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- PDB-3b18: Rv0098 of Mycobacterium tuberculosis with ordered loop between be... -

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Basic information

Entry
Database: PDB / ID: 3b18
TitleRv0098 of Mycobacterium tuberculosis with ordered loop between beta-4 and beta-5
ComponentsUncharacterized protein Rv0098/MT0107
KeywordsHYDROLASE / hot dog fold / long-chain fatty acyl-CoA thioesterase / acyl carrier protein / Mycobacterium tuberculosis
Function / homology
Function and homology information


(3R)-3-[(carboxylmethyl)amino]fatty acid synthase / palmitoyl-CoA hydrolase / fatty acyl-CoA hydrolase activity / Hydrolases; Acting on ester bonds; Thioester hydrolases / fatty acid metabolic process / fatty acid biosynthetic process / lyase activity / plasma membrane
Similarity search - Function
Rv0098, thioesterase-like hot dog domain / Long-chain fatty acyl-CoA thioesterase FcoT-like / Long-chain fatty acyl-CoA thioesterase, Rv0098-like superfamily / FcoT-like thioesterase domain / Thiol Ester Dehydrase; Chain A / Roll / Alpha Beta
Similarity search - Domain/homology
LAURIC ACID / Long-chain fatty acyl-CoA thioesterase FcoT / (2E)-enoyl-[ACP] glycyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsMaity, K. / Suguna, K.
CitationJournal: J.Biomol.Struct.Dyn. / Year: 2012
Title: Insights into the substrate specificity of a thioesterase Rv0098 of mycobacterium tuberculosis through X-ray crystallographic and molecular dynamics studies.
Authors: Maity, K. / Bajaj, P. / Surolia, N. / Surolia, A. / Suguna, K.
History
DepositionJun 26, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title
Revision 1.2Nov 1, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein Rv0098/MT0107
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7502
Polymers20,5491
Non-polymers2001
Water50428
1
A: Uncharacterized protein Rv0098/MT0107
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)124,49912
Polymers123,2976
Non-polymers1,2026
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_454-z-1/2,-x,y-1/21
crystal symmetry operation10_554-y,z+1/2,-x-1/21
crystal symmetry operation14_555-x,-y+1/2,z1
crystal symmetry operation20_455-z-1/2,x,-y1
crystal symmetry operation21_454y-1/2,z+1/2,x-1/21
2
A: Uncharacterized protein Rv0098/MT0107
hetero molecules

A: Uncharacterized protein Rv0098/MT0107
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5004
Polymers41,0992
Non-polymers4012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation14_555-x,-y+1/2,z1
Buried area2810 Å2
ΔGint-21 kcal/mol
Surface area13980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.190, 100.190, 100.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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Components

#1: Protein Uncharacterized protein Rv0098/MT0107 / Long-chain fatty acyl-CoA thioesterase Rv0098


Mass: 20549.479 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: Rv0098 / Plasmid: PET-28a(+)(NOVAGEN) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P64685, UniProt: P9WM67*PLUS
#2: Chemical ChemComp-DAO / LAURIC ACID


Mass: 200.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H24O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.04 Å3/Da / Density % sol: 39.68 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 5%-12% PEG 6000, 0.1M HEPES buffer, 5% MPD , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 15, 2006 / Details: Mirror
RadiationMonochromator: Osmic Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.75→50.1 Å / Num. obs: 4502 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 16.1 % / Biso Wilson estimate: 75.7 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 23.3
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 16.3 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 4 / Num. unique all: 648 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PFC

2pfc


Resolution: 2.75→50.01 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.913 / SU B: 12.006 / SU ML: 0.239 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.27679 205 4.6 %RANDOM
Rwork0.22421 ---
obs0.22694 4276 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 59.096 Å2
Refinement stepCycle: LAST / Resolution: 2.75→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1316 0 14 28 1358
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221367
X-RAY DIFFRACTIONr_angle_refined_deg1.7121.9711851
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9765167
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.8722.58162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.39715224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9011513
X-RAY DIFFRACTIONr_chiral_restr0.1270.2204
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211036
X-RAY DIFFRACTIONr_mcbond_it0.7311.5835
X-RAY DIFFRACTIONr_mcangle_it1.36621339
X-RAY DIFFRACTIONr_scbond_it1.6653532
X-RAY DIFFRACTIONr_scangle_it2.8864.5511
LS refinement shellResolution: 2.752→2.823 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.56 13 -
Rwork0.2 311 -
obs--100 %

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