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- PDB-8ahq: VirD/holo-ACP5b of Streptomyces virginiae complex -

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Basic information

Entry
Database: PDB / ID: 8ahq
TitleVirD/holo-ACP5b of Streptomyces virginiae complex
Components
  • Enoyl-CoA hydratase
  • Hybrid polyketide synthase-non ribosomal peptide synthetase
KeywordsBIOSYNTHETIC PROTEIN / Complex / Beta-methylation / Antibiotic / ACP / Polyketide / PKS
Function / homology
Function and homology information


toxin biosynthetic process / amide biosynthetic process / : / DIM/DIP cell wall layer assembly / organonitrogen compound biosynthetic process / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / antibiotic biosynthetic process / catalytic activity ...toxin biosynthetic process / amide biosynthetic process / : / DIM/DIP cell wall layer assembly / organonitrogen compound biosynthetic process / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / antibiotic biosynthetic process / catalytic activity / fatty acid biosynthetic process / plasma membrane / cytoplasm
Similarity search - Function
: / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Methyltransferase type 12 / Methyltransferase domain / : / Polyketide synthase dehydratase domain / PKS_PP_betabranch / Polyketide synthase dehydratase N-terminal domain / Condensation domain ...: / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Methyltransferase type 12 / Methyltransferase domain / : / Polyketide synthase dehydratase domain / PKS_PP_betabranch / Polyketide synthase dehydratase N-terminal domain / Condensation domain / Condensation domain / Amino acid adenylation domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain / KR domain / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / ANL, N-terminal domain / PKS_KR / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Chloramphenicol acetyltransferase-like domain superfamily / Putative AMP-binding domain signature. / Ketosynthase family 3 (KS3) domain profile. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / ClpP/crotonase-like domain superfamily / Phosphopantetheine attachment site / Thiolase-like / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
4'-PHOSPHOPANTETHEINE / Enoyl-CoA hydratase / Hybrid polyketide synthase-non ribosomal peptide synthetase
Similarity search - Component
Biological speciesStreptomyces virginiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 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 22, 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 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Enoyl-CoA hydratase
C: Hybrid polyketide synthase-non ribosomal peptide synthetase
B: Enoyl-CoA hydratase
D: Hybrid polyketide synthase-non ribosomal peptide synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,33115
Polymers71,1484
Non-polymers1,18311
Water5,801322
1
A: Enoyl-CoA hydratase
C: Hybrid polyketide synthase-non ribosomal peptide synthetase
B: Enoyl-CoA hydratase
D: Hybrid polyketide synthase-non ribosomal peptide synthetase
hetero molecules

A: Enoyl-CoA hydratase
C: Hybrid polyketide synthase-non ribosomal peptide synthetase
B: Enoyl-CoA hydratase
D: Hybrid polyketide synthase-non ribosomal peptide synthetase
hetero molecules

A: Enoyl-CoA hydratase
C: Hybrid polyketide synthase-non ribosomal peptide synthetase
B: Enoyl-CoA hydratase
D: Hybrid polyketide synthase-non ribosomal peptide synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,99445
Polymers213,44512
Non-polymers3,54933
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area34670 Å2
ΔGint-166 kcal/mol
Surface area71820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.878, 144.878, 88.781
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-489-

HOH

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Enoyl-CoA hydratase /


Mass: 26356.830 Da / Num. of mol.: 2
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: Protein Hybrid polyketide synthase-non ribosomal peptide synthetase


Mass: 9217.263 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces virginiae (bacteria) / Gene: virA / Plasmid: pBG102 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A4PHN0

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Non-polymers , 5 types, 333 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-PNS / 4'-PHOSPHOPANTETHEINE / Phosphopantetheine


Mass: 358.348 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H23N2O7PS / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 322 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.52 Å3/Da / Density % sol: 51.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM chloride calcium, 30% PEG 1500, 10% 2-propanol, 100 mM imidazole-HCl

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9537 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: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.1→41.85 Å / Num. obs: 40503 / % possible obs: 100 % / Redundancy: 11.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.037 / Rrim(I) all: 0.131 / Net I/σ(I): 15.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.1-2.1611.11.46733640.8970.4521100
8.91-36.23120.0495200.9960.0150.05198.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.495
Highest resolutionLowest resolution
Rotation41.85 Å3.4 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.4data scaling
MOLREPphasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: native

Resolution: 2.1→41.85 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.938 / SU B: 9.539 / SU ML: 0.129 / SU R Cruickshank DPI: 0.2083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.208 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2376 2029 5 %RANDOM
Rwork0.1828 ---
obs0.1856 38540 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 89.52 Å2 / Biso mean: 36.379 Å2 / Biso min: 20.91 Å2
Baniso -1Baniso -2Baniso -3
1--1.5 Å2-0.75 Å20 Å2
2---1.5 Å2-0 Å2
3---4.88 Å2
Refinement stepCycle: final / Resolution: 2.1→41.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4728 0 57 322 5107
Biso mean--52.76 41.98 -
Num. residues----630
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0134862
X-RAY DIFFRACTIONr_bond_other_d0.0030.0174745
X-RAY DIFFRACTIONr_angle_refined_deg1.7891.6626583
X-RAY DIFFRACTIONr_angle_other_deg1.4271.58910816
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4865631
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.34718.638279
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.2615725
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7691569
X-RAY DIFFRACTIONr_chiral_restr0.0840.2626
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025537
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021143
LS refinement shellResolution: 2.1→2.154 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.585 150 -
Rwork0.584 2860 -
all-3010 -
obs--99.87 %
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)
10.52880.07620.00371.3346-0.18220.37130.00790.15380.01-0.1230.00480.22890.0309-0.1195-0.01270.08340.0038-0.06410.12030.00990.1643-19.62591.5693-4.9936
20.89410.30260.31842.56680.37551.37580.0135-0.0815-0.1130.0284-0.00510.08950.0472-0.1129-0.00830.0295-0.0287-0.03250.0806-0.02770.23-22.0952-31.196512.9687
30.9584-0.1763-0.07970.8083-0.00830.2720.0175-0.0542-0.14490.12970.00260.11450.0294-0.0422-0.02010.1022-0.01430.0140.06550.04510.1809-11.2536-15.947236.9255
41.8495-0.11020.3713.0379-0.00262.3729-0.0728-0.2327-0.0919-0.16540.11240.46770.0626-0.3878-0.03960.0172-0.0177-0.01080.13930.02570.3037-38.03483.536719.0942
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 245
2X-RAY DIFFRACTION2C6834 - 6912
3X-RAY DIFFRACTION3B-1 - 245
4X-RAY DIFFRACTION4D6834 - 6912

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