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- PDB-5w95: Mtb Rv3802c with PEG bound -

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Basic information

Entry
Database: PDB / ID: 5w95
TitleMtb Rv3802c with PEG bound
ComponentsConserved membrane protein of uncharacterised function
KeywordsHYDROLASE / PEG / Complex
Function / homology
Function and homology information


phospholipase A1 activity / fatty acyl-CoA hydrolase activity / lipase activity / carboxylesterase activity / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / lipid catabolic process / peptidoglycan-based cell wall / hydrolase activity / extracellular region / membrane / plasma membrane
Similarity search - Function
Cutinase / Cutinase/acetylxylan esterase / Cutinase / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Cell wall synthesis protein CwsA / Carboxylesterase/lipase Culp6
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.723 Å
AuthorsGoins, C.M. / Schreidah, C.M. / Ronning, D.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI105084 United States
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structural basis for lipid binding and mechanism of the Mycobacterium tuberculosis Rv3802 phospholipase.
Authors: Goins, C.M. / Schreidah, C.M. / Dajnowicz, S. / Ronning, D.R.
History
DepositionJun 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2018Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 17, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Feb 7, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _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: Conserved membrane protein of uncharacterised function
B: Conserved membrane protein of uncharacterised function
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5536
Polymers60,6002
Non-polymers9534
Water11,674648
1
A: Conserved membrane protein of uncharacterised function
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7763
Polymers30,3001
Non-polymers4772
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Conserved membrane protein of uncharacterised function
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7763
Polymers30,3001
Non-polymers4772
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.188, 91.300, 101.391
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 Conserved membrane protein of uncharacterised function / Rv3802c


Mass: 30299.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: ERS007672_01844, ERS023446_02759, ERS024213_00010, ERS024276_01951, ERS027644_01116, ERS027646_00777, ERS027656_01063, ERS027659_00661, ERS027661_01209, ERS027666_00826, ERS031537_00520, ...Gene: ERS007672_01844, ERS023446_02759, ERS024213_00010, ERS024276_01951, ERS027644_01116, ERS027646_00777, ERS027656_01063, ERS027659_00661, ERS027661_01209, ERS027666_00826, ERS031537_00520, ERS124361_01515, SAMEA2683035_00004
Production host: Escherichia coli (E. coli) / References: UniProt: A0A045KEI3, UniProt: O53581*PLUS
#2: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 648 / 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: 2.31 Å3/Da / Density % sol: 46.66 %
Crystal growTemperature: 289.15 K / Method: evaporation
Details: 0.1 M BIS-TRIS pH 6.5, 25% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.72→44.321 Å / Num. obs: 56631 / % possible obs: 99.63 % / Redundancy: 14.8 % / Net I/σ(I): 23.23

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.723→44.321 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.183 2000 3.53 %
Rwork0.1582 --
obs0.159 56631 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.723→44.321 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3890 0 64 648 4602
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074084
X-RAY DIFFRACTIONf_angle_d1.0625571
X-RAY DIFFRACTIONf_dihedral_angle_d13.5911486
X-RAY DIFFRACTIONf_chiral_restr0.041618
X-RAY DIFFRACTIONf_plane_restr0.006752
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7227-1.76580.18431340.1573661X-RAY DIFFRACTION95
1.7658-1.81360.23121410.16153838X-RAY DIFFRACTION100
1.8136-1.86690.20711410.1633876X-RAY DIFFRACTION100
1.8669-1.92720.16881420.15993864X-RAY DIFFRACTION100
1.9272-1.99610.2081420.16063888X-RAY DIFFRACTION100
1.9961-2.0760.17431420.15753876X-RAY DIFFRACTION100
2.076-2.17050.21121420.15913882X-RAY DIFFRACTION100
2.1705-2.28490.17781430.16053921X-RAY DIFFRACTION100
2.2849-2.4280.18591430.163879X-RAY DIFFRACTION100
2.428-2.61550.20851430.16973914X-RAY DIFFRACTION100
2.6155-2.87860.20131430.17013930X-RAY DIFFRACTION100
2.8786-3.29510.20891460.17153955X-RAY DIFFRACTION100
3.2951-4.1510.14841450.14483998X-RAY DIFFRACTION100
4.151-44.3360.15581530.1464149X-RAY DIFFRACTION100

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