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- PDB-1xpm: Crystal Structure of Staphylococcus aureus HMG-COA Synthase with ... -

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Basic information

Entry
Database: PDB / ID: 1xpm
TitleCrystal Structure of Staphylococcus aureus HMG-COA Synthase with HMG-CoA and Acetoacetyl-COA and Acetylated Cysteine
Components3-hydroxy-3-methylglutaryl CoA synthase
KeywordsTRANSFERASE / HMG-COA Synthase / HMGS / Coenzyme A / Thiolase Fold / Condensing Enzyme / Cholesterol Biosynthesis
Function / homology
Function and homology information


farnesyl diphosphate biosynthetic process, mevalonate pathway / hydroxymethylglutaryl-CoA synthase activity / 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
ACETOACETYL-COENZYME A / 3-HYDROXY-3-METHYLGLUTARYL-COENZYME A / 3-hydroxy-3-methylglutaryl CoA synthase / 3-hydroxy-3-methylglutaryl CoA synthase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsTheisen, M.J. / Misra, I. / Saadat, D. / Campobasso, N. / Miziorko, H.M. / Harrison, D.H.T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: 3-hydroxy-3-methylglutaryl-CoA synthase intermediate complex observed in "real-time"
Authors: Theisen, M.J. / Misra, I. / Saadat, D. / Campobasso, N. / Miziorko, H.M. / Harrison, D.H.T.
History
DepositionOct 8, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 23, 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
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE RESULTS ARE FROM DAY THIRTY-ONE OF CRYSTALLIZATION. IN THE COORDINATE RECORDS SCY/CYS 111 ...SEQUENCE RESULTS ARE FROM DAY THIRTY-ONE OF CRYSTALLIZATION. IN THE COORDINATE RECORDS SCY/CYS 111 ISOFORMS ARE MODELED AS ALTERNATE CONFORMERS. BECAUSE OF THE FORMAT RESTRICTIONS ONLY SCY 111 ISOFORM IS REPRESENTED IN THE SEQUENCE RECORDS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)185,14320
Polymers177,3424
Non-polymers7,80116
Water19,5101083
1
A: 3-hydroxy-3-methylglutaryl CoA synthase
B: 3-hydroxy-3-methylglutaryl CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,57210
Polymers88,6712
Non-polymers3,9018
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7890 Å2
ΔGint-50 kcal/mol
Surface area28430 Å2
MethodPISA
2
C: 3-hydroxy-3-methylglutaryl CoA synthase
D: 3-hydroxy-3-methylglutaryl CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,57210
Polymers88,6712
Non-polymers3,9018
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7830 Å2
ΔGint-52 kcal/mol
Surface area28450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.119, 118.774, 121.304
Angle α, β, γ (deg.)90.00, 90.08, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe asymmetric unit contains two dimers (A/B and C/D); the dimer is the biological unit.

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Components

#1: Protein
3-hydroxy-3-methylglutaryl CoA synthase


Mass: 44335.480 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Species: Staphylococcus aureus / Strain: subsp. aureus / Gene: mvaS / Plasmid: pET23d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q79ZY6, UniProt: A0A0H3K1U2*PLUS, hydroxymethylglutaryl-CoA synthase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-HMG / 3-HYDROXY-3-METHYLGLUTARYL-COENZYME A / (S)-HMG-COA


Mass: 906.620 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H39N7O20P3S
#4: Chemical
ChemComp-CAA / ACETOACETYL-COENZYME A


Mass: 851.607 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C25H40N7O18P3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1083 / 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: 2.7 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 7.5
Details: mmonium sulfate, Tris, DTT, pH 7.5, VAPOR DIFFUSION, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Feb 28, 2004
RadiationMonochromator: Double crystal Si-220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→25 Å / Num. all: 232032 / Num. obs: 217551 / % possible obs: 89.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.6 % / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Χ2: 1.26 / Net I/σ(I): 28.3
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
1.6-1.660.605187780.66377.7
1.66-1.720.481203590.66284.4
1.72-1.80.343204950.71584.7
1.8-1.90.246208080.84886.3
1.9-2.020.177215921.1289.2
2.02-2.170.131220511.29691
2.17-2.390.109224151.58692.7
2.39-2.740.09230171.71295
2.74-3.440.07239181.96298.3
3.44-250.054241181.80598.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT1.501data extraction
HKL-2000data reduction
BEASTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XPK

1xpk


Resolution: 1.6→15 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.226 10669 random
Rwork0.21 --
all-216448 -
obs-216448 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.035 Å20 Å2-0.673 Å2
2---7.236 Å20 Å2
3---4.202 Å2
Refinement stepCycle: LAST / Resolution: 1.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13753 0 488 1083 15324
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_mcbond_it1.0821.5
X-RAY DIFFRACTIONc_mcangle_it1.6222
X-RAY DIFFRACTIONc_scbond_it1.6852
X-RAY DIFFRACTIONc_scangle_it2.442.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ligands_fromscratch.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ion.param
X-RAY DIFFRACTION5cis_peptide.param

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