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- PDB-1sfr: Crystal Structure of the Mycobacterium tuberculosis Antigen 85A P... -

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Basic information

Entry
Database: PDB / ID: 1sfr
TitleCrystal Structure of the Mycobacterium tuberculosis Antigen 85A Protein
ComponentsAntigen 85-A
KeywordsTRANSFERASE / alpha/beta hydrolase / 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 / cell wall / zymogen binding / acyltransferase activity, transferring groups other than amino-acyl groups / peptidoglycan-based cell wall / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
: / Esterase-like / Putative esterase / Twin-arginine translocation pathway, signal sequence / 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 Ag85A / Diacylglycerol acyltransferase/mycolyltransferase Ag85A
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 20, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Antigen 85-A
B: Antigen 85-A
C: Antigen 85-A


Theoretical massNumber of molelcules
Total (without water)98,2333
Polymers98,2333
Non-polymers00
Water1,04558
1
A: Antigen 85-A


Theoretical massNumber of molelcules
Total (without water)32,7441
Polymers32,7441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Antigen 85-A


Theoretical massNumber of molelcules
Total (without water)32,7441
Polymers32,7441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Antigen 85-A


Theoretical massNumber of molelcules
Total (without water)32,7441
Polymers32,7441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
A: Antigen 85-A
B: Antigen 85-A


Theoretical massNumber of molelcules
Total (without water)65,4892
Polymers65,4892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-18 kcal/mol
Surface area21690 Å2
MethodPISA
5
C: Antigen 85-A

C: Antigen 85-A


Theoretical massNumber of molelcules
Total (without water)65,4892
Polymers65,4892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area1420 Å2
ΔGint-17 kcal/mol
Surface area20620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.430, 288.662, 101.289
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly is a monomer

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Components

#1: Protein Antigen 85-A


Mass: 32744.457 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: fbpA / Plasmid: pET30b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P0A4V2, UniProt: P9WQP3*PLUS, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 5.23 Å3/Da / Density % sol: 76.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Sodium Cacodylate, Sodium Acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 14, 2000
RadiationMonochromator: Ge 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 52327 / Num. obs: 52327 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 59.1 Å2 / Rsym value: 0.069 / Net I/σ(I): 15
Reflection shellResolution: 2.7→2.8 Å / % possible all: 98

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Processing

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

1dqz


Resolution: 2.7→29.9 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 481759.2 / 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
Rfree0.254 2550 5 %RANDOM
Rwork0.222 ---
all0.226 53206 --
obs0.222 50656 95 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.2765 Å2 / ksol: 0.354084 e/Å3
Displacement parametersBiso mean: 54.2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.7→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6499 0 0 58 6557
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_mcbond_it1.221.5
X-RAY DIFFRACTIONc_mcangle_it2.042
X-RAY DIFFRACTIONc_scbond_it1.882
X-RAY DIFFRACTIONc_scangle_it2.732.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.323 375 4.8 %
Rwork0.309 7456 -
obs--89 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP

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