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- PDB-2vf2: X-ray crystal structure of HsaD from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 2vf2
TitleX-ray crystal structure of HsaD from Mycobacterium tuberculosis
Components2-HYDROXY-6-OXO-6-PHENYLHEXA-2,4-DIENOATE HYDROLASE BPHD
KeywordsHYDROLASE / META-CLEAVAGE PRODUCT HYDROLASE / HSAD / SERINE HYDROLASE
Function / homology
Function and homology information


4,9-DSHA hydrolase activity / 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase / 4,5-9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase activity / 2,6-dioxo-6-phenylhexa-3-enoate hydrolase / 2,6-dioxo-6-phenylhexa-3-enoate hydrolase activity / biological process involved in interaction with host / steroid biosynthetic process / : / lipid catabolic process / peptidoglycan-based cell wall / plasma membrane
Similarity search - Function
alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase / 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsLack, N. / Lowe, E.D. / Liu, J. / Eltis, L.D. / Noble, M.E.M. / Sim, E. / Westwood, I.M.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Structure of Hsad, a Steroid-Degrading Hydrolase, from Mycobacterium Tuberculosis.
Authors: Lack, N. / Lowe, E.D. / Liu, J. / Eltis, L.D. / Noble, M.E.M. / Sim, E. / Westwood, I.M.
History
DepositionOct 29, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-HYDROXY-6-OXO-6-PHENYLHEXA-2,4-DIENOATE HYDROLASE BPHD
B: 2-HYDROXY-6-OXO-6-PHENYLHEXA-2,4-DIENOATE HYDROLASE BPHD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6427
Polymers68,1732
Non-polymers4685
Water3,693205
1
A: 2-HYDROXY-6-OXO-6-PHENYLHEXA-2,4-DIENOATE HYDROLASE BPHD
B: 2-HYDROXY-6-OXO-6-PHENYLHEXA-2,4-DIENOATE HYDROLASE BPHD
hetero molecules

A: 2-HYDROXY-6-OXO-6-PHENYLHEXA-2,4-DIENOATE HYDROLASE BPHD
B: 2-HYDROXY-6-OXO-6-PHENYLHEXA-2,4-DIENOATE HYDROLASE BPHD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,28414
Polymers136,3474
Non-polymers93710
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y+1/2,z1
Buried area9790 Å2
ΔGint-49.7 kcal/mol
Surface area49750 Å2
MethodPQS
Unit cell
Length a, b, c (Å)82.360, 82.460, 194.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-2011-

HOH

21A-2079-

HOH

31B-2016-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.097702, 0.995102, -0.015065), (0.994522, 0.098188, 0.035851), (0.037155, -0.01148, -0.999244)
Vector: -20.3192, 17.9381, 51.7578)

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Components

#1: Protein 2-HYDROXY-6-OXO-6-PHENYLHEXA-2,4-DIENOATE HYDROLASE BPHD / 2 / 6-DIOXO-6-PHENYLHEXA-3-ENOATE HYDROLASE / 2-HYDROXY-6-PHENYLHEXA-2 / 4-DIENOIC ACID HYDROLASE


Mass: 34086.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PVLT31 / Production host: PSEUDOMONAS PUTIDA (bacteria) / Strain (production host): KT4224
References: UniProt: P96851, UniProt: P9WNH5*PLUS, 2,6-dioxo-6-phenylhexa-3-enoate hydrolase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE USED IN THIS STUDY CONTAINS N-TERMINAL HEXA- HISTIDINE TAG (20 AMINO ACIDS) WHICH WAS NOT ...SEQUENCE USED IN THIS STUDY CONTAINS N-TERMINAL HEXA- HISTIDINE TAG (20 AMINO ACIDS) WHICH WAS NOT CLEAVABLE WITH THROMBIN.

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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: 2.43 Å3/Da / Density % sol: 49.4 % / Description: NONE
Crystal growpH: 9.5 / Details: 30 % (W/V) PEG 3000, 0.1 M CHES PH 9.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.968
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 2, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 2.35→32.4 Å / Num. obs: 24657 / % possible obs: 96.7 % / Observed criterion σ(I): 1.5 / Redundancy: 3.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.9
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.5 / % possible all: 93.6

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Processing

Software
NameClassification
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1C4X AND 2OG1

1c4x

2og1


Resolution: 2.35→32.4 Å
RfactorNum. reflection% reflection
Rfree0.233 2496 5 %
Rwork0.212 --
obs-47065 92.9 %
Refinement stepCycle: LAST / Resolution: 2.35→32.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4388 0 28 205 4621

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