[English] 日本語
Yorodumi
- PDB-6edi: Crystal structure of Leishmania braziliensis glucokinase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6edi
TitleCrystal structure of Leishmania braziliensis glucokinase
ComponentsGlucokinase
KeywordsTRANSFERASE / open conformation / dimeric
Function / homology
Function and homology information


glucokinase / glucokinase activity / D-glucose binding / glycolytic process / ATP binding
Similarity search - Function
Glucokinase / Glucokinase / Hexokinase; domain 1 / Hexokinase; domain 1 - #20 / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesLeishmania braziliensis MHOM/BR/75/M2904 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsBuechner, G.S. / Millington, M.E. / Perry, K. / D'Antonio, E.L.
CitationJournal: Mol. Biochem. Parasitol. / Year: 2019
Title: The crystal structure of glucokinase from Leishmania braziliensis.
Authors: Buechner, G.S. / Millington, M.E. / Perry, K. / D'Antonio, E.L.
History
DepositionAug 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2019Group: Data collection / Database references / Category: citation
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.year
Revision 1.2Jan 9, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 23, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.4Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support
Revision 1.5Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glucokinase
B: Glucokinase


Theoretical massNumber of molelcules
Total (without water)88,6392
Polymers88,6392
Non-polymers00
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-30 kcal/mol
Surface area30860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.477, 63.261, 85.570
Angle α, β, γ (deg.)90.000, 107.810, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Glucokinase / Glucokinase 1


Mass: 44319.535 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania braziliensis MHOM/BR/75/M2904 (eukaryote)
Gene: LBRM_35_2550 / Plasmid: pET-28a(+) / Details (production host): kanamycin-resistant / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A4HPA0, glucokinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.06 Å3/Da / Density % sol: 40.41 % / Description: single crystal
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 1.0 uL 20.3 mg/mL LbGlcK in 50 mM HEPES, pH 7.5, 0.2 M imidazole, 2 mM magnesium chloride + 1.0 uL precipitant solution (26% w/v PEG3350, 0.2 M ammonium sulfate, 0.1 M Tris, pH 8.5) ...Details: 1.0 uL 20.3 mg/mL LbGlcK in 50 mM HEPES, pH 7.5, 0.2 M imidazole, 2 mM magnesium chloride + 1.0 uL precipitant solution (26% w/v PEG3350, 0.2 M ammonium sulfate, 0.1 M Tris, pH 8.5) equilibrated against 80 uL precipitant solution, 96-well sitting-drop plate (Innovadyne), 295 K
PH range: 7.5 - 8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 2, 2016
RadiationMonochromator: cryogenically-cooled single crystal Si(220) side bounce
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.84→81.47 Å / Num. obs: 58585 / % possible obs: 97.4 % / Redundancy: 3.4 % / Biso Wilson estimate: 31.4 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.062 / Rrim(I) all: 0.116 / Net I/σ(I): 10.3
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
1.84-1.883.31.1741069532460.4380.7421.3931.188.5
9.03-81.473.50.06819875610.9950.0410.0836.899.8

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.17data scaling
PHASERphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2Q2R

2q2r


Resolution: 1.85→49.966 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.46
RfactorNum. reflection% reflection
Rfree0.2618 2955 5.08 %
Rwork0.2124 --
obs0.2149 58205 97.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 84.96 Å2 / Biso mean: 35.11 Å2 / Biso min: 18.42 Å2
Refinement stepCycle: final / Resolution: 1.85→49.966 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5950 0 0 176 6126
Biso mean---35.17 -
Num. residues----788
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076066
X-RAY DIFFRACTIONf_angle_d1.1818212
X-RAY DIFFRACTIONf_chiral_restr0.072930
X-RAY DIFFRACTIONf_plane_restr0.0051054
X-RAY DIFFRACTIONf_dihedral_angle_d15.3122176
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.88040.35391410.30462537267896
1.8804-1.91280.30881260.27912637276397
1.9128-1.94760.30921320.26622609274197
1.9476-1.9850.28051250.25562630275598
1.985-2.02560.33951220.25582638276097
2.0256-2.06960.29981570.25112572272997
2.0696-2.11780.30851470.23782611275897
2.1178-2.17070.25711410.23092581272296
2.1707-2.22940.30611370.22322567270496
2.2294-2.2950.28551450.23712633277898
2.295-2.36910.28061490.23722649279898
2.3691-2.45380.29061350.2312629276499
2.4538-2.5520.30821370.22972654279198
2.552-2.66810.29641560.22712604276098
2.6681-2.80880.32331350.23682609274497
2.8088-2.98470.3071630.23922636279998
2.9847-3.21520.25641480.2232662281099
3.2152-3.53860.27971420.20712677281999
3.5386-4.05050.22691650.18912661282698
4.0505-5.10240.20571230.17092681280497
5.1024-49.98460.20531290.18642773290298

+
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