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- PDB-5hwr: MvaS in complex with coenzyme A -

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Basic information

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


hydroxymethylglutaryl-CoA synthase / hydroxymethylglutaryl-CoA synthase activity / farnesyl diphosphate biosynthetic process, mevalonate pathway / 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
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

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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)45,9968
Polymers44,6601
Non-polymers1,3367
Water6,467359
1
A: Hydroxymethylglutaryl-CoA synthase
hetero molecules

A: Hydroxymethylglutaryl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,99116
Polymers89,3192
Non-polymers2,67214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area9640 Å2
ΔGint-85 kcal/mol
Surface area27250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.162, 73.162, 276.899
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-502-

GOL

21A-732-

HOH

31A-929-

HOH

41A-933-

HOH

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Components

#1: Protein Hydroxymethylglutaryl-CoA synthase /


Mass: 44659.566 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 3.31 Å3/Da / Density % sol: 62.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2.2 M (NH4)2SO4, 0.2 M disodium tartrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.5→41.7 Å / Num. obs: 71372 / % possible obs: 99.9 % / Redundancy: 16 % / Biso Wilson estimate: 12.77 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.034 / Rrim(I) all: 0.137 / Net I/σ(I): 17.3 / Num. measured all: 1143902
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.5-1.5315.31.3525286634640.7550.3521.3982.499.5
8.22-41.713.30.03761657110.0080.03165.399.4

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.5.12data scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.5→41.697 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 13.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1569 3589 5.04 %
Rwork0.1241 67677 -
obs0.1258 71266 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 61.48 Å2 / Biso mean: 16.7744 Å2 / Biso min: 6.64 Å2
Refinement stepCycle: final / Resolution: 1.5→41.697 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3060 0 208 359 3627
Biso mean--23.68 25.95 -
Num. residues----417
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013320
X-RAY DIFFRACTIONf_angle_d1.3114543
X-RAY DIFFRACTIONf_chiral_restr0.202506
X-RAY DIFFRACTIONf_plane_restr0.008583
X-RAY DIFFRACTIONf_dihedral_angle_d14.2381972
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.51980.19481210.16362550267199
1.5198-1.54060.24281400.15792503264399
1.5406-1.56260.20121280.15312563269199
1.5626-1.58590.19961500.140825492699100
1.5859-1.61070.18541190.12992530264999
1.6107-1.63710.20931270.134125472674100
1.6371-1.66530.16531420.12725792721100
1.6653-1.69560.18231320.128725282660100
1.6956-1.72820.16651300.124425522682100
1.7282-1.76350.18151400.118125682708100
1.7635-1.80180.15171330.116425672700100
1.8018-1.84380.15571540.109825702724100
1.8438-1.88990.14131270.104925762703100
1.8899-1.9410.14461310.102725892720100
1.941-1.99810.13531370.105325692706100
1.9981-2.06260.15941430.104525962739100
2.0626-2.13630.13641480.102625832731100
2.1363-2.22180.14571460.101826252771100
2.2218-2.32290.12321340.10325792713100
2.3229-2.44540.14411330.106126562789100
2.4454-2.59860.16151330.11426192752100
2.5986-2.79920.14821370.123326542791100
2.7992-3.08080.15381510.131626552806100
3.0808-3.52640.15921570.129126752832100
3.5264-4.44210.12841450.120927352880100
4.4421-41.71330.18761510.166729603111100

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