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Yorodumi- PDB-2vpn: High-resolution structure of the periplasmic ectoine-binding prot... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vpn | ||||||
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Title | High-resolution structure of the periplasmic ectoine-binding protein from TeaABC TRAP-transporter of Halomonas elongata | ||||||
Components | PERIPLASMIC SUBSTRATE BINDING PROTEIN | ||||||
Keywords | TRANSPORT / ECTOINE / HYDROXYECTOINE / TRAP-TRANSPORTER / PERIPLASMIC BINDING PROTEIN | ||||||
Function / homology | Function and homology information C4-dicarboxylate transport / transmembrane transport / periplasmic space Similarity search - Function | ||||||
Biological species | HALOMONAS ELONGATA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.55 Å | ||||||
Authors | Kuhlmann, S.I. / Terwisscha van Scheltinga, A.C. / Bienert, R. / Kunte, H.J. / Ziegler, C. | ||||||
Citation | Journal: Biochemistry / Year: 2008 Title: 1.55 A Structure of the Ectoine Binding Protein Teaa of the Osmoregulated Trap-Transporter Teaabc from Halomonas Elongata. Authors: Kuhlmann, S.I. / Terwisscha Van Scheltinga, A.C. / Bienert, R. / Kunte, H.J. / Ziegler, C. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vpn.cif.gz | 284.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vpn.ent.gz | 233.2 KB | Display | PDB format |
PDBx/mmJSON format | 2vpn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vpn_validation.pdf.gz | 445.8 KB | Display | wwPDB validaton report |
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Full document | 2vpn_full_validation.pdf.gz | 447.8 KB | Display | |
Data in XML | 2vpn_validation.xml.gz | 30.2 KB | Display | |
Data in CIF | 2vpn_validation.cif.gz | 46.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vp/2vpn ftp://data.pdbj.org/pub/pdb/validation_reports/vp/2vpn | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: given Matrix: (-0.8924, 0.3868, 0.2323), Vector: |
-Components
#1: Protein | Mass: 35713.223 Da / Num. of mol.: 2 / Fragment: RESIDUES 26-341 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HALOMONAS ELONGATA (bacteria) / Strain: DSM 2581T / Plasmid: PET 26 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8VPB3, UniProt: E1VBK1*PLUS #2: Chemical | #3: Chemical | ChemComp-MG / #4: Water | ChemComp-HOH / | Nonpolymer details | (4S)-2-METHYL-1,4,5,6-TETRAHYDRO | |
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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: 2.14 Å3/Da / Density % sol: 42.68 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 0.1 M HEPES PH 7.5, 0.1 M MGCL2 AND 25.5 % PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9781 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 6, 2006 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9781 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→20 Å / Num. obs: 81024 / % possible obs: 93.3 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Rmerge(I) obs: 0.01 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 1.55→1.65 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.06 / Mean I/σ(I) obs: 2.3 / % possible all: 92.3 |
-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: NONE Resolution: 1.55→20 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.46 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.088 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.16 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→20 Å
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Refine LS restraints |
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