[English] 日本語
Yorodumi
- PDB-5mcf: Radiation damage to GH7 Family Cellobiohydrolase from Daphnia pul... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5mcf
TitleRadiation damage to GH7 Family Cellobiohydrolase from Daphnia pulex: Dose (DWD) 7.59 MGy
ComponentsCellobiohydrolase CHBI
KeywordsHYDROLASE / Glycoside hydrolase / Cellobiohydrolase / radiation damage
Function / homology
Function and homology information


cellulose 1,4-beta-cellobiosidase (non-reducing end) / cellulose 1,4-beta-cellobiosidase activity / glucan catabolic process / cellulose catabolic process
Similarity search - Function
1,4-Beta-D-Glucan Cellobiohydrolase I; Chain A / Glycoside hydrolase, family 7, domain / Glycoside hydrolase, family 7 / Glycoside hydrolase family 7, catalytic domain superfamily / Glycosyl hydrolase family 7 / Distorted Sandwich / Concanavalin A-like lectin/glucanase domain superfamily / Mainly Beta
Similarity search - Domain/homology
cellulose 1,4-beta-cellobiosidase (non-reducing end)
Similarity search - Component
Biological speciesDaphnia pulex (common water flea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsBury, C.S. / McGeehan, J.E. / Ebrahim, A. / Garman, E.F.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research Council United Kingdom
CitationJournal: J Synchrotron Radiat / Year: 2017
Title: OH cleavage from tyrosine: debunking a myth.
Authors: Bury, C.S. / Carmichael, I. / Garman, E.F.
History
DepositionNov 9, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Data collection / Category: diffrn_radiation_wavelength / pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Mar 11, 2020Group: Polymer sequence / Category: entity_poly / Item: _entity_poly.pdbx_seq_one_letter_code_can
Revision 2.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cellobiohydrolase CHBI
B: Cellobiohydrolase CHBI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,8336
Polymers96,4602
Non-polymers3724
Water10,359575
1
A: Cellobiohydrolase CHBI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3222
Polymers48,2301
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cellobiohydrolase CHBI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5104
Polymers48,2301
Non-polymers2803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.175, 46.715, 173.488
Angle α, β, γ (deg.)90.000, 108.230, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Cellobiohydrolase CHBI


Mass: 48230.168 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Daphnia pulex (common water flea) / Gene: CEL7A, DAPPUDRAFT_347598 / Production host: Trichoderma reesei QM6a (fungus)
References: UniProt: E9G5J5, cellulose 1,4-beta-cellobiosidase (non-reducing end)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 575 / 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: 2.54 Å3/Da / Density % sol: 51.52 % / Mosaicity: 0 °
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 900mM ammonium sulphate, 100mM monosodium citrate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.98 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→82.39 Å / Num. obs: 65997 / % possible obs: 99.8 % / Redundancy: 3.3 % / Biso Wilson estimate: 25.9 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.047 / Rrim(I) all: 0.086 / Net I/σ(I): 10 / Num. measured all: 215805 / Scaling rejects: 224
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2-2.053.40.470.8311100
9.17-82.3930.0350.984199.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
Aimless0.5.4data scaling
PHASERphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 4XNN

4xnn


Resolution: 2→82.39 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.13
RfactorNum. reflection% reflection
Rfree0.2132 3237 4.91 %
Rwork0.193 --
obs0.194 65917 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 84.81 Å2 / Biso mean: 30.946 Å2 / Biso min: 12.39 Å2
Refinement stepCycle: final / Resolution: 2→82.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6700 0 23 575 7298
Biso mean--50.34 39.98 -
Num. residues----883
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076901
X-RAY DIFFRACTIONf_angle_d1.2619367
X-RAY DIFFRACTIONf_chiral_restr0.0721005
X-RAY DIFFRACTIONf_plane_restr0.0051243
X-RAY DIFFRACTIONf_dihedral_angle_d12.362432
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.02990.27661450.252127122857100
2.0299-2.06160.25241440.256626832827100
2.0616-2.09540.27171300.250326892819100
2.0954-2.13150.31221350.246927322867100
2.1315-2.17030.26761440.237226722816100
2.1703-2.2120.27971400.233127142854100
2.212-2.25720.27341430.2292721286499
2.2572-2.30630.25341450.22226572802100
2.3063-2.35990.23761470.216727232870100
2.3599-2.4190.25281470.223227202867100
2.419-2.48440.23661380.21912675281399
2.4844-2.55750.27061440.223227172861100
2.5575-2.640.20921730.214326592832100
2.64-2.73440.26471470.21142710285799
2.7344-2.84390.25691350.201127122847100
2.8439-2.97330.20981380.203827492887100
2.9733-3.13010.19671350.193727242859100
3.1301-3.32620.21081190.18427882907100
3.3262-3.5830.1821460.167327462892100
3.583-3.94360.16461300.160327412871100
3.9436-4.51420.16881400.149827692909100
4.5142-5.68720.16751360.15927822918100
5.6872-82.46010.19941360.19362885302199

+
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