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Yorodumi- PDB-2hzb: X-Ray Crystal Structure of Protein BH3568 from Bacillus haloduran... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hzb | ||||||
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Title | X-Ray Crystal Structure of Protein BH3568 from Bacillus halodurans. Northeast Structural Genomics Consortium BhR60. | ||||||
Components | Hypothetical UPF0052 protein BH3568 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / BhR60 / NESG / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium | ||||||
Function / homology | Function and homology information LPPG:FO 2-phospho-L-lactate transferase activity / regulation of cell shape / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus halodurans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.8 Å | ||||||
Authors | Kuzin, A.P. / Chen, Y. / Seetharaman, J. / Benach, J. / Shastry, R. / Conover, K. / Ma, L.C. / Xiao, R. / Liu, J. / Baran, M.C. ...Kuzin, A.P. / Chen, Y. / Seetharaman, J. / Benach, J. / Shastry, R. / Conover, K. / Ma, L.C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: X-Ray structure of the hypothetical UPF0052 protein BH3568 from Bacillus halodurans. Northeast Structural Genomics Consortium BhR60. Authors: Kuzin, A.P. / Chen, Y. / Seetharaman, J. / Benach, J. / Shastry, R. / Conover, K. / Ma, L.C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hzb.cif.gz | 236.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hzb.ent.gz | 200.2 KB | Display | PDB format |
PDBx/mmJSON format | 2hzb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2hzb_validation.pdf.gz | 464.1 KB | Display | wwPDB validaton report |
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Full document | 2hzb_full_validation.pdf.gz | 496.9 KB | Display | |
Data in XML | 2hzb_validation.xml.gz | 46.7 KB | Display | |
Data in CIF | 2hzb_validation.cif.gz | 64.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hz/2hzb ftp://data.pdbj.org/pub/pdb/validation_reports/hz/2hzb | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 36047.461 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus halodurans (bacteria) / Gene: BH3568 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q9K706 #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: 2.92 Å3/Da / Density % sol: 57.91 % Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS |
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Crystal grow | Temperature: 277 K / pH: 7 Details: 2.4M Sodium malonate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 7.00 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9793, 0.9796, 0.9681 | ||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 5, 2006 / Details: MIRRORS | ||||||||||||
Radiation | Monochromator: SI 111 CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.8→30 Å / Num. all: 79533 / Num. obs: 71260 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 13.6 | ||||||||||||
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 3 / % possible all: 95.1 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.8→19.98 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 44670.69 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: ENGH & HUBER / Details: THE FRIEDEL PAIRS WERE USED FOR PHASING
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 18.48 Å2 / ksol: 0.33 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→19.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.97 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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