Å2 / Rsym value: 0.042 / Net I/σ(I): 17.5
Reflection shellResolution: 2.02→2.12 Å / Rsym value: 0.114 / % possible all: 83.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DZQ

1dzq


Resolution: 2.02→38.72 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 507000.61 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.211 2172 5 %RANDOM
Rwork0.187 ---
obs0.187 43409 94.6 %-
all-44080 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.9872 Å2 / ksol: 0.382039 e/Å3
Displacement parametersBiso mean: 17.3 Å2
Baniso -1Baniso -2Baniso -3
1-2.75 Å20 Å2-0.74 Å2
2---3.91 Å20 Å2
3---1.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.04 Å
Refinement stepCycle: LAST / Resolution: 2.02→38.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4406 0 80 252 4738
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_mcbond_it1.141.5
X-RAY DIFFRACTIONc_mcangle_it1.682
X-RAY DIFFRACTIONc_scbond_it1.772
X-RAY DIFFRACTIONc_scangle_it2.512.5
LS refinement shellResolution: 2.02→2.15 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.218 318 4.6 %
Rwork0.183 6561 -
obs--91 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3THIO.PARAMTHIO.TOP

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