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- PDB-7zm2: Crystal structure of HsaD from Mycobacterium tuberculosis in comp... -

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Basic information

Entry
Database: PDB / ID: 7zm2
TitleCrystal structure of HsaD from Mycobacterium tuberculosis in complex with Cyclophostin-like inhibitor CyC8b
Components4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase
KeywordsHYDROLASE / HsaD / M. tuberculosis / cholesterol / inhibitor
Function / homology
Function and homology information


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 activity / 2,6-dioxo-6-phenylhexa-3-enoate hydrolase / hydrolase activity, acting on acid carbon-carbon bonds, in ketonic substances / steroid biosynthetic process / biological process involved in interaction with host / 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
Similarity search - Domain/homology
Chem-9SW / 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBarelier, S. / Roig-Zamboni, V. / Cavalier, J.F. / Sulzenbacher, G.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) France
CitationJournal: Febs J. / Year: 2023
Title: Direct capture, inhibition and crystal structure of HsaD (Rv3569c) from M. tuberculosis.
Authors: Barelier, S. / Avellan, R. / Gnawali, G.R. / Fourquet, P. / Roig-Zamboni, V. / Poncin, I. / Point, V. / Bourne, Y. / Audebert, S. / Camoin, L. / Spilling, C.D. / Canaan, S. / Cavalier, J.F. / Sulzenbacher, G.
History
DepositionApr 19, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 29, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase
B: 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2959
Polymers65,9732
Non-polymers1,3217
Water1,946108
1
A: 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase
hetero molecules

A: 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase
hetero molecules

B: 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase
hetero molecules

B: 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,58918
Polymers131,9464
Non-polymers2,64314
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_756-x+2,y,-z+3/21
crystal symmetry operation2_775-x+2,-y+2,z+1/21
crystal symmetry operation4_576x,-y+2,-z+11
Buried area10500 Å2
ΔGint-193 kcal/mol
Surface area38910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.834, 87.187, 105.914
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221

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Components

#1: Protein 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase / 2-hydroxy-6-oxo-6-phenylhexa-2 / 4-dienoate hydrolase / HOPDA hydrolase / Meta-cleavage product ...2-hydroxy-6-oxo-6-phenylhexa-2 / 4-dienoate hydrolase / HOPDA hydrolase / Meta-cleavage product hydrolase / MCP hydrolase


Mass: 32986.594 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: hsaD, bphD, Rv3569c
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: P9WNH5, 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase, 2,6-dioxo-6-phenylhexa-3-enoate hydrolase
#2: Chemical ChemComp-9SW / methoxy-[(3~{R})-3-[(2~{R})-1-methoxy-1,3-bis(oxidanylidene)butan-2-yl]pentadecyl]phosphinic acid


Mass: 420.520 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H41O6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.69 Å3/Da / Density % sol: 54.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: MES Na 0.1 M NH4SO4 1.656 M PEG400 5.76%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980114 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980114 Å / Relative weight: 1
ReflectionResolution: 2.2→45.26 Å / Num. obs: 36843 / % possible obs: 100 % / Redundancy: 11.4 % / Biso Wilson estimate: 30.436 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.048 / Rrim(I) all: 0.165 / Net I/σ(I): 12.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.2-2.2711.41.3493556431320.6960.4131.4122.499.8
9.07-45.269.80.04760186120.9990.0150.0535.699.1

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Processing

Software
NameVersionClassification
Aimless0.7.7data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ZJT

7zjt


Resolution: 2.2→45.26 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.451 / SU ML: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.204 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2235 1853 5 %RANDOM
Rwork0.1754 ---
obs0.1779 34964 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 119.47 Å2 / Biso mean: 36.045 Å2 / Biso min: 10.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å2-0 Å2-0 Å2
2--0.29 Å20 Å2
3---0.51 Å2
Refinement stepCycle: final / Resolution: 2.2→45.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4388 0 35 108 4531
Biso mean--68.09 33.82 -
Num. residues----568
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0134524
X-RAY DIFFRACTIONr_bond_other_d0.0010.0154288
X-RAY DIFFRACTIONr_angle_refined_deg1.8081.6376126
X-RAY DIFFRACTIONr_angle_other_deg1.3891.5789806
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0715566
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.78620.645248
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.84715712
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4081540
X-RAY DIFFRACTIONr_chiral_restr0.0830.2542
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025172
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021116
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 131 -
Rwork0.249 2545 -
all-2676 -
obs--99.63 %

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