[English] 日本語
Yorodumi
- PDB-4b9p: Biomass sensoring module from putative Rsgi2 protein of Clostridi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4b9p
TitleBiomass sensoring module from putative Rsgi2 protein of Clostridium thermocellum resemble family 3 carbohydrate-binding module of cellulosome
ComponentsTYPE 3A CELLULOSE-BINDING DOMAIN PROTEIN
KeywordsCARBOHYDRATE-BINDING PROTEIN / CELLULOSE / RSGI-LIKE PROTEINS / BIOMASS SENSING SYSTEM
Function / homology
Function and homology information


cellulose binding / carbohydrate metabolic process / metal ion binding / plasma membrane
Similarity search - Function
Anti-sigma factor RsgI, N-terminal / Anti-sigma factor N-terminus / RsgI N-terminal anti-sigma domain profile. / Endoglucanase-like / Cellulose binding domain / Cellulose binding domain / Carbohydrate-binding module 3 / Carbohydrate-binding module 3 superfamily / CBM3 (carbohydrate binding type-3) domain profile. / CBM2/CBM3, carbohydrate-binding domain superfamily ...Anti-sigma factor RsgI, N-terminal / Anti-sigma factor N-terminus / RsgI N-terminal anti-sigma domain profile. / Endoglucanase-like / Cellulose binding domain / Cellulose binding domain / Carbohydrate-binding module 3 / Carbohydrate-binding module 3 superfamily / CBM3 (carbohydrate binding type-3) domain profile. / CBM2/CBM3, carbohydrate-binding domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Anti-sigma-I factor RsgI2
Similarity search - Component
Biological speciesCLOSTRIDIUM THERMOCELLUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.182 Å
AuthorsYaniv, O. / Shimon, L.J.W. / Bayer, E.A. / Lamed, R. / Frolow, F.
CitationJournal: 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
DepositionSep 6, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2014Group: Database references / Source and taxonomy
Revision 1.2Feb 26, 2014Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TYPE 3A CELLULOSE-BINDING DOMAIN PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1615
Polymers18,9251
Non-polymers2364
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.736, 62.289, 79.274
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein TYPE 3A CELLULOSE-BINDING DOMAIN PROTEIN


Mass: 18924.992 Da / Num. of mol.: 1
Fragment: FAMILY 3B CARBOHYDRATE BINDING MODULE, RESIDUES 506-671
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM THERMOCELLUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): RIL / References: UniProt: A3DC27
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.4 % / Description: NONE
Crystal growpH: 6.5
Details: 0.005 M ZNSO4, 0.1 M MES PH 6.5, 23% (V/V) PEG MME 550

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 25, 2011 / Details: MIRRORS
RadiationMonochromator: LIQUID NITROGEN COOLED CHANNEL-CUT SILICON MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.18→50 Å / Num. obs: 52558 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 18.67 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 16
Reflection shellResolution: 1.18→1.2 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 1.6 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4B97

4b97


Resolution: 1.182→48.978 Å / SU ML: 0.09 / σ(F): 1.36 / Phase error: 18.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1499 2242 5.2 %
Rwork0.124 --
obs0.1254 43413 82.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 0.1049 Å2 / ksol: 1.4007 e/Å3
Displacement parametersBiso mean: 24.686 Å2
Baniso -1Baniso -2Baniso -3
1-1.1234 Å20.5213 Å2-0.1525 Å2
2---0.0591 Å2-0.3717 Å2
3----0.8377 Å2
Refinement stepCycle: LAST / Resolution: 1.182→48.978 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1336 0 4 214 1554
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131451
X-RAY DIFFRACTIONf_angle_d1.5171995
X-RAY DIFFRACTIONf_dihedral_angle_d13.761532
X-RAY DIFFRACTIONf_chiral_restr0.106223
X-RAY DIFFRACTIONf_plane_restr0.008258
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1817-1.20730.2037130.1664232X-RAY DIFFRACTION8
1.2073-1.23540.2291390.1736669X-RAY DIFFRACTION22
1.2354-1.26630.2191810.16761265X-RAY DIFFRACTION42
1.2663-1.30060.24511010.16131955X-RAY DIFFRACTION64
1.3006-1.33880.19181470.15762843X-RAY DIFFRACTION92
1.3388-1.38210.18911590.14982982X-RAY DIFFRACTION97
1.3821-1.43150.18911690.14293045X-RAY DIFFRACTION99
1.4315-1.48880.16831690.12893063X-RAY DIFFRACTION100
1.4888-1.55650.1571460.11613108X-RAY DIFFRACTION100
1.5565-1.63860.17251730.10323069X-RAY DIFFRACTION100
1.6386-1.74130.14191700.09893096X-RAY DIFFRACTION100
1.7413-1.87570.14331640.09923098X-RAY DIFFRACTION100
1.8757-2.06450.12791720.09733117X-RAY DIFFRACTION100
2.0645-2.36320.13331640.10633138X-RAY DIFFRACTION100
2.3632-2.97740.16591810.13313172X-RAY DIFFRACTION100
2.9774-49.02040.14311940.13593319X-RAY DIFFRACTION100

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more