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Yorodumi- PDB-1xpk: CRYSTAL STRUCTURE OF STAPHYLOCOCCUS AUREUS HMG-COA SYNTHASE WITH ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xpk | ||||||
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Title | CRYSTAL 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 | ||||||
Keywords | TRANSFERASE / HMG-COA Synthase / HMGS / Coenzyme A / Thiolase Fold / Condensing Enzyme / Cholesterol Biosynthesis | ||||||
Function / homology | Function and homology information hydroxymethylglutaryl-CoA synthase activity / farnesyl diphosphate biosynthetic process, mevalonate pathway / acetyl-CoA metabolic process / ergosterol biosynthetic process Similarity search - Function | ||||||
Biological species | Staphylococcus aureus subsp. aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Theisen, M.J. / Misra, I. / Saadat, D. / Campobasso, N. / Miziorko, H.M. / Harrison, D.H.T. | ||||||
Citation | Journal: 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 |
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Remark 999 | SEQUENCE 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xpk.cif.gz | 325.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xpk.ent.gz | 261.9 KB | Display | PDB format |
PDBx/mmJSON format | 1xpk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1xpk_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 1xpk_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 1xpk_validation.xml.gz | 62.4 KB | Display | |
Data in CIF | 1xpk_validation.cif.gz | 85.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xp/1xpk ftp://data.pdbj.org/pub/pdb/validation_reports/xp/1xpk | HTTPS FTP |
-Related structure data
Related structure data | 1xplC 1xpmC 1txtS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | The asymmetric unit contains two dimers (A/B and C/D); the dimer is the biological unit. |
-Components
-3-hydroxy-3-methylglutaryl CoA ... , 2 types, 4 molecules ABDC
#1: Protein | 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 | | 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 / #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 53 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion / pH: 7.5 Details: ammonium sulfate, Tris, DTT, pH 7.5, VAPOR DIFFUSION, temperature 292K |
-Data collection
Diffraction | Mean temperature: 120 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Nov 3, 2002 / Details: Confocal mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 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 |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1TXT Resolution: 2→35 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2→35 Å
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Refine LS restraints |
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Xplor file |
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