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- PDB-3sqz: Crystal structure of HMG_CoA synthase complexed with CoA -

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Basic information

Entry
Database: PDB / ID: 3sqz
TitleCrystal structure of HMG_CoA synthase complexed with CoA
ComponentsPutative hydroxymethylglutaryl-CoA synthase
KeywordsTRANSFERASE / thiolase fold / HMG_CoA synthase
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-CoA synthase, prokaryotic / Hydroxymethylglutaryl-coenzyme A synthase, C-terminal domain / Hydroxymethylglutaryl-coenzyme A synthase C terminal / Chalcone and stilbene synthases, N-terminal domain / 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 speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsLiu, Y.H. / Fu, T.M. / Liu, X. / Su, X.D.
CitationJournal: To be Published
Title: Crystal structure of HMG-CoA synthase from Streptococcus mutans
Authors: Liu, Y.H. / Fu, T.M. / Liu, X. / Su, X.D.
History
DepositionJul 6, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Atomic model
Revision 1.2Nov 1, 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_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative hydroxymethylglutaryl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1714
Polymers47,2201
Non-polymers9523
Water6,323351
1


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

A: Putative hydroxymethylglutaryl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,3438
Polymers94,4392
Non-polymers1,9036
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y,-z-11
Buried area8720 Å2
ΔGint-15 kcal/mol
Surface area25910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.648, 56.058, 67.365
Angle α, β, γ (deg.)90.00, 117.33, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-421-

HOH

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Components

#1: Protein Putative hydroxymethylglutaryl-CoA synthase /


Mass: 47219.738 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: UA159 / Gene: SMU_943c / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8DUI5, 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-COA / COENZYME A / Coenzyme A


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


Mass: 18.015 Da / Num. of mol.: 351 / 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: 2.05 Å3/Da / Density % sol: 40.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M Na Formate, 20% (w/v) polyethylene glycerol 3350 , VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Apr 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.19→50 Å / Num. all: 122118 / Num. obs: 122118 / % possible obs: 100 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 7.1 % / Rsym value: 0.085
Reflection shellResolution: 1.19→1.21 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 6.5 / Num. unique all: 6728 / Rsym value: 0.29 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LEH

3leh


Resolution: 1.2→31.59 Å / SU ML: 0.11 / σ(F): 0 / Phase error: 11.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1548 5866 5 %random
Rwork0.1365 ---
obs0.1374 117294 98.26 %-
all-119371 --
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.403 Å2 / ksol: 0.43 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.9945 Å2-0 Å23.3983 Å2
2---0.4774 Å20 Å2
3----2.517 Å2
Refinement stepCycle: LAST / Resolution: 1.2→31.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3008 0 60 351 3419
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073184
X-RAY DIFFRACTIONf_angle_d1.2454333
X-RAY DIFFRACTIONf_dihedral_angle_d15.9361221
X-RAY DIFFRACTIONf_chiral_restr0.09495
X-RAY DIFFRACTIONf_plane_restr0.008545
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2003-1.2140.20181890.17933519X-RAY DIFFRACTION93
1.214-1.22830.19872000.16593604X-RAY DIFFRACTION96
1.2283-1.24320.16582000.1513615X-RAY DIFFRACTION96
1.2432-1.2590.17651870.13843651X-RAY DIFFRACTION97
1.259-1.27550.16242070.13643632X-RAY DIFFRACTION97
1.2755-1.2930.15822020.12863634X-RAY DIFFRACTION97
1.293-1.31150.14711690.11753705X-RAY DIFFRACTION97
1.3115-1.33110.13951890.10863662X-RAY DIFFRACTION98
1.3311-1.35190.12311730.10373733X-RAY DIFFRACTION98
1.3519-1.3740.13742000.10193680X-RAY DIFFRACTION98
1.374-1.39770.11712030.10383725X-RAY DIFFRACTION98
1.3977-1.42310.13772060.09923643X-RAY DIFFRACTION98
1.4231-1.45050.13032080.10193689X-RAY DIFFRACTION99
1.4505-1.48010.13172030.10083767X-RAY DIFFRACTION99
1.4801-1.51230.13312000.0993723X-RAY DIFFRACTION99
1.5123-1.54750.13151950.10093743X-RAY DIFFRACTION99
1.5475-1.58620.13421870.10383763X-RAY DIFFRACTION99
1.5862-1.62910.12571730.10553765X-RAY DIFFRACTION99
1.6291-1.6770.11872170.10663769X-RAY DIFFRACTION100
1.677-1.73110.13062020.10943758X-RAY DIFFRACTION100
1.7311-1.7930.14671720.12033785X-RAY DIFFRACTION100
1.793-1.86480.14882230.12343763X-RAY DIFFRACTION100
1.8648-1.94960.15861880.1293783X-RAY DIFFRACTION100
1.9496-2.05240.17181960.13483782X-RAY DIFFRACTION100
2.0524-2.1810.13852200.13493780X-RAY DIFFRACTION100
2.181-2.34930.14231970.14093772X-RAY DIFFRACTION100
2.3493-2.58560.17651910.14793819X-RAY DIFFRACTION100
2.5856-2.95950.17381990.15823808X-RAY DIFFRACTION100
2.9595-3.72770.17021830.15283814X-RAY DIFFRACTION99
3.7277-31.60130.16831870.16743542X-RAY DIFFRACTION91

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