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Yorodumi- PDB-1zxo: X-ray Crystal Structure of Protein Q8A1P1 from Bacteroides thetai... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zxo | ||||||
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Title | X-ray Crystal Structure of Protein Q8A1P1 from Bacteroides thetaiotaomicron. Northeast Structural Genomics Consortium Target BtR25. | ||||||
Components | conserved hypothetical protein Q8A1P1 | ||||||
Keywords | UNKNOWN FUNCTION / NESG / BtR25 / Structural Genomics / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium | ||||||
Function / homology | Function and homology information Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 - #160 / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Bacteroides thetaiotaomicron (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.2 Å | ||||||
Authors | Kuzin, A.P. / Yong, W. / Forouhar, F. / Vorobiev, S. / Xiao, R. / Ma, C. / Acton, T. / Montelione, G.T. / Hunt, J. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: X-Ray structure of the hypothetical protein Q8A1P1 at the resolution 3.2A. Northeast Structural Genomics Consortium target BtR25. Authors: Kuzin, A.P. / Yong, W. / Forouhar, F. / Vorobiev, S. / Xiao, R. / Ma, C. / Acton, T. / Montelione, G.T. / Hunt, J. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zxo.cif.gz | 319.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zxo.ent.gz | 273.6 KB | Display | PDB format |
PDBx/mmJSON format | 1zxo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zxo_validation.pdf.gz | 480.8 KB | Display | wwPDB validaton report |
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Full document | 1zxo_full_validation.pdf.gz | 564.8 KB | Display | |
Data in XML | 1zxo_validation.xml.gz | 68.1 KB | Display | |
Data in CIF | 1zxo_validation.cif.gz | 92.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zx/1zxo ftp://data.pdbj.org/pub/pdb/validation_reports/zx/1zxo | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 32492.658 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria) Production host: Escherichia coli (E. coli) / References: UniProt: Q8A1P1 #2: 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: 3.4 Å3/Da / Density % sol: 64 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: 8% PEG8K, 0.1M NaHepes, 8% Ethyl-Glycol , pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97908,0.97932,0.96797 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 15, 2005 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 3→30 Å / Num. all: 102631 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.79 % / Biso Wilson estimate: 32.2 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 24.64 | ||||||||||||
Reflection shell | Resolution: 3→3.11 Å / Rmerge(I) obs: 0.549 / Mean I/σ(I) obs: 3.2 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 3.2→25.56 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 165787.62 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.24546 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 60.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.2→25.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.4 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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