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- PDB-2f9a: HMG-CoA synthase from Brassica juncea in complex with F-244 -

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Basic information

Entry
Database: PDB / ID: 2f9a
TitleHMG-CoA synthase from Brassica juncea in complex with F-244
Components3-Hydroxy-3-methylglutaryl coenzyme A synthase 1
KeywordsTRANSFERASE / HMGS1 / F-244
Function / homology
Function and homology information


hydroxymethylglutaryl-CoA synthase / hydroxymethylglutaryl-CoA synthase activity / farnesyl diphosphate biosynthetic process, mevalonate pathway / acetyl-CoA metabolic process / sterol 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
Chem-F24 / Hydroxymethylglutaryl-CoA synthase
Similarity search - Component
Biological speciesBrassica juncea (brown mustard)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 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 5, 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: Advisory / Derived calculations / Version format compliance
Revision 1.3May 23, 2012Group: Non-polymer description
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-Hydroxy-3-methylglutaryl coenzyme A synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3522
Polymers50,0261
Non-polymers3261
Water4,918273
1
A: 3-Hydroxy-3-methylglutaryl coenzyme A synthase 1
hetero molecules

A: 3-Hydroxy-3-methylglutaryl coenzyme A synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,7054
Polymers100,0522
Non-polymers6532
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area7970 Å2
ΔGint-15 kcal/mol
Surface area27270 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)61.170, 61.170, 412.590
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 3-Hydroxy-3-methylglutaryl coenzyme A synthase 1


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: Chemical ChemComp-F24 / (7R,12R,13R)-13-formyl-12,14-dihydroxy-3,5,7-trimethyltetradeca-2,4-dienoic acid / Antibiotic 1233A, Bound Form


Mass: 326.428 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H30O5 / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 2.23 Å3/Da / Density % sol: 44.75 %
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: BM30A / Wavelength: 0.979754 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 14, 2005
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979754 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 16476 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.6 % / Rsym value: 0.1 / Net I/σ(I): 19.93
Reflection shellResolution: 2.5→2.65 Å / Mean I/σ(I) obs: 4.89 / Rsym value: 0.4 / % possible all: 83.4

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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: 2F82

2f82


Resolution: 2.51→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.902 / SU B: 19.027 / SU ML: 0.19 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.069 / ESU R Free: 0.299 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23644 839 5.1 %RANDOM
Rwork0.15404 ---
all0.15805 15746 --
obs0.15805 15746 97.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.914 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20.06 Å20 Å2
2--0.11 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 2.51→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3139 0 23 273 3435
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223607
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7061.9754868
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9825447
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.49924.516155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.15715622
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2631513
X-RAY DIFFRACTIONr_chiral_restr0.1170.2537
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022694
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2520.21749
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.22461
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2273
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.2107
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8381.52287
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.44423578
X-RAY DIFFRACTIONr_scbond_it2.19131497
X-RAY DIFFRACTIONr_scangle_it3.3944.51290
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.506→2.571 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 56 -
Rwork0.218 872 -
obs--75.63 %
Refinement TLS params.Method: refined / Origin x: 18.5066 Å / Origin y: 7.0515 Å / Origin z: 18.0639 Å
111213212223313233
T0.0126 Å2-0.0354 Å20.0084 Å2-0.0071 Å2-0.025 Å2---0.0099 Å2
L0.2151 °20.1399 °2-0.1076 °2-0.2902 °20.0354 °2--0.2684 °2
S-0.0395 Å °0.0274 Å °0.0009 Å °-0.0556 Å °0.0448 Å °-0.017 Å °0.0072 Å °-0.0119 Å °-0.0053 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 4511 - 450
2X-RAY DIFFRACTION1AC501 - 773

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