[English] 日本語
Yorodumi
- PDB-7ec9: Structure of the Thermotoga maritima Family 5 endo-glucanase in c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ec9
TitleStructure of the Thermotoga maritima Family 5 endo-glucanase in complex with 1-deoxynojiromycin
ComponentsEndoglucanase
KeywordsHYDROLASE / Family 5 Glycosyl hydrolase / Inhibitor complex / TIM-barrel fold / beta-glycosidase
Function / homology
Function and homology information


glucan catabolic process / beta-glucosidase activity / cell surface / extracellular region
Similarity search - Function
Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycoside hydrolase superfamily
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / 1-DEOXYNOJIRIMYCIN / Endoglucanase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsManoj, N. / Garg, P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR-13040/FNS/20/416/2009 India
CitationJournal: Biochimie / Year: 2023
Title: Structure of an iminosugar complex of a glycoside hydrolase family 5 lichenase provides insights into the active site.
Authors: Garg, P. / Manoj, N.
History
DepositionMar 11, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jan 25, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Nov 29, 2023Group: 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
A: Endoglucanase
B: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,0786
Polymers81,6312
Non-polymers4474
Water16,177898
1
A: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0393
Polymers40,8151
Non-polymers2232
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area380 Å2
ΔGint3 kcal/mol
Surface area13550 Å2
MethodPISA
2
B: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0393
Polymers40,8151
Non-polymers2232
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area380 Å2
ΔGint3 kcal/mol
Surface area13360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.330, 62.280, 202.690
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Endoglucanase


Mass: 40815.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_1752 / Plasmid: pMH4 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9X274
#2: Chemical ChemComp-NOJ / 1-DEOXYNOJIRIMYCIN / MORANOLINE


Mass: 163.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4 / Feature type: SUBJECT OF INVESTIGATION / Comment: inhibitor*YM
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 898 / 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: 2.37 Å3/Da / Density % sol: 48.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM sodium citrate tribasic dihydrate (pH 5.8-6.2), 8-14% (v/v) isopropanol, 8-16% (w/v) PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 14, 2014 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→42.72 Å / Num. obs: 69266 / % possible obs: 95 % / Redundancy: 7.2 % / Biso Wilson estimate: 14.91 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.018 / Rrim(I) all: 0.054 / Net I/σ(I): 24.7 / Num. measured all: 496396 / Scaling rejects: 703
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.8-1.843.50.1811069730190.9640.1110.2136.171.5
9-42.7212.40.04186196940.9990.0120.04251.899.2

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.5.17data scaling
PHENIX1.11.1refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VJZ

