[English] 日本語
Yorodumi
- PDB-5ont: Crystal structure of Mycolicibacterium hassiacum glucosylglycerat... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ont
TitleCrystal structure of Mycolicibacterium hassiacum glucosylglycerate hydrolase(MhGgH) E419A variant in complex with glucosylglycerol
ComponentsUncharacterized protein
KeywordsHYDROLASE / Mycobacterium
Function / homology
Function and homology information


glucosylglycerate hydrolase / glucosylglycerate hydrolase activity / Glc3Man9GlcNAc2 oligosaccharide glucosidase activity / oligosaccharide metabolic process
Similarity search - Function
Glycoside hydrolase family 63 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
1,3-dihydroxypropan-2-yl alpha-D-glucopyranoside / Glucosylglycerate hydrolase
Similarity search - Component
Biological speciesMycobacterium hassiacum
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsCereija, T.B. / Macedo-Ribeiro, S. / Pereira, P.J.B.
Funding support Portugal, 2items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a TecnologiaPOCI-01-0145-FEDER-007274 Portugal
Norte Portugal Regional Operational Programme NORTE 2020Norte-01-0145-FEDER-000012 Portugal
CitationJournal: Iucrj / Year: 2019
Title: The structural characterization of a glucosylglycerate hydrolase provides insights into the molecular mechanism of mycobacterial recovery from nitrogen starvation.
Authors: Cereija, T.B. / Alarico, S. / Lourenco, E.C. / Manso, J.A. / Ventura, M.R. / Empadinhas, N. / Macedo-Ribeiro, S. / Pereira, P.J.B.
History
DepositionAug 4, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1May 15, 2019Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_database_proc / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _struct.title
Revision 1.2Jul 31, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 2.0Jul 29, 2020Group: Atomic model / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,04412
Polymers101,7992
Non-polymers1,24510
Water10,196566
1
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,08824
Polymers203,5984
Non-polymers2,49020
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area12480 Å2
ΔGint-23 kcal/mol
Surface area60590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.898, 158.760, 87.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Uncharacterized protein


Mass: 50899.461 Da / Num. of mol.: 2 / Mutation: E419A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium hassiacum (strain DSM 44199 / CIP 105218 / JCM 12690 / 3849) (bacteria)
Gene: C731_0006 / Production host: Escherichia coli (E. coli) / References: UniProt: K5BDL0
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Sugar ChemComp-A0K / 1,3-dihydroxypropan-2-yl alpha-D-glucopyranoside / (2~{S},3~{R},4~{S},5~{S},6~{R})-2-[1,3-bis(oxidanyl)propan-2-yloxy]-6-(hydroxymethyl)oxane-3,4,5-triol / 1,3-dihydroxypropan-2-yl alpha-D-glucoside / 1,3-dihydroxypropan-2-yl D-glucoside / 1,3-dihydroxypropan-2-yl glucoside


Type: D-saccharide / Mass: 254.234 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H18O8 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 566 / 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: 2.98 Å3/Da / Density % sol: 58.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Tris-Bicine pH 8.5, amino acids, PEG 4000, glycerol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Oct 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.05→45.313 Å / Num. obs: 76309 / % possible obs: 99.4 % / Redundancy: 4.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.049 / Rrim(I) all: 0.104 / Net I/σ(I): 9.4
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.901 / Mean I/σ(I) obs: 1.6 / CC1/2: 0.552 / Rpim(I) all: 0.488 / Rrim(I) all: 1.027 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OHZ

