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- PDB-1xpk: CRYSTAL STRUCTURE OF STAPHYLOCOCCUS AUREUS HMG-COA SYNTHASE WITH ... -

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Basic information

Entry
Database: PDB / ID: 1xpk
TitleCRYSTAL STRUCTURE OF STAPHYLOCOCCUS AUREUS HMG-COA SYNTHASE WITH HMG-CoA AND WITH ACETOACETYL-COA AND ACETYLATED CYSTEINE
Components(3-hydroxy-3-methylglutaryl CoA ...) x 2
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 / MOLECULAR REPLACEMENT / Resolution: 2 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 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Derived calculations
Revision 1.4Oct 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 1.5Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 1.6Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.7Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE RESULTS ARE FROM DAY FIVE OF CRYSTALLIZATION. IN THE COORDINATE RECORDS FOR CHAINS A AND ...SEQUENCE RESULTS ARE FROM DAY FIVE OF CRYSTALLIZATION. IN THE COORDINATE RECORDS FOR CHAINS A AND D, SCY/CYS 111 ISOFORMS ARE MODELED AS ALTERNATE CONFORMERS. BECAUSE OF THE FORMAT RESTRICTIONS ONLY SCY 111 ISOFORM IS REPRESENTED IN THE SEQUENCE RECORDS. RESIDUES 111 OF CHAINS B AND C ARE MODELED WITH ONLY SCY AND CYS, RESPECTIVELY.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)179,17918
Polymers173,1354
Non-polymers6,04314
Water10,395577
1
A: 3-hydroxy-3-methylglutaryl CoA synthase
B: 3-hydroxy-3-methylglutaryl CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,5839
Polymers86,5892
Non-polymers2,9947
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6650 Å2
ΔGint-54 kcal/mol
Surface area26670 Å2
MethodPISA, PQS
2
C: 3-hydroxy-3-methylglutaryl CoA synthase
D: 3-hydroxy-3-methylglutaryl CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,5969
Polymers86,5472
Non-polymers3,0497
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8210 Å2
ΔGint-51 kcal/mol
Surface area27390 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)64.271, 84.612, 94.633
Angle α, β, γ (deg.)84.25, 72.52, 70.44
Int Tables number1
Space group name H-MP1
DetailsThe asymmetric unit contains two dimers (A/B and C/D); the dimer is the biological unit.

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Components

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3-hydroxy-3-methylglutaryl CoA ... , 2 types, 4 molecules ABDC

#1: Protein 3-hydroxy-3-methylglutaryl CoA synthase / HMG-COA SYNTHASE


Mass: 43294.367 Da / Num. of mol.: 3
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: Protein 3-hydroxy-3-methylglutaryl CoA synthase / HMG-COA SYNTHASE


Mass: 43252.328 Da / Num. of mol.: 1
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

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Non-polymers , 4 types, 591 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 906.620 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H39N7O20P3S
#5: Chemical ChemComp-CAA / ACETOACETYL-COENZYME A


Mass: 851.607 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C25H40N7O18P3S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 577 / 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: 2.7 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 7.5
Details: ammonium sulfate, Tris, DTT, pH 7.5, VAPOR DIFFUSION, temperature 292K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Nov 3, 2002 / Details: Confocal mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→35 Å / Num. all: 119970 / Num. obs: 94526 / % possible obs: 78.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 1.7 % / Rmerge(I) obs: 0.028 / Rsym value: 0.028 / Χ2: 1.132 / Net I/σ(I): 27
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.070.13238650.79132.2
2.07-2.150.10753770.837145
2.15-2.250.08577890.963165
2.25-2.370.073104771.011187
2.37-2.520.059108921.035191.3
2.52-2.710.047112311.039193.3
2.71-2.990.036112401.189193.8
2.99-3.420.028110871.292192.4
3.42-4.310.022112871.255194
4.31-350.016112811.437194

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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 1TXT

1txt


Resolution: 2→35 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.234 4609 random
Rwork0.198 --
all-92374 -
obs-92374 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.611 Å22.293 Å2-0.4 Å2
2---0.374 Å20 Å2
3---4.985 Å2
Refinement stepCycle: LAST / Resolution: 2→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11900 0 376 577 12853
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_mcbond_it1.2241.5
X-RAY DIFFRACTIONc_mcangle_it1.7782
X-RAY DIFFRACTIONc_scbond_it1.8282
X-RAY DIFFRACTIONc_scangle_it2.4722.5
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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