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- PDB-8s81: VirC mutant C114A-Q334A-R335A-R338A -

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Basic information

Entry
Database: PDB / ID: 8s81
TitleVirC mutant C114A-Q334A-R335A-R338A
ComponentsHMG-CoA synthase-like protein
KeywordsTRANSFERASE / 3-hydroxy-3-methylglutaryl-CoA synthase / conformational flexibility / substrate specificity
Function / homology
Function and homology information


farnesyl diphosphate biosynthetic process, mevalonate pathway / hydroxymethylglutaryl-CoA synthase activity / acetyl-CoA metabolic process / acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
Hydroxymethylglutaryl-coenzyme A synthase, N-terminal / Hydroxymethylglutaryl-coenzyme A synthase, C-terminal domain / Hydroxymethylglutaryl-coenzyme A synthase N terminal / Hydroxymethylglutaryl-coenzyme A synthase C terminal / Thiolase-like
Similarity search - Domain/homology
HMG-CoA synthase-like protein
Similarity search - Component
Biological speciesStreptomyces virginiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsCollin, S. / Gruez, A. / Weissman, K.J.
Funding support France, 3items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-20-CE93-0002-01 France
Agence Nationale de la Recherche (ANR)ANR-16- CE92-0006-01 France
Agence Nationale de la Recherche (ANR)ANR-11-JSV8-003-01 France
CitationJournal: Jacs Au / Year: 2024
Title: Structural Plasticity within 3-Hydroxy-3-Methylglutaryl Synthases Catalyzing the First Step of beta-Branching in Polyketide Biosynthesis Underpins a Dynamic Mechanism of Substrate Accommodation.
Authors: Collin, S. / Weissman, K.J. / Gruez, A.
History
DepositionMar 5, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HMG-CoA synthase-like protein
B: HMG-CoA synthase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,7905
Polymers92,6032
Non-polymers1863
Water6,648369
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-19 kcal/mol
Surface area27320 Å2
Unit cell
Length a, b, c (Å)126.350, 126.350, 324.940
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein HMG-CoA synthase-like protein


Mass: 46301.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces virginiae (bacteria) / Gene: virC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A4PHM8
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.7 Å3/Da / Density % sol: 54.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 11% PEG 3350, 12.5% 2-methyl-2,4-pentanediol, 100 mM amino acids (0.02 M DL-glutamic acid monohydrate, 0.02 M glycine, 0.02 M DL-serine, 0.02 M DL-alanine, 0.2 M DL-lysine monohydrochloride) ...Details: 11% PEG 3350, 12.5% 2-methyl-2,4-pentanediol, 100 mM amino acids (0.02 M DL-glutamic acid monohydrate, 0.02 M glycine, 0.02 M DL-serine, 0.02 M DL-alanine, 0.2 M DL-lysine monohydrochloride), 100 mM MES-imidazole buffer, pH 6.5.

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980112195015 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980112195015 Å / Relative weight: 1
ReflectionResolution: 1.99→45.42 Å / Num. obs: 68537 / % possible obs: 99.2 % / Redundancy: 39.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.023 / Rrim(I) all: 0.147 / Χ2: 0.99 / Net I/σ(I): 22.6
Reflection shellResolution: 1.99→2.04 Å / % possible obs: 96 % / Redundancy: 39 % / Rmerge(I) obs: 1.551 / Num. measured all: 190088 / Num. unique obs: 4880 / CC1/2: 0.859 / Rpim(I) all: 0.245 / Rrim(I) all: 1.57 / Χ2: 0.82 / Net I/σ(I) obs: 2.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→45.42 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.286 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20644 3427 5 %RANDOM
Rwork0.17208 ---
obs0.1738 65110 99.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.641 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.99→45.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6031 0 12 369 6412
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0136166
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175816
X-RAY DIFFRACTIONr_angle_refined_deg1.7591.6468359
X-RAY DIFFRACTIONr_angle_other_deg1.441.57413345
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0715788
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.43220.769325
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.52415916
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5881553
X-RAY DIFFRACTIONr_chiral_restr0.0850.2804
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027037
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021445
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7863.2223164
X-RAY DIFFRACTIONr_mcbond_other2.7563.223162
X-RAY DIFFRACTIONr_mcangle_it3.5714.8153948
X-RAY DIFFRACTIONr_mcangle_other3.5764.8153948
X-RAY DIFFRACTIONr_scbond_it3.6743.6353002
X-RAY DIFFRACTIONr_scbond_other3.6743.6363003
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2725.2954412
X-RAY DIFFRACTIONr_long_range_B_refined6.28639.4046858
X-RAY DIFFRACTIONr_long_range_B_other6.25839.2086787
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.99→2.037 Å
RfactorNum. reflection% reflection
Rfree0.393 244 -
Rwork0.388 4634 -
obs--95.91 %

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