5ohz


Resolution: 2.05→45.313 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.33
RfactorNum. reflection% reflection
Rfree0.195 3909 5.13 %
Rwork0.1542 --
obs0.1563 76246 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.05→45.313 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7055 0 82 566 7703
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017610
X-RAY DIFFRACTIONf_angle_d1.01110387
X-RAY DIFFRACTIONf_dihedral_angle_d19.3194471
X-RAY DIFFRACTIONf_chiral_restr0.0591067
X-RAY DIFFRACTIONf_plane_restr0.0071361
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.0750.32141630.26442551X-RAY DIFFRACTION100
2.075-2.10130.2951450.24522563X-RAY DIFFRACTION100
2.1013-2.12890.30161190.24032615X-RAY DIFFRACTION100
2.1289-2.15810.24691300.22662539X-RAY DIFFRACTION100
2.1581-2.18890.28261520.21362568X-RAY DIFFRACTION100
2.1889-2.22160.23811210.19792566X-RAY DIFFRACTION100
2.2216-2.25630.26731040.19452620X-RAY DIFFRACTION100
2.2563-2.29330.26391540.19192574X-RAY DIFFRACTION100
2.2933-2.33290.20021500.1822556X-RAY DIFFRACTION100
2.3329-2.37530.23251500.17462558X-RAY DIFFRACTION100
2.3753-2.4210.22331410.17172559X-RAY DIFFRACTION99
2.421-2.47040.20041330.16452525X-RAY DIFFRACTION99
2.4704-2.52410.22261300.1652549X-RAY DIFFRACTION98
2.5241-2.58280.20611480.16162556X-RAY DIFFRACTION99
2.5828-2.64740.20061070.15792608X-RAY DIFFRACTION99
2.6474-2.7190.20911210.15122584X-RAY DIFFRACTION99
2.719-2.79890.23321240.1572613X-RAY DIFFRACTION100
2.7989-2.88930.22451120.1482578X-RAY DIFFRACTION99
2.8893-2.99250.19581130.15622551X-RAY DIFFRACTION97
2.9925-3.11230.17571550.15212409X-RAY DIFFRACTION93
3.1123-3.25390.19331560.14382534X-RAY DIFFRACTION98
3.2539-3.42540.17291490.14642586X-RAY DIFFRACTION100
3.4254-3.63990.15871470.13752616X-RAY DIFFRACTION100
3.6399-3.92080.17991680.12892604X-RAY DIFFRACTION100
3.9208-4.31510.15121570.11512614X-RAY DIFFRACTION100
4.3151-4.93890.18741430.11932658X-RAY DIFFRACTION100
4.9389-6.21990.1831550.1552688X-RAY DIFFRACTION100
6.2199-45.32380.1751620.16722795X-RAY DIFFRACTION100
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)
10.96271.3537-0.22695.7274-2.65314.9661-0.04970.1231-0.0351-0.28980.15410.23350.0673-0.2011-0.0840.15770.01740.00520.1553-0.03020.213142.51139.076737.3997
23.6563-1.92022.33473.2549-2.38216.66620.16120.39510.0097-0.627-0.13410.009-0.0032-0.0819-0.06580.3191-0.00770.02680.1869-0.02630.212846.640721.382328.1304
33.2281-1.25620.34462.3927-0.32431.68440.03850.29770.0809-0.3606-0.05130.2637-0.248-0.11160.00580.322-0.0049-0.01480.20050.01390.239141.133830.15732.4584
41.25070.1323-0.0911.69690.09051.13830.0022-0.06890.13820.05670.01320.3078-0.2101-0.1533-0.02550.2280.03070.00690.1913-0.00080.249337.873825.881449.1548
51.46232.27641.7375.69781.93785.54470.2792-0.2362-0.1590.5843-0.1067-0.22590.2840.234-0.1580.2511-0.04720.0060.28810.02880.215249.62186.519580.3654
62.28220.4841-0.21491.5123-0.10171.93020.1879-0.58160.00220.4581-0.2412-0.215-0.22960.32920.05360.4387-0.1458-0.04450.42430.00090.245660.658524.308483.9707
71.82220.4103-0.0773.0532-0.8721.77430.0519-0.0612-0.23740.0213-0.1307-0.36890.05110.26730.06790.188-0.0231-0.0210.25810.00310.229663.270711.947366.8926
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 69 )
2X-RAY DIFFRACTION2chain 'A' and (resid 70 through 134 )
3X-RAY DIFFRACTION3chain 'A' and (resid 135 through 272 )
4X-RAY DIFFRACTION4chain 'A' and (resid 273 through 446 )
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 69 )
6X-RAY DIFFRACTION6chain 'B' and (resid 70 through 320 )
7X-RAY DIFFRACTION7chain 'B' and (resid 321 through 446 )

+
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