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Yorodumi- PDB-3k9u: Crystal structure of paia acetyltransferase (ta0374) from thermop... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3k9u | ||||||
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Title | Crystal structure of paia acetyltransferase (ta0374) from thermoplasma acidophilum | ||||||
Components | PaiA Acetyltransferase | ||||||
Keywords | TRANSFERASE / THERMOPLASMA ACIDOPHILUM / ACETYLTRANSFERASE / STRUCTURAL GENOMICS / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information negative regulation of sporulation / diamine N-acetyltransferase / diamine N-acetyltransferase activity Similarity search - Function | ||||||
Biological species | Thermoplasma acidophilum (acidophilic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Filippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: Proteins / Year: 2011 Title: Crystal structure of the novel PaiA N-acetyltransferase from Thermoplasma acidophilum involved in the negative control of sporulation and degradative enzyme production. Authors: Filippova, E.V. / Shuvalova, L. / Minasov, G. / Kiryukhina, O. / Zhang, Y. / Clancy, S. / Radhakrishnan, I. / Joachimiak, A. / Anderson, W.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3k9u.cif.gz | 84 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3k9u.ent.gz | 62.8 KB | Display | PDB format |
PDBx/mmJSON format | 3k9u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3k9u_validation.pdf.gz | 1000.7 KB | Display | wwPDB validaton report |
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Full document | 3k9u_full_validation.pdf.gz | 1002.7 KB | Display | |
Data in XML | 3k9u_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | 3k9u_validation.cif.gz | 19.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k9/3k9u ftp://data.pdbj.org/pub/pdb/validation_reports/k9/3k9u | HTTPS FTP |
-Related structure data
Related structure data | 3f0aSC 3fixC 3ne7C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: 6 / Auth seq-ID: 1 - 159 / Label seq-ID: 1 - 159
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Details | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). GENERATING THE BIOMOLECULE COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. BIOMOLECULE: 1 APPLY THE FOLLOWING TO CHAINS: A, B, G, H, L, C, F BIOMT1 1 1.000000 0.000000 0.000000 0.00000 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 18808.830 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Gene: Ta0374 / Plasmid: pMCSG7 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): Bl21magic / References: UniProt: Q9HL57 |
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-Non-polymers , 5 types, 82 molecules
#2: Chemical | #3: Chemical | ChemComp-NI / | #4: Chemical | ChemComp-BR / | #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: 2.89 Å3/Da / Density % sol: 57.44 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M Sodium Bromide, 20% PEG 3350, 0.1 M Bis-Tris propane, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97872 Å |
Detector | Detector: CCD / Date: Mar 16, 2009 / Details: MIRROR |
Radiation | Monochromator: SI-111 CHANNEL / Protocol: MOLECULAR REPLACEMENT / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→54.98 Å / Num. all: 19708 / Num. obs: 19708 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 17.469 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.185 / Mean I/σ(I) obs: 10.2 / Rsym value: 0.185 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3F0A Resolution: 2.3→54.98 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.903 / SU B: 10.592 / SU ML: 0.148 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.28 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.28 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→54.98 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Number: 2278 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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