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Yorodumi- PDB-2a6a: Crystal structure of Glycoprotein endopeptidase (tm0874) from THE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2a6a | ||||||
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Title | Crystal structure of Glycoprotein endopeptidase (tm0874) from THERMOTOGA MARITIMA at 2.50 A resolution | ||||||
Components | hypothetical protein TM0874Hypothesis | ||||||
Keywords | HYDROLASE / tm0874 / Glycoprotein endopeptidase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2010 Title: Structure of an essential bacterial protein YeaZ (TM0874) from Thermotoga maritima at 2.5 A resolution. Authors: Xu, Q. / McMullan, D. / Jaroszewski, L. / Krishna, S.S. / Elsliger, M.A. / Yeh, A.P. / Abdubek, P. / Astakhova, T. / Axelrod, H.L. / Carlton, D. / Chiu, H.J. / Clayton, T. / Duan, L. / ...Authors: Xu, Q. / McMullan, D. / Jaroszewski, L. / Krishna, S.S. / Elsliger, M.A. / Yeh, A.P. / Abdubek, P. / Astakhova, T. / Axelrod, H.L. / Carlton, D. / Chiu, H.J. / Clayton, T. / Duan, L. / Feuerhelm, J. / Grant, J. / Han, G.W. / Jin, K.K. / Klock, H.E. / Knuth, M.W. / Miller, M.D. / Morse, A.T. / Nigoghossian, E. / Okach, L. / Oommachen, S. / Paulsen, J. / Reyes, R. / Rife, C.L. / van den Bedem, H. / Hodgson, K.O. / Wooley, J. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Wilson, I.A. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...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). THE BIOLOGICAL UNIT IS A TETRAMER WITH 222 POINT SYMMETRY, FORMED BY CRYSTALLOGRAPHIC SYMMETRY, AS ADJUDGED BY EXTENSIVE HYDROPHOBIC CONTACTS BETWEEN THESE UNITS. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2a6a.cif.gz | 83.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2a6a.ent.gz | 65.3 KB | Display | PDB format |
PDBx/mmJSON format | 2a6a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a6/2a6a ftp://data.pdbj.org/pub/pdb/validation_reports/a6/2a6a | HTTPS FTP |
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-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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3 |
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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 label comp-ID: MSE / End label comp-ID: GLU / Auth seq-ID: 1 - 187 / Label seq-ID: 13 - 199
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Details | THE BIOLOGICAL UNIT IS A TETRAMER WITH 222 POINT SYMMETRY, FORMED BY CRYSTALLOGRAPHIC SYMMETRY, AS ADJUDGED BY EXTENSIVE HYDROPHOBIC CONTACTS BETWEEN THESE UNITS. |
-Components
#1: Protein | Mass: 24623.162 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: tm0874 / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: GenBank: 15643636, UniProt: Q9WZX7*PLUS #2: Chemical | Num. of mol.: 2 / Source method: obtained synthetically #3: 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: 3.25 Å3/Da / Density % sol: 61.87 % |
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Crystal grow | Temperature: 273 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 4 Details: 10.0% MPD, 0.1M Citrate pH 4.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 273K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979413, 0.918370 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 3, 2005 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.5→29.24 Å / Num. obs: 18685 / % possible obs: 99.6 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 11.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.5→29.24 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / SU B: 18.431 / SU ML: 0.186 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.333 / ESU R Free: 0.242 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.618 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→29.24 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2742 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.5→2.588 Å / Total num. of bins used: 15
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Selection: all
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