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Yorodumi- PDB-2raq: Crystal structure of the MTH889 protein from Methanothermobacter ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2raq | ||||||
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Title | Crystal structure of the MTH889 protein from Methanothermobacter thermautotrophicus. Northeast Structural Genomics Consortium target TT205 | ||||||
Components | Conserved protein MTH889 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta protein / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | MTH889-like domain / Protein of unknown function DUF211 / MTH889-like domain superfamily / Uncharacterized ArCR, COG1888 / Alpha-Beta Plaits / 2-Layer Sandwich / metal ion binding / Alpha Beta / Conserved protein Function and homology information | ||||||
Biological species | Methanothermobacter thermautotrophicus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.11 Å | ||||||
Authors | Forouhar, F. / Su, M. / Xu, X. / Seetharaman, J. / Mao, L. / Xiao, R. / Ma, L.-C. / Conover, K. / Baran, M.C. / Acton, T.B. ...Forouhar, F. / Su, M. / Xu, X. / Seetharaman, J. / Mao, L. / Xiao, R. / Ma, L.-C. / Conover, K. / Baran, M.C. / Acton, T.B. / Montelione, G.T. / Arrowsmith, C.H. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of the MTH889 protein from Methanothermobacter thermautotrophicus. Authors: Forouhar, F. / Su, M. / Xu, X. / Seetharaman, J. / Mao, L. / Xiao, R. / Ma, L.-C. / Conover, K. / Baran, M.C. / Acton, T.B. / Montelione, G.T. / Arrowsmith, C.H. / Hunt, J.F. / Tong, L. | ||||||
History |
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Remark 999 | SEQUENCE A 25-AA N-TERMINAL TAG WAS CLEAVED BY THROMBIN. IN RESULT, THE FINAL PURIFIED PROTEIN HAD ... SEQUENCE A 25-AA N-TERMINAL TAG WAS CLEAVED BY THROMBIN. IN RESULT, THE FINAL PURIFIED PROTEIN HAD ONLY MODIFICATION FOR ITS METHIONINE RESIDUES TO SE-MET RESIDUES. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2raq.cif.gz | 133.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2raq.ent.gz | 112.8 KB | Display | PDB format |
PDBx/mmJSON format | 2raq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2raq_validation.pdf.gz | 472.6 KB | Display | wwPDB validaton report |
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Full document | 2raq_full_validation.pdf.gz | 513.6 KB | Display | |
Data in XML | 2raq_validation.xml.gz | 29.8 KB | Display | |
Data in CIF | 2raq_validation.cif.gz | 40.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ra/2raq ftp://data.pdbj.org/pub/pdb/validation_reports/ra/2raq | 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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Unit cell |
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Details | 14-mer oligomer made of two heptameric rings that are mediated by many calcium ions. |
-Components
#1: Protein | Mass: 10962.974 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea) Strain: Delta H / Gene: MTH889 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) gold magic / References: UniProt: O26975 #2: Chemical | ChemComp-CA / #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: 2.41 Å3/Da / Density % sol: 48.88 % |
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Crystal grow | Temperature: 291 K / Method: microbatch under oil / pH: 7.5 Details: Protein solution: 10 mM Tris-HCl pH 7.5, 100 mM NaCl, 5 mM DTT. Reservoir solution: 100 mM HEPES pH 7.5, 18% PEG 400, 200 mM CaCl2, 3% 1,6-Hexanediol, MICROBATCH UNDER OIL, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 13, 2007 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→80.58 Å / Num. all: 25673 / Num. obs: 25673 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.085 / Rsym value: 0.068 / Net I/σ(I): 26.13 |
Reflection shell | Resolution: 3.1→3.21 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 6.13 / Num. unique all: 2573 / Rsym value: 0.282 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3.11→80.58 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.862 / SU B: 43.319 / SU ML: 0.386 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.553 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Program CNS_1.2 has also been used in refinement
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.914 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.11→80.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.11→3.19 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 19.4402 Å / Origin y: 75.2137 Å / Origin z: -7.4043 Å
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Refinement TLS group |
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