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- PDB-5hwq: MvaS in complex with acetoacetyl coenzyme A -

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Basic information

Entry
Database: PDB / ID: 5hwq
TitleMvaS in complex with acetoacetyl coenzyme A
ComponentsHydroxymethylglutaryl-CoA synthase
KeywordsTRANSFERASE / MvaS / Myxococcus xanthus / Biosynthesis
Function / homology
Function and homology information


hydroxymethylglutaryl-CoA synthase / hydroxymethylglutaryl-CoA synthase activity / acetyl-CoA metabolic process
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/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETOACETYL-COENZYME A / Hydroxymethylglutaryl-CoA synthase
Similarity search - Component
Biological speciesMyxococcus xanthus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.5 Å
AuthorsBock, T. / Kasten, J. / Blankenfeldt, W.
CitationJournal: Chembiochem / Year: 2016
Title: Crystal Structure of the HMG-CoA Synthase MvaS from the Gram-Negative Bacterium Myxococcus xanthus.
Authors: Bock, T. / Kasten, J. / Muller, R. / Blankenfeldt, W.
History
DepositionJan 29, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2016Group: Database references
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_close_contact
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_validate_close_contact.auth_atom_id_2
Revision 2.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hydroxymethylglutaryl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7647
Polymers44,4481
Non-polymers1,3166
Water7,530418
1
A: Hydroxymethylglutaryl-CoA synthase
hetero molecules

A: Hydroxymethylglutaryl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,52914
Polymers88,8972
Non-polymers2,63212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area7420 Å2
ΔGint-46 kcal/mol
Surface area30260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.514, 73.514, 277.552
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-503-

GOL

21A-720-

HOH

31A-916-

HOH

41A-921-

HOH

51A-969-

HOH

61A-985-

HOH

71A-998-

HOH

81A-1012-

HOH

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Components

#1: Protein Hydroxymethylglutaryl-CoA synthase


Mass: 44448.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myxococcus xanthus (strain DK 1622) (bacteria)
Strain: DK 1622 / Gene: mvaS, MXAN_4267 / Plasmid: pET19m / Production host: Escherichia coli (E. coli)
References: UniProt: Q1D4I1, hydroxymethylglutaryl-CoA synthase
#2: Chemical ChemComp-CAA / ACETOACETYL-COENZYME A


Mass: 851.607 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H40N7O18P3S
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / Source method: isolated from a natural source / Formula: H2O
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: 2.42 Å3/Da / Density % sol: 49.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1 M Li2SO4, 0.1 M trisodium-citrate, 0.5 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.5→46.91 Å / Num. obs: 72387 / % possible obs: 100 % / Redundancy: 17.7 % / Biso Wilson estimate: 14.57 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.025 / Rrim(I) all: 0.107 / Net I/σ(I): 18 / Num. measured all: 1280707 / Scaling rejects: 23
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.5-1.53161.0185563434870.7970.261.0532.6100
8.22-46.9116.80.0498405850.9990.010.04149.599.5

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.5.17data scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.5→46.911 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1675 3637 5.04 %
Rwork0.1408 68588 -
obs0.1422 72225 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.77 Å2 / Biso mean: 18.5285 Å2 / Biso min: 8.07 Å2
Refinement stepCycle: final / Resolution: 1.5→46.911 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3083 0 151 418 3652
Biso mean--25.55 28.2 -
Num. residues----418
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053311
X-RAY DIFFRACTIONf_angle_d0.8984515
X-RAY DIFFRACTIONf_chiral_restr0.046506
X-RAY DIFFRACTIONf_plane_restr0.005586
X-RAY DIFFRACTIONf_dihedral_angle_d12.9982006
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.5-1.51970.24711250.196425972722
1.5197-1.54060.22551320.172525752707
1.5406-1.56260.22651350.170925722707
1.5626-1.58590.19071420.168825842726
1.5859-1.61070.23081370.169625862723
1.6107-1.63710.23571320.165326102742
1.6371-1.66530.231330.162325682701
1.6653-1.69560.22161470.16625932740
1.6956-1.72820.21141180.153726102728
1.7282-1.76350.17361520.147525772729
1.7635-1.80180.19471320.148326202752
1.8018-1.84380.18521490.145425902739
1.8438-1.88990.1751410.13626122753
1.8899-1.9410.15291280.132426272755
1.941-1.99810.17921380.137225902728
1.9981-2.06260.15891380.129826292767
2.0626-2.13630.14691580.134226132771
2.1363-2.22180.16931510.129326212772
2.2218-2.32290.13661390.125426422781
2.3229-2.44540.15541250.127126792804
2.4454-2.59860.15671350.130426522787
2.5986-2.79920.1531390.133626712810
2.7992-3.08090.16431520.140427082860
3.0809-3.52660.16491590.135527002859
3.5266-4.44260.14321470.126127582905
4.4426-46.93390.16211530.159430043157

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