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Yorodumi- PDB-5d6a: 2.7 Angstrom Crystal Structure of ABC transporter ATPase from Vib... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5d6a | ||||||
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Title | 2.7 Angstrom Crystal Structure of ABC transporter ATPase from Vibrio vulnificus in Complex with Adenylyl-imidodiphosphate (AMP-PNP) | ||||||
Components | Predicted ATPase of the ABC class | ||||||
Keywords | HYDROLASE / ABC transporter ATPase / AMP-PNP / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | ABC transporter, ATPase, putative / P-loop domain / nucleotide binding / P-loop containing nucleoside triphosphate hydrolase / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Predicted ATPase of the ABC class Function and homology information | ||||||
Biological species | Vibrio vulnificus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å | ||||||
Authors | Minasov, G. / Wawrzak, Z. / Shuvalova, L. / Dubrovska, I. / Flores, K. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To Be Published Title: 2.7 Angstrom Crystal Structure of ABC transporter ATPase from Vibrio vulnificus in Complex with Adenylyl-imidodiphosphate (AMP-PNP) Authors: Minasov, G. / Wawrzak, Z. / Shuvalova, L. / Dubrovska, I. / Flores, K. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5d6a.cif.gz | 230.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5d6a.ent.gz | 192.2 KB | Display | PDB format |
PDBx/mmJSON format | 5d6a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d6/5d6a ftp://data.pdbj.org/pub/pdb/validation_reports/d6/5d6a | 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 64915.957 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio vulnificus (bacteria) / Strain: YJ016 / Gene: VVA0769 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic / References: UniProt: Q7MEA1 |
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#2: Chemical | ChemComp-NA / |
#3: Chemical | ChemComp-ANP / |
#4: Water | ChemComp-HOH / |
Sequence details | The sequence has not yet been deposited to UniProt. See WP_011081233.1 database reference |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.5 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5 Details: Protein: 5.9 mg/ml, 0.5M Sodium chloride, 0.01M Tris-HCL (pH 8.3), 1mM AMPPNP; Screen: PACT (C2), 0.1M PCB buffer (pH 5.0), 25% (w/v) PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 17, 2014 |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. all: 15243 / Num. obs: 15243 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 11 % / Biso Wilson estimate: 57.9 Å2 / Rmerge(I) obs: 0.117 / Rsym value: 0.117 / Net I/σ(I): 32.5 |
Reflection shell | Resolution: 2.7→2.75 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.621 / Mean I/σ(I) obs: 5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.7→28.55 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.908 / SU B: 28.361 / SU ML: 0.283 / Cross valid method: THROUGHOUT / ESU R Free: 0.407 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 55.709 Å2
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Refinement step | Cycle: 1 / Resolution: 2.7→28.55 Å
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