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- PDB-2f82: HMG-CoA synthase from Brassica juncea in the apo-form -

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Basic information

Entry
Database: PDB / ID: 2f82
TitleHMG-CoA synthase from Brassica juncea in the apo-form
ComponentsHMG-CoA synthase
KeywordsTRANSFERASE / HMGS1
Function / homology
Function and homology information


hydroxymethylglutaryl-CoA synthase / hydroxymethylglutaryl-CoA synthase activity / farnesyl diphosphate biosynthetic process, mevalonate pathway / acetyl-CoA metabolic process / ergosterol biosynthetic process / identical protein binding
Similarity search - Function
Hydroxymethylglutaryl-coenzyme A synthase, active site / Hydroxymethylglutaryl-CoA synthase, eukaryotic / Hydroxymethylglutaryl-coenzyme A synthase active site. / 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 ...Hydroxymethylglutaryl-coenzyme A synthase, active site / Hydroxymethylglutaryl-CoA synthase, eukaryotic / Hydroxymethylglutaryl-coenzyme A synthase active site. / 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
Hydroxymethylglutaryl-CoA synthase
Similarity search - Component
Biological speciesBrassica juncea (brown mustard)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPojer, F. / Ferrer, J.L. / Richard, S.B. / Noel, J.P.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Structural basis for the design of potent and species-specific inhibitors of 3-hydroxy-3-methylglutaryl CoA synthases.
Authors: Pojer, F. / Ferrer, J.L. / Richard, S.B. / Nagegowda, D.A. / Chye, M.L. / Bach, T.J. / Noel, J.P.
History
DepositionDec 1, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 30, 2023Group: 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

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Assembly

Deposited unit
A: HMG-CoA synthase


Theoretical massNumber of molelcules
Total (without water)50,0261
Polymers50,0261
Non-polymers00
Water2,756153
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: HMG-CoA synthase

A: HMG-CoA synthase


Theoretical massNumber of molelcules
Total (without water)100,0522
Polymers100,0522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area6140 Å2
ΔGint-21 kcal/mol
Surface area31080 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)61.130, 61.130, 433.670
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein HMG-CoA synthase


Mass: 50025.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brassica juncea (brown mustard) / Plasmid: pHis8 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9M6U3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.34 Å3/Da / Density % sol: 47.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 17% PEG 20K, 0.25M TMAO, 100mM PIPES, 2mM dithiothreitol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 4, 2004
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 29580 / Num. obs: 29353 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.072 / Net I/σ(I): 20.16
Reflection shellResolution: 2.1→2.22 Å / Mean I/σ(I) obs: 4.88 / Num. unique all: 4188 / Rsym value: 0.314 / % possible all: 89.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
NEMOdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry: 1TXT

1txt


Resolution: 2.1→47.67 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.925 / SU B: 10.302 / SU ML: 0.126 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.219 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23958 1472 5 %RANDOM
Rwork0.195 ---
all0.19724 29353 --
obs0.19724 27963 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.864 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20.05 Å20 Å2
2--0.09 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.1→47.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3510 0 0 153 3663
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223591
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5461.9684851
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5575450
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.53724.516155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.24615623
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1281513
X-RAY DIFFRACTIONr_chiral_restr0.0990.2531
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022702
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2150.21746
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22475
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2224
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.283
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1130.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9251.52306
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.49723591
X-RAY DIFFRACTIONr_scbond_it2.3931480
X-RAY DIFFRACTIONr_scangle_it3.4284.51260
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 98 -
Rwork0.196 1867 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 15.5972 Å / Origin y: 6.0307 Å / Origin z: 19.6222 Å
111213212223313233
T0.0287 Å2-0.0186 Å20.0455 Å2--0.0636 Å2-0.0529 Å2---0.0295 Å2
L0.2671 °2-0.0791 °2-0.2693 °2-0.5713 °20.1867 °2--0.505 °2
S0.0186 Å °-0.0521 Å °0.0196 Å °-0.1722 Å °0.0436 Å °-0.0561 Å °-0.0427 Å °-0.0039 Å °-0.0623 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 4511 - 450
2X-RAY DIFFRACTION1AB452 - 604

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