[English] 日本語
Yorodumi
- PDB-4eyz: Crystal structure of an uncommon cellulosome-related protein modu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4eyz
TitleCrystal structure of an uncommon cellulosome-related protein module from Ruminococcus flavefaciens that resembles papain-like cysteine peptidases
ComponentsCellulosome-related protein module from Ruminococcus flavefaciens that resembles papain-like cysteine peptidases
KeywordsHYDROLASE / Putative protease
Function / homologyCellulosome-related protein module from Ruminococcus flavefaciens that resembles papain-like cysteine peptidases
Function and homology information
Biological speciesRuminococcus flavefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.383 Å
AuthorsFrolow, F. / Voronov-Goldman, M. / Bayer, E. / Lamed, R.
CitationJournal: Plos One / Year: 2013
Title: Crystal Structure of an Uncommon Cellulosome-Related Protein Module from Ruminococcus flavefaciens That Resembles Papain-Like Cysteine Peptidases.
Authors: Levy-Assaraf, M. / Voronov-Goldman, M. / Rozman Grinberg, I. / Weiserman, G. / Shimon, L.J. / Jindou, S. / Borovok, I. / White, B.A. / Bayer, E.A. / Lamed, R. / Frolow, F.
History
DepositionMay 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cellulosome-related protein module from Ruminococcus flavefaciens that resembles papain-like cysteine peptidases
B: Cellulosome-related protein module from Ruminococcus flavefaciens that resembles papain-like cysteine peptidases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0555
Polymers54,8692
Non-polymers1863
Water12,971720
1
A: Cellulosome-related protein module from Ruminococcus flavefaciens that resembles papain-like cysteine peptidases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4962
Polymers27,4341
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cellulosome-related protein module from Ruminococcus flavefaciens that resembles papain-like cysteine peptidases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5583
Polymers27,4341
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.811, 60.605, 66.126
Angle α, β, γ (deg.)90.00, 107.66, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Cellulosome-related protein module from Ruminococcus flavefaciens that resembles papain-like cysteine peptidases


Mass: 27434.309 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus flavefaciens (bacteria) / Strain: FD-1 / Gene: NlpC/P60_2 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: M9MMP4*PLUS
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 720 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 0.2M ammonium acetate, 0.1M BIS-TRIS and 25% w/v polyethylene glycol 3350, pH 6.5, VAPOR DIFFUSION, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 20, 2008
RadiationProtocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionRedundancy: 7.3 % / Av σ(I) over netI: 37.5 / Number: 715274 / Rmerge(I) obs: 0.051 / Χ2: 0.94 / D res high: 1.38 Å / D res low: 50 Å / Num. obs: 97755 / % possible obs: 95.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.755096.110.0260.7417.2
2.973.7596.610.031.0157.1
2.62.9798.610.0371.1357.3
2.362.698.410.0431.2027.5
2.192.3697.810.0431.147.5
2.062.1997.910.0471.1067.5
1.962.0697.510.0531.0497.5
1.871.9697.110.0641.0127.6
1.81.8796.910.0760.9427.6
1.741.896.910.0940.97.6
1.681.7496.310.1160.8637.6
1.641.6896.210.1420.8487.6
1.591.649610.1710.8547.6
1.551.5995.910.2080.8397.6
1.521.5595.410.2460.8537.6
1.491.5295.310.2980.8517.4
1.461.4995.110.340.8437.2
1.431.4695.210.3940.8366.9
1.41.4394.610.4150.8366.5
1.381.483.510.4490.8385.6
ReflectionResolution: 1.38→50 Å / Num. obs: 182049 / % possible obs: 95.9 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 15.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.38-1.45.60.449183.5
1.4-1.436.50.415194.6
1.43-1.466.90.394195.2
1.46-1.497.20.34195.1
1.49-1.527.40.298195.3
1.52-1.557.60.246195.4
1.55-1.597.60.208195.9
1.59-1.647.60.171196
1.64-1.687.60.142196.2
1.68-1.747.60.116196.3
1.74-1.87.60.094196.9
1.8-1.877.60.076196.9
1.87-1.967.60.064197.1
1.96-2.067.50.053197.5
2.06-2.197.50.047197.9
2.19-2.367.50.043197.8
2.36-2.67.50.043198.4
2.6-2.977.30.037198.6
2.97-3.757.10.03196.6
3.75-507.20.026196.1

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
SHELXphasing
PHENIXdev_1180refinement
PDB_EXTRACT3.11data extraction
DNAdata collection
DENZOdata reduction
SHELXCDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.383→38.935 Å / Occupancy max: 1 / Occupancy min: 0.2 / SU ML: 0.1 / σ(F): 1.37 / Phase error: 14.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1524 2002 2.1 %
Rwork0.1265 --
obs0.1271 182049 91.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.123 Å2
Refinement stepCycle: LAST / Resolution: 1.383→38.935 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3808 0 12 720 4540
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094119
X-RAY DIFFRACTIONf_angle_d1.1955626
X-RAY DIFFRACTIONf_dihedral_angle_d12.7031427
X-RAY DIFFRACTIONf_chiral_restr0.071564
X-RAY DIFFRACTIONf_plane_restr0.006729
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3825-1.40.1779910.15693907X-RAY DIFFRACTION54
1.4-1.41850.2105850.15084881X-RAY DIFFRACTION68
1.4185-1.43790.16491090.15455372X-RAY DIFFRACTION74
1.4379-1.45840.1961290.15465745X-RAY DIFFRACTION80
1.4584-1.48020.19061260.14696108X-RAY DIFFRACTION84
1.4802-1.50330.18621450.1436289X-RAY DIFFRACTION87
1.5033-1.5280.14771520.13756501X-RAY DIFFRACTION90
1.528-1.55430.17431420.13386604X-RAY DIFFRACTION92
1.5543-1.58260.17241510.13316759X-RAY DIFFRACTION93
1.5826-1.6130.15631490.13066815X-RAY DIFFRACTION95
1.613-1.6460.18281470.12766905X-RAY DIFFRACTION95
1.646-1.68180.14661550.12776892X-RAY DIFFRACTION96
1.6818-1.72090.16221410.12216975X-RAY DIFFRACTION96
1.7209-1.76390.15731500.12226920X-RAY DIFFRACTION97
1.7639-1.81160.13831550.11726971X-RAY DIFFRACTION97
1.8116-1.86490.15731550.1137132X-RAY DIFFRACTION97
1.8649-1.92510.13781440.1126920X-RAY DIFFRACTION97
1.9251-1.99390.12961580.11037117X-RAY DIFFRACTION97
1.9939-2.07370.16581440.11147019X-RAY DIFFRACTION98
2.0737-2.16810.1381520.11197087X-RAY DIFFRACTION98
2.1681-2.28240.15731500.11277078X-RAY DIFFRACTION98
2.2824-2.42540.13251580.11587163X-RAY DIFFRACTION99
2.4254-2.61260.13311400.12727061X-RAY DIFFRACTION98
2.6126-2.87550.15021620.12897130X-RAY DIFFRACTION98
2.8755-3.29140.161490.12597074X-RAY DIFFRACTION98
3.2914-4.1460.13991420.11826905X-RAY DIFFRACTION96
4.146-38.950.16541440.15846894X-RAY DIFFRACTION95

+
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