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Yorodumi- PDB-6cum: Crystal structure of a C-terminal proteolytic fragment of a prote... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6cum | ||||||
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Title | Crystal structure of a C-terminal proteolytic fragment of a protein annotated as an LAO/AO transport system ATPase but likely MeaB and MMAA-like GTPase from Mycobacterium smegmatis | ||||||
Components | LAO/AO transport system ATPase | ||||||
Keywords | TRANSFERASE / SSGCID / proteolytic fragment / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease | ||||||
Function / homology | Function and homology information Transferases; Transferring phosphorus-containing groups / transferase activity / GTPase activity / GTP binding Similarity search - Function | ||||||
Biological species | Mycobacterium smegmatis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: Acta Crystallogr F Struct Biol Commun / Year: 2018 Title: Ab initio structure solution of a proteolytic fragment using ARCIMBOLDO. Authors: Abendroth, J. / Sankaran, B. / Myler, P.J. / Lorimer, D.D. / Edwards, T.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6cum.cif.gz | 43.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cum.ent.gz | 25.4 KB | Display | PDB format |
PDBx/mmJSON format | 6cum.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6cum_validation.pdf.gz | 426.7 KB | Display | wwPDB validaton report |
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Full document | 6cum_full_validation.pdf.gz | 426.7 KB | Display | |
Data in XML | 6cum_validation.xml.gz | 5.2 KB | Display | |
Data in CIF | 6cum_validation.cif.gz | 6.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cu/6cum ftp://data.pdbj.org/pub/pdb/validation_reports/cu/6cum | 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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-Components
#1: Protein | Mass: 32667.145 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_4869 / Plasmid: MysmA.00200.a.A1 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Strain (production host): BL21(DE3) References: UniProt: A0R1T8, Transferases; Transferring phosphorus-containing groups | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7 Details: RigakuReagents JCSG+ screen, condition G7: 15% PEG 3350, 100mM succinic acid / NaOH pH 7.0: MysmA.00200.a.A1.PS00535 at 60.5mg/ml: cryo: 25% EG: tray: 215267 G7: puck DZB0-10: no protease was intentionally added |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9999 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 10, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.6→19.622 Å / Num. obs: 10171 / % possible obs: 99.1 % / Redundancy: 4.624 % / Biso Wilson estimate: 22.03 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.033 / Rrim(I) all: 0.037 / Χ2: 0.959 / Net I/σ(I): 24.59 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2x 10-residue helices via Acrimboldo Resolution: 1.6→19.622 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.9
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 70.11 Å2 / Biso mean: 32.4202 Å2 / Biso min: 18.98 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.6→19.622 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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