[English] 日本語
Yorodumi
- PDB-7vt4: Crystal structure of mutant E393Q of MtGlu5 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7vt4
TitleCrystal structure of mutant E393Q of MtGlu5
ComponentsEndoglucanase H
KeywordsHYDROLASE / cellulase / GH5 / Meiothermus taiwanensis WR-220 / endo-beta-1 / 4-glucanase
Function / homologyGlycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / cellulase / cellulase activity / Glycoside hydrolase superfamily / carbohydrate metabolic process / Endoglucanase H
Function and homology information
Biological speciesMeiothermus taiwanensis WR-220 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsYe, T.J. / Ko, P.T. / Huang, K.F. / Wu, S.H.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Synergic action of an inserted carbohydrate-binding module in a glycoside hydrolase family 5 endoglucanase.
Authors: Ye, T.J. / Huang, K.F. / Ko, T.P. / Wu, S.H.
History
DepositionOct 28, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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 H
B: Endoglucanase H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,75421
Polymers105,9522
Non-polymers1,80119
Water27,7431540
1
A: Endoglucanase H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,92511
Polymers52,9761
Non-polymers94910
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18270 Å2
MethodPISA
2
B: Endoglucanase H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,82910
Polymers52,9761
Non-polymers8539
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-17 kcal/mol
Surface area18170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.249, 114.350, 80.149
Angle α, β, γ (deg.)90.000, 103.235, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: PRO / End label comp-ID: PRO / Auth seq-ID: 16 - 452 / Label seq-ID: 16 - 452

Dom-IDComponent-IDSelection detailsAuth asym-IDLabel asym-ID
11(chain 'A' and resid 16 through 452)AA
22chain 'B'BB

-
Components

#1: Protein Endoglucanase H


Mass: 52976.133 Da / Num. of mol.: 2 / Mutation: E393Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Meiothermus taiwanensis WR-220 (bacteria)
Production host: Escherichia coli B (bacteria) / References: UniProt: A0A399DY85, cellulase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1540 / 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: 3.22 Å3/Da / Density % sol: 61.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1M citric acid, 0.7M ammonium sulfate, 20% PEG 400, pH 5.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Oct 31, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 97424 / % possible obs: 99.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 19.61 Å2 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.035 / Rrim(I) all: 0.068 / Χ2: 0.913 / Net I/σ(I): 22.06
Reflection shellResolution: 1.93→2 Å / Rmerge(I) obs: 0.059 / Num. unique obs: 9740 / Rpim(I) all: 0.035 / Rrim(I) all: 0.872

