[English] 日本語
Yorodumi
- PDB-7pho: Crystal structure of Mycobacterium hassiacum glucosyl-3-phosphogl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7pho
TitleCrystal structure of Mycobacterium hassiacum glucosyl-3-phosphoglycerate synthase at pH 7.1 in complex with 4-hydroxybenzaldehyde
ComponentsGlucosyl-3-phosphoglycerate synthase
KeywordsTRANSFERASE / Glucose / UDP / thermostable / GTA-fold
Function / homology
Function and homology information


glucosyl-3-phosphoglycerate synthase / glycosyltransferase activity / nucleotide binding / metal ion binding
Similarity search - Function
: / Glycosyltransferase 2-like / Glycosyl transferase family 2 / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
BICARBONATE ION / P-HYDROXYBENZALDEHYDE / D-MALATE / Glucosyl-3-phosphoglycerate synthase
Similarity search - Component
Biological speciesMycolicibacterium hassiacum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 Å
AuthorsNunes-Costa, D. / Silva, A. / Barbosa Pereira, P.J. / Macedo-Ribeiro, S.
Funding support Portugal, 1items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a TecnologiaPTDC/BTM-TEC/29221/2017 (POCI-01-0145-FEDER-029221) Portugal
CitationJournal: To Be Published
Title: Crystal structure of Mycobacterium hassiacum glucosyl-3-phosphoglycerate synthase at pH 7.1 in complex with 4-hydroxybenzaldehyde
Authors: Nunes-Costa, D. / Silva, A. / Barbosa Pereira, P.J. / Macedo-Ribeiro, S.
History
DepositionAug 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: 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: Glucosyl-3-phosphoglycerate synthase
B: Glucosyl-3-phosphoglycerate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,53613
Polymers70,3022
Non-polymers1,23411
Water8,161453
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Alarico S, Nunes-Costa D, Silva A, Costa M, Macedo-Ribeiro S, Empadinhas N. A genuine mycobacterial thermophile: Mycobacterium hassiacum growth, survival and GpgS stability ...Evidence: gel filtration, Alarico S, Nunes-Costa D, Silva A, Costa M, Macedo-Ribeiro S, Empadinhas N. A genuine mycobacterial thermophile: Mycobacterium hassiacum growth, survival and GpgS stability at near-pasteurization temperatures. Microbiology (Reading). 2020 May;166(5):474-483. doi: 10.1099/mic.0.000898. PMID: 32100712.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5880 Å2
ΔGint-11 kcal/mol
Surface area25330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.548, 90.542, 95.340
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Glucosyl-3-phosphoglycerate synthase


Mass: 35151.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The C-terminal KLAAALEHHHHHH sequence corresponds to a linker followed by an hexahistidine tag used for protein purification
Source: (gene. exp.) Mycolicibacterium hassiacum (strain DSM 44199 / CIP 105218 / JCM 12690 / 3849) (bacteria)
Strain: DSM 44199 / CIP 105218 / JCM 12690 / 3849 / Gene: gpgS, C731_3243, MHAS_02845 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: K5B7Z4, glucosyl-3-phosphoglycerate synthase

-
Non-polymers , 5 types, 464 molecules

#2: Chemical
ChemComp-HBA / P-HYDROXYBENZALDEHYDE


Mass: 122.121 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C7H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 453 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.1 / Details: 0.15 M DL-Malic Acid pH 7.1; 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.268→65.654 Å / Num. obs: 161347 / % possible obs: 99.9 % / Redundancy: 5.4 % / Biso Wilson estimate: 16.59 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.017 / Rrim(I) all: 0.04 / Net I/σ(I): 18.2
Reflection shellResolution: 1.268→1.29 Å / Redundancy: 5 % / Rmerge(I) obs: 1.115 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 8041 / CC1/2: 0.579 / Rpim(I) all: 0.552 / Rrim(I) all: 1.248 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7P5L

7p5l


Resolution: 1.27→65.65 Å / SU ML: 0.1329 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.7427
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1641 7947 4.93 %
Rwork0.145 153389 -
obs0.1459 161336 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.87 Å2
Refinement stepCycle: LAST / Resolution: 1.27→65.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4499 0 88 453 5040
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00764883
X-RAY DIFFRACTIONf_angle_d0.93156703
X-RAY DIFFRACTIONf_chiral_restr0.075804
X-RAY DIFFRACTIONf_plane_restr0.0147869
X-RAY DIFFRACTIONf_dihedral_angle_d11.22971867
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.27-1.280.33372560.30275076X-RAY DIFFRACTION99.96
1.28-1.30.29722420.27115059X-RAY DIFFRACTION99.96
1.3-1.310.28112960.24165064X-RAY DIFFRACTION99.96
1.31-1.330.25862630.2275107X-RAY DIFFRACTION99.96
1.33-1.350.24462570.21775033X-RAY DIFFRACTION99.98
1.35-1.370.2282570.20775084X-RAY DIFFRACTION99.98
1.37-1.390.23232720.19835069X-RAY DIFFRACTION99.94
1.39-1.410.23022690.19165066X-RAY DIFFRACTION100
1.41-1.430.19462370.18335081X-RAY DIFFRACTION99.96
1.43-1.450.20652780.17615067X-RAY DIFFRACTION99.89
1.45-1.480.18422650.1645079X-RAY DIFFRACTION100
1.48-1.50.16692670.14535093X-RAY DIFFRACTION99.98
1.5-1.530.15142520.13955087X-RAY DIFFRACTION99.94
1.53-1.560.17693020.12825055X-RAY DIFFRACTION99.96
1.56-1.60.15092610.12135065X-RAY DIFFRACTION99.91
1.6-1.640.14512820.1165072X-RAY DIFFRACTION99.98
1.64-1.680.14882640.11715135X-RAY DIFFRACTION99.98
1.68-1.720.15182590.1195091X-RAY DIFFRACTION99.93
1.72-1.770.15962530.12385118X-RAY DIFFRACTION99.96
1.77-1.830.16312780.13165079X-RAY DIFFRACTION99.94
1.83-1.890.16082510.1335115X-RAY DIFFRACTION100
1.89-1.970.1422820.12645123X-RAY DIFFRACTION99.94
1.97-2.060.13692550.11595113X-RAY DIFFRACTION99.8
2.06-2.170.13192420.11825152X-RAY DIFFRACTION99.72
2.17-2.30.13222440.12055160X-RAY DIFFRACTION99.83
2.3-2.480.14172520.12565160X-RAY DIFFRACTION99.83
2.48-2.730.15382700.13765171X-RAY DIFFRACTION99.63
2.73-3.130.16882790.14735170X-RAY DIFFRACTION99.6
3.13-3.940.16632700.14765246X-RAY DIFFRACTION99.58
3.94-65.650.16982920.16495399X-RAY DIFFRACTION99.25

+
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