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- PDB-8ahz: Native VirD of Streptomyces virginiae -

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Basic information

Entry
Database: PDB / ID: 8ahz
TitleNative VirD of Streptomyces virginiae
ComponentsEnoyl-CoA hydratase
KeywordsBIOSYNTHETIC PROTEIN / Enoyl-CoA hydratase / Beta-methylation / Antibiotic / ACP / Polyketide / PKS
Function / homology
Function and homology information


: / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
IMIDAZOLE / Enoyl-CoA hydratase
Similarity search - Component
Biological speciesStreptomyces virginiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsCollin, S. / Gruez, A.
Funding support France, 3items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-11-JSV8-003-01 France
Agence Nationale de la Recherche (ANR)ANR-16-CE92-0006-01 France
Agence Nationale de la Recherche (ANR)ANR-20-CE93-0002-01 France
CitationJournal: Nat Commun / Year: 2023
Title: Decrypting the programming of beta-methylation in virginiamycin M biosynthesis.
Authors: Collin, S. / Cox, R.J. / Paris, C. / Jacob, C. / Chagot, B. / Weissman, K.J. / Gruez, A.
History
DepositionJul 25, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: Enoyl-CoA hydratase
B: Enoyl-CoA hydratase
C: Enoyl-CoA hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,48043
Polymers79,0703
Non-polymers2,41040
Water7,891438
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.310, 84.310, 230.190
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Enoyl-CoA hydratase


Mass: 26356.830 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces virginiae (bacteria) / Gene: virD / Plasmid: pBG102 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A4PHM7
#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 438 / 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: 2.59 Å3/Da / Density % sol: 52.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 20% PEG 400, 20% PEG 800, 100 mM Tris-HCl

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.953709 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 29, 2017
RadiationMonochromator: crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953709 Å / Relative weight: 1
ReflectionResolution: 1.7→59.62 Å / Num. obs: 87602 / % possible obs: 99 % / Redundancy: 12.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.021 / Rrim(I) all: 0.074 / Net I/σ(I): 19.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.76-1.8111.60.75351710.810.2260.78885.9
2-2.110.20.0311100.9990.0150.03299.9

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.29data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→57.78 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.964 / WRfactor Rfree: 0.1798 / WRfactor Rwork: 0.1592 / FOM work R set: 0.9221 / SU B: 2.737 / SU ML: 0.045 / SU R Cruickshank DPI: 0.083 / SU Rfree: 0.0802 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1798 4525 4.9 %RANDOM
Rwork0.1592 ---
obs0.1602 87602 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.26 Å2 / Biso mean: 27.189 Å2 / Biso min: 17.09 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20 Å20 Å2
2--0.67 Å20 Å2
3----1.34 Å2
Refinement stepCycle: final / Resolution: 1.7→57.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5090 0 152 438 5680
Biso mean--46.2 38.62 -
Num. residues----684
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0135459
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175484
X-RAY DIFFRACTIONr_angle_refined_deg1.5171.6657365
X-RAY DIFFRACTIONr_angle_other_deg1.4291.57712497
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9215725
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.04517.391322
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.28415839
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6861592
X-RAY DIFFRACTIONr_chiral_restr0.0790.2691
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026214
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021334
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 307 -
Rwork0.247 6365 -
all-6672 -
obs--99.96 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5950.0374-0.17580.3395-0.25010.93320.03370.0483-0.0178-0.01660.00780.05990.0266-0.1278-0.04150.03880.0043-0.0030.0231-0.00440.029321.018739.025615.965
20.68910.31130.06490.5121-0.02740.80720.0338-0.06790.01880.1039-0.02240.0368-0.0207-0.027-0.01140.0654-0.01660.01490.0131-0.00190.030424.295531.888347.738
30.36320.09410.14070.65-0.17431.24250.03910.0174-0.0224-0.0019-0.0443-0.0982-0.01260.23320.00520.0067-0.00690.00520.07-0.00660.037551.056242.574930.7295
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-3 - 240
2X-RAY DIFFRACTION2B-3 - 229
3X-RAY DIFFRACTION3C-3 - 233

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