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- PDB-1ysl: Crystal structure of HMG-CoA synthase from Enterococcus faecalis ... -

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Basic information

Entry
Database: PDB / ID: 1ysl
TitleCrystal structure of HMG-CoA synthase from Enterococcus faecalis with AcetoAcetyl-CoA ligand.
Components(HMG-CoA synthase) x 2
KeywordsLYASE / Thiolase family / CoEnzymeA
Function / homology
Function and homology information


hydroxymethylglutaryl-CoA synthase / hydroxymethylglutaryl-CoA synthase activity / acetyl-CoA metabolic process / isoprenoid biosynthetic 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
ACETOACETIC ACID / COENZYME A / : / Hydroxymethylglutaryl-CoA synthase
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSteussy, C.N. / Vartia, A.A. / Burgner II, J.W. / Sutherlin, A. / Rodwell, V.W. / Stauffacher, C.V.
CitationJournal: Biochemistry / Year: 2005
Title: X-ray Crystal Structures of HMG-CoA Synthase from Enterococcus faecalis and a Complex with Its Second Substrate/Inhibitor Acetoacetyl-CoA.
Authors: Steussy, C.N. / Vartia, A.A. / Burgner II, J.W. / Sutherlin, A. / Rodwell, V.W. / Stauffacher, C.V.
History
DepositionFeb 8, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_poly_seq_scheme / 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 / _pdbx_poly_seq_scheme.auth_seq_num / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / struct_conn
Remark 400COMPOUND THE ACETOACETYL MOLECULE, AAE IS COVALENTLY ATTACHED TO CYSTEINE B111 WITH 50% OCCUPANCY. ...COMPOUND THE ACETOACETYL MOLECULE, AAE IS COVALENTLY ATTACHED TO CYSTEINE B111 WITH 50% OCCUPANCY. THE REMAINING PORTION OF CYSTEINE B111 IS OXIDIZED TO SULFONATE (CSD). CYSTEINE A 111 IS ENTIRELY OXIDIZED (CSD).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HMG-CoA synthase
B: HMG-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,8308
Polymers88,5842
Non-polymers1,2466
Water9,404522
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7000 Å2
ΔGint-35 kcal/mol
Surface area24730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.300, 109.013, 140.799
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11B-700-

HOH

DetailsThe asymmetric unit contains a homodimer that is believed to be the biologically active unit.

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein HMG-CoA synthase


Mass: 44307.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21[DE3]
References: GenBank: 9937383, UniProt: Q9FD71*PLUS, EC: 4.1.3.5
#2: Protein HMG-CoA synthase


Mass: 44275.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21[DE3]
References: GenBank: 9937383, UniProt: Q9FD71*PLUS, EC: 4.1.3.5

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Non-polymers , 5 types, 528 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#6: Chemical ChemComp-AAE / ACETOACETIC ACID


Mass: 102.089 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 522 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.39 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 2.4M ammonium sulfate, 100 mM MES, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 30, 2004 / Details: Bent conical Si-mirror (Rh coating)
RadiationMonochromator: Bent Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.9→28 Å / Num. all: 63975 / Num. obs: 63975 / % possible obs: 100 % / Observed criterion σ(F): 63975 / Observed criterion σ(I): 63975
Reflection shellResolution: 1.9→1.95 Å / % possible all: 100

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1x9e

1x9e


Resolution: 1.9→28 Å / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2008 2565 4 %Random
Rwork0.179 ---
obs0.18 63975 99.8 %-
all-63975 --
Refinement stepCycle: LAST / Resolution: 1.9→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5948 0 76 522 6546
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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