[English] 日本語
Yorodumi
- PDB-8anx: E329A Mutant Thermogutta terrifontis endoglucanase catalytic doma... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8anx
TitleE329A Mutant Thermogutta terrifontis endoglucanase catalytic domain with C-linker from glycoside hydrolase family 5 (TtEnd5A-CDC-E329A)
ComponentsEndoglucanaseCellulase
KeywordsHYDROLASE / endoglucanase / endocellulase / inactive mutant
Function / homologyorganic substance metabolic process / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / cellulase / cellulase activity / Glycoside hydrolase superfamily / Endoglucanase
Function and homology information
Biological speciesThermogutta terrifontis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsHussain, N. / Mikolajek, H. / Naismith, J.H.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Commonwealth Scholarship Commission (United Kingdom)PKCN-2019-176 United Kingdom
Wellcome Trust100209/Z/12/Z United Kingdom
CitationJournal: To Be Published
Title: TtEnd5A-CDC-E329A
Authors: Hussain, N. / Mikolajek, H. / Naismith, J.H.
History
DepositionAug 6, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Endoglucanase


Theoretical massNumber of molelcules
Total (without water)39,8321
Polymers39,8321
Non-polymers00
Water6,756375
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13790 Å2
Unit cell
Length a, b, c (Å)60.390, 69.590, 81.920
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Endoglucanase / Cellulase


Mass: 39831.727 Da / Num. of mol.: 1 / Mutation: E329A
Source method: isolated from a genetically manipulated source
Details: TtEnd5A-CDC-E329A is an inactive mutant of TtEnd5A-CD, in which glutamic acid (E329) has been mutated with alanine (329A). TtEnd5A-CDC itself a truncated variant of our previously deposited ...Details: TtEnd5A-CDC-E329A is an inactive mutant of TtEnd5A-CD, in which glutamic acid (E329) has been mutated with alanine (329A). TtEnd5A-CDC itself a truncated variant of our previously deposited Thermogutta terrifontis endoglucanase from glycoside hydrolase family 5 (TtEnd5A). TtEnd5A-CDC-E329A is comprised of a catalytic domain and a linker at C-terminal (186-531 amino caids).
Source: (gene. exp.) Thermogutta terrifontis (bacteria) / Gene: THTE_1171 / Plasmid: pEHISTEV vector
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3) / Variant (production host): OverExpress C43(DE3) / References: UniProt: A0A286RCT9, cellulase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 375 / 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: 2.16 Å3/Da / Density % sol: 43.08 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.2M NH4Cl and 20%W/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Sep 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.13→69.59 Å / Num. obs: 125321 / % possible obs: 96.8 % / Redundancy: 11.6 % / Biso Wilson estimate: 13.69 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.013 / Rrim(I) all: 0.047 / Χ2: 0.94 / Net I/σ(I): 18.9
Reflection shellResolution: 1.13→1.16 Å / Redundancy: 4.6 % / Rmerge(I) obs: 1.646 / Num. unique obs: 7072 / CC1/2: 0.392 / Χ2: 0.83 / % possible all: 75.2

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8AG9

8ag9


Resolution: 1.2→69.59 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.976 / SU B: 0.958 / SU ML: 0.019 / Cross valid method: FREE R-VALUE / ESU R: 0.03 / ESU R Free: 0.032
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1484 5308 4.913 %
Rwork0.1199 102734 -
all0.121 --
obs-108042 99.712 %
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 16.638 Å2
Baniso -1Baniso -2Baniso -3
1--0.468 Å20 Å2-0 Å2
2---0.339 Å20 Å2
3---0.808 Å2
Refinement stepCycle: LAST / Resolution: 1.2→69.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2719 0 0 375 3094
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132896
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172574
X-RAY DIFFRACTIONr_angle_refined_deg1.4361.6393975
X-RAY DIFFRACTIONr_angle_other_deg1.51.5765964
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4075359
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.24521.297185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.81515446
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6531527
X-RAY DIFFRACTIONr_chiral_restr0.0750.2359
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023340
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02689
X-RAY DIFFRACTIONr_nbd_refined0.2240.2573
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.22470
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21384
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.21241
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2232
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1390.216
X-RAY DIFFRACTIONr_nbd_other0.1960.247
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.4410.258
X-RAY DIFFRACTIONr_mcbond_it1.0041.4981363
X-RAY DIFFRACTIONr_mcbond_other0.9991.4951362
X-RAY DIFFRACTIONr_mcangle_it1.3532.2581709
X-RAY DIFFRACTIONr_mcangle_other1.3542.261710
X-RAY DIFFRACTIONr_scbond_it1.5711.7541533
X-RAY DIFFRACTIONr_scbond_other1.5691.7531533
X-RAY DIFFRACTIONr_scangle_it1.9452.5452252
X-RAY DIFFRACTIONr_scangle_other1.9472.5482253
X-RAY DIFFRACTIONr_lrange_it2.67118.813449
X-RAY DIFFRACTIONr_lrange_other2.33617.9843357
X-RAY DIFFRACTIONr_rigid_bond_restr1.1935470
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.2-1.2310.2593740.24772450.24879060.8420.85196.36980.227
1.231-1.2650.2274150.19773140.19977450.9040.91299.79340.172
1.265-1.3020.1773510.16271530.16275050.9410.94499.98670.137
1.302-1.3420.1713390.13470130.13673520.9520.961000.111
1.342-1.3860.1423400.11567010.11670410.9670.9731000.093
1.386-1.4340.1523640.10765340.10968990.9670.97799.98550.087
1.434-1.4880.1313050.09663010.09766060.9770.9831000.078
1.488-1.5490.1282850.08461080.08563930.9810.9861000.07
1.549-1.6180.1222860.0858490.08261350.9820.9881000.068
1.618-1.6970.1182980.0855610.08258590.9840.9891000.07
1.697-1.7890.113060.0852870.08155930.9860.991000.071
1.789-1.8970.1152480.08850610.08953090.9850.9881000.081
1.897-2.0280.1182610.147240.10149850.9840.9861000.094
2.028-2.190.1332420.11244080.11346500.9790.9841000.109
2.19-2.3990.142080.10841010.10943090.9770.9831000.108
2.399-2.6820.1321750.11537350.11639100.9810.9831000.121
2.682-3.0960.1421720.12432970.12534690.9780.9811000.135
3.096-3.790.1541370.12828220.12929590.9750.9811000.147
3.79-5.3510.1751220.13822190.1423420.9770.9899.95730.17
5.351-69.590.215770.19812850.19913660.970.97299.70720.238

+
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