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Yorodumi- PDB-5anp: CRYSTAL STRUCTURE OF THE BA41 PROTEIN FROM BIZIONIA ARGENTINENSIS -
+Open data
-Basic information
Entry | Database: PDB / ID: 5anp | ||||||
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Title | CRYSTAL STRUCTURE OF THE BA41 PROTEIN FROM BIZIONIA ARGENTINENSIS | ||||||
Components | BA41 | ||||||
Keywords | UNKNOWN FUNCTION / ANTARCTIC BACTERIA / BA41 | ||||||
Function / homology | Diaminopimelate Epimerase; Chain A, domain 1 - #50 / TPM domain / TPM domain / Diaminopimelate Epimerase; Chain A, domain 1 / membrane => GO:0016020 / Roll / Alpha Beta / TPM domain-containing protein Function and homology information | ||||||
Biological species | BIZIONIA ARGENTINENSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Otero, L.H. / Cerutti, M.L. / Goldbaum, F.A. / Klinke, S. | ||||||
Citation | Journal: J. Struct. Biol. / Year: 2017 Title: Structural and functional characterization of a cold adapted TPM-domain with ATPase/ADPase activity. Authors: Cerutti, M.L. / Otero, L.H. / Smal, C. / Pellizza, L. / Goldbaum, F.A. / Klinke, S. / Aran, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5anp.cif.gz | 76.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5anp.ent.gz | 56.2 KB | Display | PDB format |
PDBx/mmJSON format | 5anp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/an/5anp ftp://data.pdbj.org/pub/pdb/validation_reports/an/5anp | HTTPS FTP |
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-Related structure data
Related structure data | 2kw7S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 29161.879 Da / Num. of mol.: 2 / Fragment: TPM DOMAIN, UNP RESIDUES 29-178 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BIZIONIA ARGENTINENSIS (bacteria) / Strain: JUB59 / Plasmid: PDEST527 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYS / References: UniProt: G2EA44 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.82 Å3/Da / Density % sol: 32.53 % / Description: NONE |
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Crystal grow | pH: 6.1 Details: 23% PEG 5000 MME, 2% PEG 400, 0.1M IMIDAZOLE PH 6.1 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.82656 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS |
Radiation | Monochromator: CHANNEL CUT CRYOGENICALLY COOLED MONOCROMATOR CRYSTAL Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.82656 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→34.43 Å / Num. obs: 46549 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Biso Wilson estimate: 13.43 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.2 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2KW7 Resolution: 1.4→34.43 Å / Cor.coef. Fo:Fc: 0.9569 / Cor.coef. Fo:Fc free: 0.9535 / SU R Cruickshank DPI: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.067 / SU Rfree Blow DPI: 0.063 / SU Rfree Cruickshank DPI: 0.062
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Displacement parameters | Biso mean: 17.29 Å2
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Refine analyze | Luzzati coordinate error obs: 0.154 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→34.43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.44 Å / Total num. of bins used: 20
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