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- PDB-1tvz: Crystal structure of 3-hydroxy-3-methylglutaryl-coenzyme A syntha... -

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Basic information

Entry
Database: PDB / ID: 1tvz
TitleCrystal structure of 3-hydroxy-3-methylglutaryl-coenzyme A synthase from Staphylococcus aureus
Components3-hydroxy-3-methylglutaryl-CoA synthase
KeywordsLYASE / HMG-CoA synthase / HMGS / coenzyme A / thiolase fold / condensing enzyme / cholesterol biosynthesis
Function / homology
Function and homology information


hydroxymethylglutaryl-CoA synthase activity / farnesyl diphosphate biosynthetic process, mevalonate pathway / acetyl-CoA metabolic process
Similarity search - Function
Hydroxymethylglutaryl-CoA synthase, prokaryotic / 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
: / HMG-CoA synthase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2 Å
AuthorsCampobasso, N. / Patel, M. / Wilding, I.E. / Kallender, H. / Rosenberg, M. / Gwynn, M.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Staphylococcus aureus 3-hydroxy-3-methylglutaryl-CoA synthase: crystal structure and mechanism
Authors: Campobasso, N. / Patel, M. / Wilding, I.E. / Kallender, H. / Rosenberg, M. / Gwynn, M.
History
DepositionJun 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-hydroxy-3-methylglutaryl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4222
Polymers43,3261
Non-polymers961
Water3,567198
1
A: 3-hydroxy-3-methylglutaryl-CoA synthase
hetero molecules

A: 3-hydroxy-3-methylglutaryl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,8454
Polymers86,6532
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
Buried area5210 Å2
ΔGint-30 kcal/mol
Surface area26860 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)119.401, 119.401, 114.115
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Cell settinghexagonal
Space group name H-MP6422
DetailsThe biological assembly is a dimer generated from the monomer in the asymmetric unit by the operation: -x+1, -y, z

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Components

#1: Protein 3-hydroxy-3-methylglutaryl-CoA synthase / E.C.4.1.3.5 / HMG-CoA synthase


Mass: 43326.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: mvaS / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli)
References: GenBank: 9937361, UniProt: Q9FD87*PLUS, EC: 4.1.3.5
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.7 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: TRIS, ammonium sulfate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 10, 2000
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→99 Å / Num. obs: 32374 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Biso Wilson estimate: 23.9 Å2 / Rsym value: 0.048 / Net I/σ(I): 15.7
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 6.5 / Rsym value: 0.27 / % possible all: 95

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
MLPHAREphasing
REFMAC5.1.24refinement
HKL-2000data reduction
RefinementMethod to determine structure: MIR / Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.911 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 4 / σ(I): 2 / ESU R: 0.151 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19144 1577 5 %RANDOM
Rwork0.16546 ---
obs0.16679 29725 95.08 %-
all-33021 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.907 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å2-0.06 Å20 Å2
2---0.12 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3040 0 5 198 3243
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0213106
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3371.9474211
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6945386
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0990.2462
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022398
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.21492
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.2189
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.249
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.6311.51923
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.21323083
X-RAY DIFFRACTIONr_scbond_it2.17131183
X-RAY DIFFRACTIONr_scangle_it3.4964.51128
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.221 115
Rwork0.187 2024

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