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3mmu

3mmu


Resolution: 1.93→26.97 Å / SU ML: 0.1786 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.0525
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1968 4288 4.91 %
Rwork0.1581 83083 -
obs0.16 87371 89.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.54 Å2
Refinement stepCycle: LAST / Resolution: 1.93→26.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7033 0 101 1550 8684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00837323
X-RAY DIFFRACTIONf_angle_d0.9499984
X-RAY DIFFRACTIONf_chiral_restr0.06171016
X-RAY DIFFRACTIONf_plane_restr0.00641309
X-RAY DIFFRACTIONf_dihedral_angle_d17.32762604
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.950.2278680.20441147X-RAY DIFFRACTION36.72
1.95-1.980.2235890.2181257X-RAY DIFFRACTION41.96
1.98-20.2406700.20021512X-RAY DIFFRACTION48.66
2-2.020.27981050.19971682X-RAY DIFFRACTION55.51
2.02-2.050.28851200.21252023X-RAY DIFFRACTION65.42
2.05-2.080.2341030.20672301X-RAY DIFFRACTION74.57
2.08-2.110.21681340.20032562X-RAY DIFFRACTION82.88
2.11-2.140.21851520.20052710X-RAY DIFFRACTION88.83
2.14-2.170.25381470.19182873X-RAY DIFFRACTION93.7
2.17-2.210.25141510.18563025X-RAY DIFFRACTION97.78
2.21-2.250.22731530.19013088X-RAY DIFFRACTION99.51
2.25-2.290.23011470.18223135X-RAY DIFFRACTION100
2.29-2.330.23681490.17823088X-RAY DIFFRACTION100
2.33-2.380.20411570.17143063X-RAY DIFFRACTION100
2.38-2.430.24091610.16643103X-RAY DIFFRACTION100
2.43-2.490.20231840.16353074X-RAY DIFFRACTION100
2.49-2.550.20831440.16183068X-RAY DIFFRACTION100
2.55-2.620.20181670.16293069X-RAY DIFFRACTION100
2.62-2.70.21541630.16053107X-RAY DIFFRACTION100
2.7-2.780.20831690.16023084X-RAY DIFFRACTION100
2.78-2.880.20391570.15823113X-RAY DIFFRACTION100
2.88-30.18951650.15793062X-RAY DIFFRACTION99.97
3-3.130.1891540.15993101X-RAY DIFFRACTION99.94
3.13-3.30.18871330.15073124X-RAY DIFFRACTION99.97
3.3-3.510.18841450.143134X-RAY DIFFRACTION99.97
3.51-3.780.16811610.1273098X-RAY DIFFRACTION99.97
3.78-4.150.14451650.12013112X-RAY DIFFRACTION100
4.15-4.750.15751670.1183097X-RAY DIFFRACTION99.97
4.75-5.980.17491490.14593136X-RAY DIFFRACTION99.88
5.98-26.970.18961590.18283135X-RAY DIFFRACTION98.71
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.026048239883-0.00857583036414-0.0088090810770.0339714247818-0.02628456245950.0781451592423-0.001874224795560.0365944981950.0208730877583-0.00579247836244-0.0655692080203-0.05183789141370.001101850067180.113486296517-0.1406567483830.0612248581822-0.00425148491620.01102090326360.165130759675-0.009391207795480.084224278795417.4171377106-2.4577284833434.1111355115
20.004556467354250.002403687030540.0002596922227410.00446273010220.001120157778040.003786992756430.0292232185465-0.0880333710748-0.0395564628988-0.002621144216030.0257624664769-0.01183158770790.020748041058-0.03771199492470.007521653228950.113400585942-0.0160125428038-0.04507636657030.22348616395-0.0373996015720.160190557929-19.2264003735-4.6859878194427.813122305
30.01759770693930.0007413809177940.00237336606020.008484625723610.01510306788450.0281279433987-0.013158074309-0.03663407556080.06212395542940.00139616625958-0.0391064575828-0.00241791411568-0.0349246068772-0.0293323997367-0.04872159440110.0940002795377-0.01211814647150.001091591783680.100111113218-0.03821078139180.08109321770946.331580539199.8374606412435.8358845337
40.0217157360190.0110250451146-0.006190042653470.02791474599850.01866418850750.0424299691252-0.0314955624221-0.0425874386768-0.0219252576410.0243088527569-0.02276119627480.05703388545910.0984121418786-0.0570043943513-0.07819670585650.0353446745841-0.1045671131160.0317244082582-0.0899275768316-0.007746386161320.08158798736219.965154516-0.771295281264-2.30368230071
50.00394341482454-7.17784670776E-5-0.004668382389160.02518358100190.007850594137810.01069483373150.02449885840420.0194898855825-0.00351767362697-0.03071677843270.02648674521250.006184330322370.0179509356092-0.004016453080860.02880232403960.225774399952-0.0220729983126-0.06669439393430.01978427536430.003280909866410.20408276669154.4627299115-20.4993446609-2.21734339346
60.0110960270277-0.007186538388450.007699768077010.00921895633763-0.008492129741930.0108125326107-0.000907485982420.009386215885860.0545345539242-0.0264645970327-0.0233128061817-0.04508733740630.02109455533660.0380096137229-0.002006985423230.0726110904102-0.0002216392143730.01161382600930.0423014431299-0.006850089276380.06924992797835.79021760184.49492953721-3.02767706617
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 242 )
2X-RAY DIFFRACTION2chain 'A' and (resid 243 through 363 )
3X-RAY DIFFRACTION3chain 'A' and (resid 364 through 452 )
4X-RAY DIFFRACTION4chain 'B' and (resid 16 through 242 )
5X-RAY DIFFRACTION5chain 'B' and (resid 243 through 363 )
6X-RAY DIFFRACTION6chain 'B' and (resid 364 through 452 )

+
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