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Yorodumi- PDB-2wib: Crystal Structures of the N-terminal Intracellular Domain of FeoB... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wib | ||||||
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Title | Crystal Structures of the N-terminal Intracellular Domain of FeoB from Klebsiella Pneumoniae in GDP binding state | ||||||
Components | FERROUS IRON TRANSPORT PROTEIN B | ||||||
Keywords | METAL TRANSPORT / SIGNAL TRANSDUCTION / FERROUS IRON TRANSPORT / MEMBRANE PROTEIN / G PROTEIN | ||||||
Function / homology | Function and homology information ferrous iron transmembrane transporter activity / GTP binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | KLEBSIELLA PNEUMONIAE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.56 Å | ||||||
Authors | Hung, K.-W. / Chang, Y.-W. / Chen, J.-H. / Chen, Y.-C. / Sun, Y.-J. / Hsiao, C.-D. / Huang, T.-H. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2010 Title: Structural Fold, Conservation and Fe(II) Binding of the Intracellular Domain of Prokaryote Feob. Authors: Hung, K.-W. / Chang, Y.-W. / Eng, E.T. / Chen, J.-H. / Chen, Y.-C. / Sun, Y.-J. / Hsiao, C.-D. / Dong, G. / Spasov, K.A. / Unger, V.M. / Huang, T.-H. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wib.cif.gz | 105.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wib.ent.gz | 85.8 KB | Display | PDB format |
PDBx/mmJSON format | 2wib.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wi/2wib ftp://data.pdbj.org/pub/pdb/validation_reports/wi/2wib | HTTPS FTP |
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-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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-Components
#1: Protein | Mass: 29133.160 Da / Num. of mol.: 2 / Fragment: N-TERMINAL INTRACELLULAR DOMAIN, RESIDUES 1-267 Source method: isolated from a genetically manipulated source Source: (gene. exp.) KLEBSIELLA PNEUMONIAE (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A6TF32 #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | THE GENE AND PROTEIN SEQUENCE OF KLEBSIELLA PNEUMONIAE FEOB WERE PROVIDED BY DR. SHIH-FENG TASI. ...THE GENE AND PROTEIN SEQUENCE OF KLEBSIELLA | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.7 % / Description: NONE |
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Crystal grow | Details: 100 MM TRIS-HCL PH 8.5, 30% PEG8000, 150 MM (NH4)2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.56→19.53 Å / Num. obs: 19651 / % possible obs: 94.5 % / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Biso Wilson estimate: 35.4 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 23.7 |
Reflection shell | Resolution: 2.56→2.65 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.9 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: STRUCTURE OF FEOB IN GMPPNP STATE Resolution: 2.56→19.53 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 60552.9 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 Details: BULK SOLVENT MODEL USED SIDECHAINS OF RESIDUES K3, V36, I66, S67, S68, Q69, E74, Q75, E126, R131, R152, R154, E173, H176, L187, Q190, Q191, S193, R202, I213, Y214, R216, D221, D224, K225, ...Details: BULK SOLVENT MODEL USED SIDECHAINS OF RESIDUES K3, V36, I66, S67, S68, Q69, E74, Q75, E126, R131, R152, R154, E173, H176, L187, Q190, Q191, S193, R202, I213, Y214, R216, D221, D224, K225, D227, I228, L230, L233, S234, E236, I237, D238, N261 OF CHAIN A, AND R29, N32, V36, T37, V38, E39, E42, T65, I66, L72, E74, Q75, I76, R100, R131, R152, R154, D171, E173, H176, R183, Q190, Q191, R202, I213, Y214, S215, R216, Y218, D221, D224, K225, L226, I228, L230, L233, S234, D235, E236, I237, D238, Y249, N261, T262 OF CHAIN B ARE DISORDERED. FULL RESIDUES OF T262 TO P267 IN CHAIN A AND S67 TO S71, L263 TO P267 IN CHAIN B ARE DISORDERED.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.7078 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.56→19.53 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.56→2.7 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
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Xplor file |
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