[English] 日本語
Yorodumi
- PDB-1vjz: Crystal structure of Endoglucanase (TM1752) from Thermotoga marit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1vjz
TitleCrystal structure of Endoglucanase (TM1752) from Thermotoga maritima at 2.05 A resolution
Componentsendoglucanase
KeywordsENDOGLUCANASE / TM1752 / STRUCTURAL GENOMICS / JCSG / PSI / Protein Structure Initiative / Joint Center for Structural Genomics
Function / homology
Function and homology information


glucan exo-1,3-beta-glucosidase activity / glucan catabolic process / cellulose catabolic process
Similarity search - Function
: / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.05 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Endoglucanase (TM1752) from Thermotoga maritima at 2.05 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 8, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
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_ref_seq_dif.details
Revision 1.5Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: endoglucanase


Theoretical massNumber of molelcules
Total (without water)41,0971
Polymers41,0971
Non-polymers00
Water3,819212
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.684, 64.684, 202.189
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-503-

HOH

-
Components

#1: Protein endoglucanase


Mass: 41096.855 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM1752 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X274, cellulase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.5351.06
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2771vapor diffusion, sitting drop, nanodrop9Bicine pH 9, 2% Dioxane, 10% PEG-20000, pH 9.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
2772vapor diffusion, sitting drop, nanodrop9Bicine pH 9, 2% Dioxane, 10% PEG-20000, pH 9.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONAPS 19-BM10.980502
SYNCHROTRONAPS 19-BM20.964063, 0.979292
Detector
TypeIDDetectorDateDetails
APS-11CCDFeb 20, 2004water cooled, sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
APS-12CCDFeb 20, 2004water cooled, sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Rosenbaum-Rock double-crystal monochromatorMADMx-ray1
2Rosenbaum-Rock double-crystal monochromatorMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9805021
20.9640631
30.9792921
ReflectionResolution: 2.05→50 Å / Num. obs: 26538 / % possible obs: 94.64 % / Redundancy: 3.82 % / Biso Wilson estimate: 34.42 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 14.57
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 2.75 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 3 / Num. unique all: 2053 / % possible all: 75.23

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
SOLOMONphasing
REFMAC5.2.0001refinement
RefinementMethod to determine structure: MAD / Resolution: 2.05→32.34 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.94 / SU B: 7.85 / SU ML: 0.108 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.155
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.21244 1336 5 %RANDOM
Rwork0.16804 ---
obs0.17021 25186 94.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.751 Å2
Baniso -1Baniso -2Baniso -3
1-1.49 Å20 Å20 Å2
2--1.49 Å20 Å2
3----2.99 Å2
Refinement stepCycle: LAST / Resolution: 2.05→32.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2737 0 0 212 2949
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222861
X-RAY DIFFRACTIONr_angle_refined_deg1.4331.9123884
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.595324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.61323.4150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.48815491
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0871519
X-RAY DIFFRACTIONr_chiral_restr0.1030.2399
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022211
X-RAY DIFFRACTIONr_nbd_refined0.1980.21368
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2244
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2420.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.25
X-RAY DIFFRACTIONr_mcbond_it2.07531678
X-RAY DIFFRACTIONr_mcangle_it2.96752662
X-RAY DIFFRACTIONr_scbond_it5.47381398
X-RAY DIFFRACTIONr_scangle_it7.209111222
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.192 69 4.68 %
Rwork0.195 1405 -
Refinement TLS params.Method: refined / Origin x: 7.864 Å / Origin y: 26.646 Å / Origin z: 47.722 Å
111213212223313233
T0.0505 Å2-0.0335 Å20.0072 Å2-0.0212 Å20.0157 Å2--0.0761 Å2
L0.5077 °20.1897 °2-0.3738 °2-0.6271 °2-0.7043 °2--3.6131 °2
S-0.0493 Å °-0.0042 Å °-0.0197 Å °-0.0303 Å °0.0039 Å °-0.0145 Å °0.2778 Å °-0.0023 Å °0.0454 Å °
Refinement TLS groupSelection: ALL

+
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