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Yorodumi- PDB-1tm0: Crystal Structure of the putative proline racemase from Brucella ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tm0 | ||||||
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Title | Crystal Structure of the putative proline racemase from Brucella melitensis, Northeast Structural Genomics Target LR31 | ||||||
Components | PROLINE RACEMASE | ||||||
Keywords | ISOMERASE / STRUCTURAL GENOMICS / alpha-beta protein that resembles double-beta barrel / in each of which an alpha helix is sandwiched / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | 4-hydroxyproline epimerase / 4-hydroxyproline epimerase activity / Proline racemase family / Proline racemase / Diaminopimelate Epimerase; Chain A, domain 1 / Diaminopimelate Epimerase; Chain A, domain 1 / Roll / Alpha Beta / Protein BMEI1586 Function and homology information | ||||||
Biological species | Brucella melitensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å | ||||||
Authors | Forouhar, F. / Chen, Y. / Xiao, R. / Ho, C.K. / Ma, L.-C. / Cooper, B. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: J.STRUCT.FUNCT.GENOM. / Year: 2007 Title: Functional insights from structural genomics. Authors: Forouhar, F. / Kuzin, A. / Seetharaman, J. / Lee, I. / Zhou, W. / Abashidze, M. / Chen, Y. / Yong, W. / Janjua, H. / Fang, Y. / Wang, D. / Cunningham, K. / Xiao, R. / Acton, T.B. / ...Authors: Forouhar, F. / Kuzin, A. / Seetharaman, J. / Lee, I. / Zhou, W. / Abashidze, M. / Chen, Y. / Yong, W. / Janjua, H. / Fang, Y. / Wang, D. / Cunningham, K. / Xiao, R. / Acton, T.B. / Pichersky, E. / Klessig, D.F. / Porter, C.W. / Montelione, G.T. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tm0.cif.gz | 124.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tm0.ent.gz | 103.4 KB | Display | PDB format |
PDBx/mmJSON format | 1tm0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1tm0_validation.pdf.gz | 444.2 KB | Display | wwPDB validaton report |
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Full document | 1tm0_full_validation.pdf.gz | 469.8 KB | Display | |
Data in XML | 1tm0_validation.xml.gz | 26.5 KB | Display | |
Data in CIF | 1tm0_validation.cif.gz | 35.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tm/1tm0 ftp://data.pdbj.org/pub/pdb/validation_reports/tm/1tm0 | HTTPS FTP |
-Related structure data
Related structure data | 1rtyC 1sqsC 1zbpC 2hd3C 2nv4C 2oysC 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 38559.449 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brucella melitensis (bacteria) / Strain: 16M / Plasmid: pET21(BL21) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q8YFD6, proline racemase #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: 2.25 Å3/Da / Density % sol: 44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20% PEG 3350, pH 7, 200mM potassium thiocyanate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97904 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 4, 2004 / Details: Mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97904 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→28.57 Å / Num. all: 29250 / Num. obs: 26270 / % possible obs: 84.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 9.3 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.076 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2.8→2.98 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.181 / Mean I/σ(I) obs: 5.1 / Num. unique all: 2887 / Rsym value: 0.182 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.8→28.57 Å / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure.
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Displacement parameters | Biso mean: 33.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→28.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.028
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