1vjz


Resolution: 1.8→39.306 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1681 2104 3.04 %
Rwork0.1409 67032 -
obs0.1417 69136 94.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.07 Å2 / Biso mean: 17.7993 Å2 / Biso min: 6.14 Å2
Refinement stepCycle: final / Resolution: 1.8→39.306 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5384 0 72 898 6354
Biso mean--20.95 26.67 -
Num. residues----646
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055615
X-RAY DIFFRACTIONf_angle_d0.8087631
X-RAY DIFFRACTIONf_chiral_restr0.052782
X-RAY DIFFRACTIONf_plane_restr0.005966
X-RAY DIFFRACTIONf_dihedral_angle_d10.5283232
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8-1.84190.26461070.1743328771
1.8419-1.8880.17851230.1567376081
1.888-1.9390.20821230.1713403587
1.939-1.99610.18121410.147423191
1.9961-2.06050.20741100.14445995
2.0605-2.13410.19851650.1354454398
2.1341-2.21960.19391510.1415460599
2.2196-2.32060.18341390.14724661100
2.3206-2.44290.17611490.13154699100
2.4429-2.59590.15011570.13474698100
2.5959-2.79630.1791430.13864714100
2.7963-3.07760.16651500.14044735100
3.0776-3.52270.15951410.14154766100
3.5227-4.43730.13921280.12534846100
4.4373-39.3060.13991770.14884993100
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)
10.4610.2649-0.12630.5354-0.24831.23090.0178-0.01230.03220.102-0.0443-0.1078-0.05960.1350.03020.1127-0.0219-0.01750.09320.00170.118614.710712.101723.2414
21.06730.02540.0390.2195-0.01310.87320.0433-0.1456-0.04450.101-0.0507-0.06070.0079-0.00560.00480.1387-0.0257-0.00280.0831-0.0050.0963.74935.130632.1817
30.82490.64960.36971.11010.2490.67220.1004-0.14010.13560.21950.00120.1301-0.0924-0.0684-0.07070.1735-0.01330.04430.1057-0.02840.1229-2.044912.158233.4553
40.85440.1070.21450.8233-0.09031.16740.01270.0227-0.07370.0229-0.02510.05350.1775-0.14530.03090.0879-0.0222-0.00110.0810.0140.1099-3.77660.636812.1298
51.0691-0.3071-0.22651.1333-0.17591.06390.02990.07610.04110.04390.01130.0639-0.0534-0.1277-0.03880.0741-0.00360.00070.07830.00340.0883-4.595910.3399.3664
60.80160.0724-0.31410.5546-0.04240.8582-0.02330.11880.0273-0.0598-0.0090.0101-0.00710.04240.02920.086-0.0152-0.0030.09190.00530.091211.893310.50364.3778
70.74390.0393-0.1110.50260.00931.15770.0169-0.0671-0.1014-0.0028-0.00640.01140.127-0.0605-0.00740.1002-0.0381-0.00630.10420.00720.1014-24.0955-30.01326.1413
80.60240.0535-0.03751.0817-0.04591.0713-0.02040.0262-0.0274-0.11610.0050.06660.0056-0.12320.01590.0929-0.0181-0.01950.10310.00270.1011-24.4122-21.05217.6475
91.09720.58210.16051.07950.23521.1951-0.02140.14670.1134-0.05450.0580.1376-0.1403-0.1533-0.02930.09-0.0102-0.01910.13980.0240.1176-27.5899-15.294516.8369
101.09620.3431-0.04490.94650.06310.8530.0232-0.01980.08850.0748-0.0579-0.0451-0.14480.10010.04490.1163-0.0150.01510.1124-0.00750.1129-16.9766-12.367237.8961
110.986-0.08940.42140.523-0.02541.1842-0.0622-0.18860.17340.00620.0454-0.0047-0.1964-0.23910.0220.11960.02420.00250.1464-0.02160.1271-26.1495-10.948337.489
120.68260.04980.08320.6013-0.15691.3122-0.0128-0.2127-0.00910.1080.04250.04840.0033-0.2584-0.03070.0969-0.0170.00250.19810.0140.0887-25.6304-24.717646.7287
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 87 )A7 - 87
2X-RAY DIFFRACTION2chain 'A' and (resid 88 through 149 )A88 - 149
3X-RAY DIFFRACTION3chain 'A' and (resid 150 through 181 )A150 - 181
4X-RAY DIFFRACTION4chain 'A' and (resid 182 through 234 )A182 - 234
5X-RAY DIFFRACTION5chain 'A' and (resid 235 through 285 )A235 - 285
6X-RAY DIFFRACTION6chain 'A' and (resid 286 through 329 )A286 - 329
7X-RAY DIFFRACTION7chain 'B' and (resid 7 through 106 )B7 - 106
8X-RAY DIFFRACTION8chain 'B' and (resid 107 through 149 )B107 - 149
9X-RAY DIFFRACTION9chain 'B' and (resid 150 through 181 )B150 - 181
10X-RAY DIFFRACTION10chain 'B' and (resid 182 through 234 )B182 - 234
11X-RAY DIFFRACTION11chain 'B' and (resid 235 through 267 )B235 - 267
12X-RAY DIFFRACTION12chain 'B' and (resid 268 through 329 )B268 - 329

+
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://pdbjlvh1.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