[English] 日本語
Yorodumi
- PDB-1zv9: Crystal structure analysis of a type II cohesin domain from the c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1zv9
TitleCrystal structure analysis of a type II cohesin domain from the cellulosome of Acetivibrio cellulolyticus- SeMet derivative
ComponentsCellulosomal scaffoldin adaptor protein B
Keywordscellulosome / cohesins II
Function / homology
Function and homology information


polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / extracellular region / metal ion binding
Similarity search - Function
: / Immunoglobulin-like - #680 / Cellulosome anchoring protein, cohesin domain / Cohesin domain / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily ...: / Immunoglobulin-like - #680 / Cellulosome anchoring protein, cohesin domain / Cohesin domain / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETIC ACID / FORMIC ACID / NITRATE ION / 1,3-PROPANDIOL / : / Cellulosomal scaffoldin adaptor protein B
Similarity search - Component
Biological speciesAcetivibrio cellulolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å
AuthorsNoach, I. / Rosenheck, S. / Lamed, R. / Shimon, L. / Bayer, E. / Frolow, F.
Citation
Journal: J.Mol.Biol. / Year: 2009
Title: Intermodular linker flexibility revealed from crystal structures of adjacent cellulosomal cohesins of Acetivibrio cellulolyticus.
Authors: Noach, I. / Frolow, F. / Alber, O. / Lamed, R. / Shimon, L.J. / Bayer, E.A.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Preliminary X-ray characterisation and phasing of a type II cohesin domain from the cellulosome of Acetivibrio cellulolyticus
Authors: Noach, I. / Lamed, R. / Xu, Q. / Rosenheck, S. / Shimon, L.J.W. / Bayer, E. / Frolow, F.
History
DepositionJun 1, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cellulosomal scaffoldin adaptor protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,26813
Polymers18,5291
Non-polymers73912
Water5,314295
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.858, 53.858, 111.964
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Cell settingtrigonal
Space group name H-MP3121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Cellulosomal scaffoldin adaptor protein B / ScaB


Mass: 18529.287 Da / Num. of mol.: 1 / Fragment: cohesin II domain from cellulosome assembly / Mutation: MET41MSE,MET63MSE,MET139MSE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acetivibrio cellulolyticus (bacteria) / Gene: ScaB / Plasmid: pet28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: GenBank: 31540575, UniProt: Q7WYN3*PLUS

-
Non-polymers , 6 types, 307 molecules

#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PDO / 1,3-PROPANDIOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 51.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6
Details: Ammonium sulfate, pH 6, vapor diffusion, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 16, 2003 / Details: Mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.28→50 Å / Num. all: 49349 / Num. obs: 48796 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 12.8 % / Biso Wilson estimate: 19.2 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Χ2: 1.23 / Net I/σ(I): 24.2
Reflection shellResolution: 1.28→1.3 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.6 / Num. unique all: 2340 / Rsym value: 0.49 / Χ2: 0.841 / % possible all: 97.1

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT1.401data extraction
ProDCdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QZN

1qzn


Resolution: 1.28→46.63 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.182 / SU ML: 0.023 / SU R Cruickshank DPI: 0.035 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.039 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.158 2462 5.1 %RANDOM
Rwork0.116 ---
all0.118 48796 --
obs0.118 48747 98.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.949 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å2-0.13 Å20 Å2
2---0.26 Å20 Å2
3---0.39 Å2
Refinement stepCycle: LAST / Resolution: 1.28→46.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1328 0 32 316 1676
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONr_bond_refined_d0.01513940.022
X-RAY DIFFRACTIONr_bond_other_d0.0019280.02
X-RAY DIFFRACTIONr_angle_refined_deg1.47218821.986
X-RAY DIFFRACTIONr_angle_other_deg0.98923043
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5051845
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.0555226.538
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.84924115
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.027315
X-RAY DIFFRACTIONr_chiral_restr0.0872260.2
X-RAY DIFFRACTIONr_gen_planes_refined0.00715280.02
X-RAY DIFFRACTIONr_gen_planes_other0.0012380.02
X-RAY DIFFRACTIONr_nbd_refined0.2362160.2
X-RAY DIFFRACTIONr_nbd_other0.1989500.2
X-RAY DIFFRACTIONr_nbtor_refined0.1646760.2
X-RAY DIFFRACTIONr_nbtor_other0.0837230.2
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1741940.2
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3100.2
X-RAY DIFFRACTIONr_symmetry_vdw_other0.278280.2
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.155380.2
X-RAY DIFFRACTIONr_mcbond_it6.83210903
X-RAY DIFFRACTIONr_mcbond_other3.4183543
X-RAY DIFFRACTIONr_mcangle_it7.38914435
X-RAY DIFFRACTIONr_scbond_it11.1965587
X-RAY DIFFRACTIONr_scangle_it13.03743210
X-RAY DIFFRACTIONr_rigid_bond_restr5.6627013
X-RAY DIFFRACTIONr_sphericity_free29731.928
X-RAY DIFFRACTIONr_sphericity_bonded230910.211
LS refinement shellResolution: 1.28→1.312 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.219 187 -
Rwork0.168 3230 -
obs-3230 94.68 %

+
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