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Yorodumi- PDB-3c37: X-ray structure of the putative Zn-dependent peptidase Q74D82 at ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3c37 | ||||||
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Title | X-ray structure of the putative Zn-dependent peptidase Q74D82 at the resolution 1.7 A. Northeast Structural Genomics Consortium target GsR143A | ||||||
Components | Peptidase, M48 familyProtease | ||||||
Keywords | HYDROLASE / Q74D82 / GsR143A / Peptidase / M48 family / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Metalloprotease / Protease | ||||||
Function / homology | Peptidase M48 / Peptidase family M48 / metalloendopeptidase activity / metal ion binding / DI(HYDROXYETHYL)ETHER / Peptidase lipoprotein, M48 family Function and homology information | ||||||
Biological species | Geobacter sulfurreducens PCA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å | ||||||
Authors | Kuzin, A.P. / Chen, Y. / Seetharaman, J. / Vorobiev, S.M. / Forouhar, F. / Wang, D. / Mao, L. / Maglaqui, M. / Xiao, R. / Liu, J. ...Kuzin, A.P. / Chen, Y. / Seetharaman, J. / Vorobiev, S.M. / Forouhar, F. / Wang, D. / Mao, L. / Maglaqui, M. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: X-ray structure of the putative Zn-dependent peptidase Q74D82 at the resolution 1.7 A. Authors: Kuzin, A.P. / Chen, Y. / Seetharaman, J. / Vorobiev, S.M. / Forouhar, F. / Wang, D. / Mao, L. / Maglaqui, M. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3c37.cif.gz | 102.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3c37.ent.gz | 83.4 KB | Display | PDB format |
PDBx/mmJSON format | 3c37.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c3/3c37 ftp://data.pdbj.org/pub/pdb/validation_reports/c3/3c37 | 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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Unit cell |
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-Components
#1: Protein | Mass: 28906.326 Da / Num. of mol.: 2 / Fragment: Residues 21-264 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacter sulfurreducens PCA (bacteria) Species: Geobacter sulfurreducens / Strain: PCA / DSM 12127 / Gene: GSU1437 / Production host: Escherichia coli (E. coli) / References: UniProt: Q74D82 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 1.791 Å3/Da / Density % sol: 31.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1M Ammonium thiocyanate, 0.1M Sodium citrate, 40% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 1.7→30 Å / Num. obs: 84304 / % possible obs: 94.7 % / Observed criterion σ(I): -3 / Redundancy: 1.92 % / Rsym value: 0.024 / Net I/σ(I): 30.2 | |||||||||||||||
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 1.93 % / Mean I/σ(I) obs: 3.9 / Rsym value: 0.167 / % possible all: 86.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.7→27.43 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.917 / SU B: 2.544 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: The Friedel pairs were used in phasing
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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: 25.071 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→27.43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.74 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 18.189 Å / Origin y: 7.005 Å / Origin z: 18.244 Å
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