[English] 日本語
Yorodumi
- PDB-6gt9: Crystal structure of GanP, a glucose-galactose binding protein fr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6gt9
TitleCrystal structure of GanP, a glucose-galactose binding protein from Geobacillus stearothermophilus, in complex with galactose
ComponentsPutative sugar binding protein
KeywordsSUGAR BINDING PROTEIN / Glucose-galactose binding protein / Geobacillus stearothermophilus / three-component sensing system / galactan utilization system
Function / homology
Function and homology information


carbohydrate binding
Similarity search - Function
Periplasmic binding protein / Periplasmic binding protein domain / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
beta-D-galactopyranose / Putative sugar binding protein
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.894 Å
AuthorsSherf, D. / Lansky, S. / Zehavi, A. / Shoham, Y. / Shoham, G.
CitationJournal: To Be Published
Title: The crystal structure of GanP, a glucose-galactose binding protein from Geobacillus stearothermophilus, in complex with galactose
Authors: Sherf, D. / Zehavi, A. / Lansky, S. / Shoham, Y. / Shoham, G.
History
DepositionJun 16, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Jan 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: Putative sugar binding protein
B: Putative sugar binding protein
C: Putative sugar binding protein
D: Putative sugar binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,19512
Polymers142,0904
Non-polymers1,1058
Water13,944774
1
A: Putative sugar binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7993
Polymers35,5221
Non-polymers2762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative sugar binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7993
Polymers35,5221
Non-polymers2762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Putative sugar binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7993
Polymers35,5221
Non-polymers2762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Putative sugar binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7993
Polymers35,5221
Non-polymers2762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.520, 88.890, 88.880
Angle α, β, γ (deg.)90.00, 95.41, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Putative sugar binding protein


Mass: 35522.449 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: ganP / Production host: Escherichia coli (E. coli) / References: UniProt: W8QN64
#2: Sugar
ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 774 / 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: 1.98 Å3/Da / Density % sol: 37.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.1 M sodium acetate (pH 4 buffer), 26%-28% w/v PEG MME 2K, 0.2 M ammonium sulfate.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.89→88.89 Å / Num. obs: 87725 / % possible obs: 99.6 % / Redundancy: 7.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.119 / Net I/σ(I): 12
Reflection shellResolution: 1.89→1.93 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.824 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4369 / CC1/2: 0.866 / % possible all: 97.4

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C6Q

3c6q


Resolution: 1.894→58.217 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.72
RfactorNum. reflection% reflection
Rfree0.2391 1999 2.28 %
Rwork0.1916 --
obs0.1926 87582 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.894→58.217 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8812 0 68 774 9654
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079098
X-RAY DIFFRACTIONf_angle_d0.88112359
X-RAY DIFFRACTIONf_dihedral_angle_d16.975571
X-RAY DIFFRACTIONf_chiral_restr0.0551467
X-RAY DIFFRACTIONf_plane_restr0.0051575
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.894-1.94140.40261390.32325976X-RAY DIFFRACTION98
1.9414-1.99390.31811420.28216078X-RAY DIFFRACTION100
1.9939-2.05250.33131430.25836104X-RAY DIFFRACTION100
2.0525-2.11880.25231440.23386123X-RAY DIFFRACTION100
2.1188-2.19450.26461420.21756111X-RAY DIFFRACTION100
2.1945-2.28240.29031430.20736105X-RAY DIFFRACTION100
2.2824-2.38630.29141420.19916087X-RAY DIFFRACTION100
2.3863-2.51210.25061420.19326121X-RAY DIFFRACTION100
2.5121-2.66950.24081440.19546141X-RAY DIFFRACTION100
2.6695-2.87560.2421430.19866133X-RAY DIFFRACTION100
2.8756-3.16490.25131440.19266134X-RAY DIFFRACTION100
3.1649-3.62280.23691430.17876135X-RAY DIFFRACTION100
3.6228-4.56410.20151430.14976151X-RAY DIFFRACTION99
4.5641-58.2450.15471450.15036184X-RAY DIFFRACTION98

+
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