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- PDB-5hwo: MvaS in complex with 3-hydroxy-3-methylglutaryl coenzyme A -

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Basic information

Entry
Database: PDB / ID: 5hwo
TitleMvaS in complex with 3-hydroxy-3-methylglutaryl 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
3-HYDROXY-3-METHYLGLUTARYL-COENZYME A / Hydroxymethylglutaryl-CoA synthase
Similarity search - Component
Biological speciesMyxococcus xanthus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 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 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)46,0958
Polymers44,6281
Non-polymers1,4677
Water9,116506
1
A: Hydroxymethylglutaryl-CoA synthase
hetero molecules

A: Hydroxymethylglutaryl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,18916
Polymers89,2552
Non-polymers2,93414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_676x-y+1,-y+2,-z+11
Buried area7640 Å2
ΔGint-47 kcal/mol
Surface area30080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.349, 73.349, 277.276
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-504-

GOL

21A-955-

HOH

31A-1043-

HOH

41A-1048-

HOH

51A-1054-

HOH

61A-1086-

HOH

71A-1106-

HOH

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Components

#1: Protein Hydroxymethylglutaryl-CoA synthase


Mass: 44627.566 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-HMG / 3-HYDROXY-3-METHYLGLUTARYL-COENZYME A / (S)-HMG-COA


Mass: 906.620 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H39N7O20P3S
#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.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 506 / Source method: isolated from a natural source / Formula: H2O

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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: 2.41 Å3/Da / Density % sol: 49.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 2.2 M (NH4)2SO4, 0.1 M MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.48→46.213 Å / Num. obs: 74847 / % possible obs: 100 % / Redundancy: 10.7 % / Biso Wilson estimate: 10.33 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.164 / Net I/σ(I): 12.3
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
1.48-1.5110.71.1583858836070.7620.3671.2162.399.9
8.11-46.218.70.031524060310.0110.03347.699.4

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Processing

Software
NameVersionClassification
Aimless0.5.12data scaling
PHENIXrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1tvz

1tvz


Resolution: 1.48→46.213 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 13.11
RfactorNum. reflection% reflection
Rfree0.157 3763 5.04 %
Rwork0.1276 --
obs0.1291 74699 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 53.43 Å2 / Biso mean: 13.0975 Å2 / Biso min: 4.01 Å2
Refinement stepCycle: final / Resolution: 1.48→46.213 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3086 0 155 510 3751
Biso mean--16.57 25.41 -
Num. residues----418
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083286
X-RAY DIFFRACTIONf_angle_d1.1644477
X-RAY DIFFRACTIONf_chiral_restr0.074500
X-RAY DIFFRACTIONf_plane_restr0.007581
X-RAY DIFFRACTIONf_dihedral_angle_d16.3871199
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.48-1.49870.21311330.176425572690
1.4987-1.51850.21381250.173125752700
1.5185-1.53930.22261390.166625852724
1.5393-1.56130.21761270.166925912718
1.5613-1.58460.22671480.154225632711
1.5846-1.60930.20141310.152725702701
1.6093-1.63570.19181370.152325832720
1.6357-1.66390.20041330.141725852718
1.6639-1.69420.1871430.138325792722
1.6942-1.72680.16561170.131325862703
1.7268-1.7620.15421520.125826032755
1.762-1.80030.16971340.119525822716
1.8003-1.84220.16231510.123625962747
1.8422-1.88830.1641340.122825992733
1.8883-1.93930.15181270.111826182745
1.9393-1.99640.1461420.113125962738
1.9964-2.06080.13741380.113226042742
2.0608-2.13450.13471540.111626002754
2.1345-2.21990.13711500.104726272777
2.2199-2.3210.12031380.102726202758
2.321-2.44330.13381270.104426852812
2.4433-2.59640.14011340.10926362770
2.5964-2.79690.1421380.118926682806
2.7969-3.07830.16061540.127826882842
3.0783-3.52360.15581570.126126932850
3.5236-4.43870.12781480.118627562904
4.4387-46.23520.17941520.164829913143

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