[English] 日本語
Yorodumi
- PDB-5oj4: Crystal structure of Mycolicibacterium hassiacum glucosylglycerat... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5oj4
TitleCrystal structure of Mycolicibacterium hassiacum glucosylglycerate hydrolase (MhGgH) D182A variant in complex with mannosylglycerate
ComponentsHydrolase
KeywordsHYDROLASE / Mycobacterium
Function / homology
Function and homology information


glucosylglycerate hydrolase / glucosylglycerate hydrolase activity / Glc3Man9GlcNAc2 oligosaccharide glucosidase activity / oligosaccharide metabolic process
Similarity search - Function
Mannosylglycerate hydrolase MGH1-like glycoside hydrolase domain / 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
Chem-2M8 / GLYCINE / DI(HYDROXYETHYL)ETHER / Glucosylglycerate hydrolase
Similarity search - Component
Biological speciesMycobacterium hassiacum DSM 44199 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 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
DepositionJul 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2018Group: Data collection / Database references / Category: pdbx_related_exp_data_set / Item: _pdbx_related_exp_data_set.data_reference
Revision 1.2May 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 1.3Jul 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: Hydrolase
B: Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,21324
Polymers101,8272
Non-polymers2,38622
Water15,241846
1
A: Hydrolase
B: Hydrolase
hetero molecules

A: Hydrolase
B: Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,42748
Polymers203,6544
Non-polymers4,77344
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Unit cell
Length a, b, c (Å)85.329, 159.632, 91.169
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

-
Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Hydrolase


Mass: 50913.484 Da / Num. of mol.: 2 / Mutation: D182A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium hassiacum DSM 44199 (bacteria)
Gene: C731_0006 / Production host: Escherichia coli (E. coli) / References: UniProt: K5BDL0
#5: Sugar ChemComp-2M8 / (2R)-3-hydroxy-2-(alpha-D-mannopyranosyloxy)propanoic acid / 2-O-ALPHA-MANNOSYL-D-GLYCERATE / (2R)-3-hydroxy-2-(alpha-D-mannosyloxy)propanoic acid / (2R)-3-hydroxy-2-(D-mannosyloxy)propanoic acid / (2R)-3-hydroxy-2-(mannosyloxy)propanoic acid


Type: D-saccharide, alpha linking / Mass: 268.218 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16O9

-
Non-polymers , 4 types, 866 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 846 / 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: 3.06 Å3/Da / Density % sol: 59.79 %
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-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.79→49.11 Å / Num. obs: 117039 / % possible obs: 99.4 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.031 / Rrim(I) all: 0.08 / Net I/σ(I): 16.5
Reflection shellResolution: 1.79→1.85 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.052 / Mean I/σ(I) obs: 1.7 / CC1/2: 0.66 / Rpim(I) all: 0.436 / Rrim(I) all: 1.141 / % possible all: 95.9

-
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: 1.79→49.11 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1729 5861 5.01 %
Rwork0.144 --
obs0.1454 116974 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.79→49.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7160 0 157 846 8163
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017800
X-RAY DIFFRACTIONf_angle_d0.98610626
X-RAY DIFFRACTIONf_dihedral_angle_d19.8644600
X-RAY DIFFRACTIONf_chiral_restr0.0621087
X-RAY DIFFRACTIONf_plane_restr0.0071393
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.81030.29732020.28273496X-RAY DIFFRACTION95
1.8103-1.83160.30581810.25743498X-RAY DIFFRACTION96
1.8316-1.8540.28941920.24473566X-RAY DIFFRACTION97
1.854-1.87740.22991730.22043630X-RAY DIFFRACTION98
1.8774-1.90220.22422060.20563589X-RAY DIFFRACTION98
1.9022-1.92820.24541870.20513657X-RAY DIFFRACTION99
1.9282-1.95580.22652170.19073668X-RAY DIFFRACTION100
1.9558-1.9850.21562240.18643666X-RAY DIFFRACTION100
1.985-2.0160.20191950.17593700X-RAY DIFFRACTION100
2.016-2.0490.18872160.16083631X-RAY DIFFRACTION100
2.049-2.08440.18481830.15673724X-RAY DIFFRACTION100
2.0844-2.12230.18221800.1553719X-RAY DIFFRACTION100
2.1223-2.16310.18722030.14953681X-RAY DIFFRACTION100
2.1631-2.20720.17191950.14333687X-RAY DIFFRACTION100
2.2072-2.25520.20481970.14393701X-RAY DIFFRACTION100
2.2552-2.30770.16121780.13813745X-RAY DIFFRACTION100
2.3077-2.36540.15461860.13523702X-RAY DIFFRACTION100
2.3654-2.42930.18862010.14323701X-RAY DIFFRACTION100
2.4293-2.50080.17082040.1373709X-RAY DIFFRACTION100
2.5008-2.58150.17382090.14243724X-RAY DIFFRACTION100
2.5815-2.67380.19031940.14073719X-RAY DIFFRACTION100
2.6738-2.78080.17831940.13693742X-RAY DIFFRACTION100
2.7808-2.90740.16072170.13713708X-RAY DIFFRACTION100
2.9074-3.06070.16322000.13453764X-RAY DIFFRACTION100
3.0607-3.25240.16331900.1323732X-RAY DIFFRACTION100
3.2524-3.50340.16721910.13093753X-RAY DIFFRACTION100
3.5034-3.85590.13731680.12033814X-RAY DIFFRACTION100
3.8559-4.41350.12811840.11023829X-RAY DIFFRACTION100
4.4135-5.55930.14662020.12793829X-RAY DIFFRACTION100
5.5593-49.12870.1841920.16664029X-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)
10.5080.29060.80083.8772-0.9473.10810.01120.0127-0.0734-0.13060.06680.09480.0706-0.0869-0.06330.07870.01250.00970.119-0.01510.169641.74478.727339.3349
20.80780.01210.05481.094-0.10861.20810.01120.07130.1158-0.07730.00960.1102-0.2365-0.067-0.01840.17350.01820.00880.12840.0140.192539.871726.518641.2196
31.94481.12991.37441.95970.91043.35360.1808-0.3115-0.05760.4911-0.1701-0.05120.08280.0932-0.00770.3236-0.0920.00910.26450.03160.1752.046511.672388.1979
41.43210.19410.06851.322-0.07181.40640.1292-0.25230.0760.3716-0.1477-0.1975-0.23980.23980.0260.3488-0.1215-0.03710.2732-0.00610.192460.111324.871783.417
51.0045-0.04880.25672.4553-0.89981.92910.07410.0065-0.09910.0251-0.108-0.25760.06090.26710.02250.1478-0.0241-0.01320.1934-0.01090.185362.120512.16568.6728
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 446 )
3X-RAY DIFFRACTION3chain 'B' and (resid 2 through 117 )
4X-RAY DIFFRACTION4chain 'B' and (resid 118 through 320 )
5X-RAY DIFFRACTION5chain '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