[English] 日本語
Yorodumi
- PDB-6zz3: RBcel1 cellulase variant Y201F with cellotriose covalently bound -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zz3
TitleRBcel1 cellulase variant Y201F with cellotriose covalently bound
ComponentsEndoglucanaseCellulase
KeywordsHYDROLASE / Cellulase / Complex / cellotriose / Y201F variant
Function / homologyorganic substance metabolic process / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / cellulase / cellulase activity / Glycoside hydrolase superfamily / alpha-cellotriose / Endoglucanase
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.095 Å
AuthorsCollet, L. / Dutoit, R.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2021
Title: Glycoside hydrolase family 5: structural snapshots highlighting the involvement of two conserved residues in catalysis.
Authors: Collet, L. / Vander Wauven, C. / Oudjama, Y. / Galleni, M. / Dutoit, R.
History
DepositionAug 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Endoglucanase
B: Endoglucanase
C: Endoglucanase
D: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,0889
Polymers144,9484
Non-polymers2,1405
Water8,413467
1
A: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8643
Polymers36,2371
Non-polymers6272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7412
Polymers36,2371
Non-polymers5041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7412
Polymers36,2371
Non-polymers5041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7412
Polymers36,2371
Non-polymers5041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.000, 61.890, 177.260
Angle α, β, γ (deg.)90.000, 97.110, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 17 or (resid 18...
21(chain B and ((resid 1 and (name CA or name...
31(chain C and ((resid 1 and (name CA or name...
41(chain D and ((resid 1 and (name CA or name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERGLYGLY(chain A and (resid 1 through 17 or (resid 18...AA1 - 171 - 17
12LYSLYSLYSLYS(chain A and (resid 1 through 17 or (resid 18...AA1818
13SERSERLYSLYS(chain A and (resid 1 through 17 or (resid 18...AA1 - 3191 - 319
21SERSERSERSER(chain B and ((resid 1 and (name CA or name...BB11
22SERSERALAALA(chain B and ((resid 1 and (name CA or name...BB1 - 3201 - 320
23SERSERALAALA(chain B and ((resid 1 and (name CA or name...BB1 - 3201 - 320
31SERSERSERSER(chain C and ((resid 1 and (name CA or name...CC11
32SERSERLYSLYS(chain C and ((resid 1 and (name CA or name...CC1 - 3191 - 319
33SERSERLYSLYS(chain C and ((resid 1 and (name CA or name...CC1 - 3191 - 319
41SERSERSERSER(chain D and ((resid 1 and (name CA or name...DD11
42SERSERALAALA(chain D and ((resid 1 and (name CA or name...DD1 - 3201 - 320
43SERSERALAALA(chain D and ((resid 1 and (name CA or name...DD1 - 3201 - 320

-
Components

#1: Protein
Endoglucanase / Cellulase


Mass: 36236.938 Da / Num. of mol.: 4 / Mutation: Y201F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Plasmid: pBad / Production host: Escherichia coli MC1061 (bacteria) / References: UniProt: C1JI15, cellulase
#2: Polysaccharide
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 504.438 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-cellotriose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1a_1-5][a2122h-1b_1-5]/1-2-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 467 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.59 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20.5% PEG600, 100mM Tris, 1mM 2-Chloro-4-nitrophenyl-b-cellotrioside

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 15, 2018
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.095→45.101 Å / Num. obs: 72131 / % possible obs: 99.5 % / Redundancy: 6.921 % / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Rrim(I) all: 0.094 / Χ2: 1.016 / Net I/σ(I): 11.93
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.1-2.156.681.3021.2633332528749900.511.40994.4
2.15-2.217.1131.1341.5637549528452790.6371.22399.9
2.21-2.277.0060.9961.8235361504550470.6741.076100
2.27-2.346.8530.7112.5933109483348310.8180.77100
2.34-2.426.5490.5223.3731048474547410.8790.56899.9
2.42-2.56.9060.4214.2831886461946170.9180.456100
2.5-2.66.6870.325.3429926447844750.9550.34899.9
2.6-2.77.1850.2576.9430801428342870.9710.278100
2.7-2.827.2320.2048.829515408440810.9810.2299.9
2.82-2.967.1770.15411.2928193392839280.9890.166100
2.96-3.127.0330.11814.3526253373437330.9940.128100
3.12-3.316.870.09617.4424376354835480.9950.104100
3.31-3.546.5990.07521.2221955333033270.9970.08199.9
3.54-3.836.7250.06823.6221124314731410.9970.07399.8
3.83-4.197.2120.05429.5820510284328440.9980.058100
4.19-4.687.2460.04732.918840260126000.9990.05100
4.68-5.417.1140.04433.4916285229022890.9990.047100
5.41-6.636.6040.04531.1412963196319630.9980.049100
6.63-9.376.760.03734.9610478154915500.9990.04100
9.37-45.1016.6830.03238.0357478738600.9990.03498.5

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.66 Å45.1 Å
Translation4.66 Å45.1 Å

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASER2.7.15phasing
PHENIX1.11-2563refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ee9

4ee9


Resolution: 2.095→45.101 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2287 3604 5 %
Rwork0.1954 68488 -
obs0.197 72092 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.77 Å2 / Biso mean: 48.4076 Å2 / Biso min: 23.31 Å2
Refinement stepCycle: final / Resolution: 2.095→45.101 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10084 0 140 467 10691
Biso mean--45.93 48.78 -
Num. residues----1278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610659
X-RAY DIFFRACTIONf_angle_d0.87514513
X-RAY DIFFRACTIONf_chiral_restr0.0541495
X-RAY DIFFRACTIONf_plane_restr0.0071886
X-RAY DIFFRACTIONf_dihedral_angle_d3.928564
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5565X-RAY DIFFRACTION8.076TORSIONAL
12B5565X-RAY DIFFRACTION8.076TORSIONAL
13C5565X-RAY DIFFRACTION8.076TORSIONAL
14D5565X-RAY DIFFRACTION8.076TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0951-2.12270.35291230.309233889
2.1227-2.15180.33291380.29132624100
2.1518-2.18250.33731390.28762628100
2.1825-2.21510.32221390.27932640100
2.2151-2.24970.33061370.2712607100
2.2497-2.28660.27261400.25972666100
2.2866-2.3260.30281360.24782586100
2.326-2.36830.31841410.24892667100
2.3683-2.41390.32191360.24412598100
2.4139-2.46310.30271410.2332671100
2.4631-2.51670.29611370.23662595100
2.5167-2.57520.27841400.22442660100
2.5752-2.63960.29671380.22332621100
2.6396-2.7110.27581400.2272675100
2.711-2.79070.25671360.23462588100
2.7907-2.88080.27131400.23572657100
2.8808-2.98380.26961400.22162654100
2.9838-3.10320.24621390.21842643100
3.1032-3.24440.26261400.20942649100
3.2444-3.41540.24841380.21492624100
3.4154-3.62930.24791400.19532666100
3.6293-3.90930.18921400.17692652100
3.9093-4.30250.1581400.15282658100
4.3025-4.92440.17171410.14392686100
4.9244-6.20170.19111420.15842702100
6.2017-45.1010.1851430.1634273399

+
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