[English] 日本語
Yorodumi- PDB-4b97: Biomass sensing modules from putative Rsgi-like proteins of Clost... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4b97 | ||||||
---|---|---|---|---|---|---|---|
Title | Biomass sensing modules from putative Rsgi-like proteins of Clostridium thermocellum resemble family 3 carbohydrate-binding module of cellulosome | ||||||
Components | CELLULOSE BINDING DOMAIN-CONTAINING PROTEIN | ||||||
Keywords | SUGAR BINDING PROTEIN / BIOMASS SENSORING SYSTEM | ||||||
Function / homology | Endoglucanase-like / Immunoglobulin-like / Sandwich / Mainly Beta / : Function and homology information | ||||||
Biological species | CLOSTRIDIUM THERMOCELLUM (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.276 Å | ||||||
Authors | Yaniv, O. / Fichman, G. / Shimon, L.J.W. / Bayer, E.A. / Lamed, R. / Frolow, F. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Fine-Structural Variance of Family 3 Carbohydrate-Binding Modules as Extracellular Biomass-Sensing Components of Clostridium Thermocellum Anti-Sigma(I) Factors. Authors: Yaniv, O. / Fichman, G. / Borovok, I. / Shoham, Y. / Bayer, E.A. / Lamed, R. / Shimon, L.J.W. / Frolow, F. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4b97.cif.gz | 80.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4b97.ent.gz | 59.9 KB | Display | PDB format |
PDBx/mmJSON format | 4b97.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4b97_validation.pdf.gz | 419.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4b97_full_validation.pdf.gz | 420.3 KB | Display | |
Data in XML | 4b97_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | 4b97_validation.cif.gz | 13.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b9/4b97 ftp://data.pdbj.org/pub/pdb/validation_reports/b9/4b97 | HTTPS FTP |
-Related structure data
Related structure data | 4b9cC 4b9pC 2wnxS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 17263.957 Da / Num. of mol.: 1 Fragment: FAMILY 3B CARBOHYDRATE BINDING MODULE, RESIDUES 374-522 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CLOSTRIDIUM THERMOCELLUM (bacteria) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): RIL / References: UniProt: D1NLR4 |
---|---|
#2: Chemical | ChemComp-CA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.84 Å3/Da / Density % sol: 33.08 % / Description: NONE |
---|---|
Crystal grow | pH: 5.6 Details: 0.2 M AMMONIUM ACETATE, 0.1 M TRI-SODIUM CITRATE PH 5.6, 30 % (V/V) PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97622 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 23, 2011 / Details: MIRRORS |
Radiation | Monochromator: LIQUID NITROGEN COOLED CHANNEL-CUT SILICON MONOCHROMATOR Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97622 Å / Relative weight: 1 |
Reflection | Resolution: 1.28→50 Å / Num. obs: 33242 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 6.83 % / Biso Wilson estimate: 14.71 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 30.8 |
Reflection shell | Resolution: 1.28→1.3 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.3 / % possible all: 96.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WNX Resolution: 1.276→42.331 Å / SU ML: 0.1 / σ(F): 1.11 / Phase error: 12.76 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 0.6105 Å2 / ksol: 1.3634 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.85 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.276→42.331 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|