[English] 日本語
Yorodumi
- PDB-3hqq: Crystal structure of Leishmania mexicana pyruvate kinase (LmPYK) ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3hqq
TitleCrystal structure of Leishmania mexicana pyruvate kinase (LmPYK) in complex with Fructose 2,6 bisphosphate
ComponentsPyruvate kinase
KeywordsTRANSFERASE / TIM BARREL / T-STATE ENZYME / Allosteric enzyme / Glycolysis / Kinase / Magnesium / Metal-binding / Pyruvate
Function / homology
Function and homology information


pyruvate kinase / pyruvate kinase activity / potassium ion binding / kinase activity / magnesium ion binding / ATP binding
Similarity search - Function
Pyruvate kinase, active site / Pyruvate kinase active site signature. / Pyruvate kinase / Pyruvate kinase, barrel / Pyruvate kinase, insert domain superfamily / Pyruvate kinase, barrel domain / Pyruvate kinase, C-terminal / Pyruvate kinase, C-terminal domain superfamily / Pyruvate kinase, alpha/beta domain / Pyruvate kinase-like, insert domain superfamily ...Pyruvate kinase, active site / Pyruvate kinase active site signature. / Pyruvate kinase / Pyruvate kinase, barrel / Pyruvate kinase, insert domain superfamily / Pyruvate kinase, barrel domain / Pyruvate kinase, C-terminal / Pyruvate kinase, C-terminal domain superfamily / Pyruvate kinase, alpha/beta domain / Pyruvate kinase-like, insert domain superfamily / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily
Similarity search - Domain/homology
2,6-di-O-phosphono-beta-D-fructofuranose / Pyruvate kinase
Similarity search - Component
Biological speciesLeishmania mexicana (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5.07 Å
AuthorsMorgan, H.P. / Walkinshaw, M.D.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: The allosteric mechanism of pryuvate kinase from Leishmania mexicana: a rock and lock model
Authors: Morgan, H.P. / McNae, I.W. / Nowicki, M.W. / Hannaert, V. / Michels, P.A.M. / Fothergill-Gilmore, L.A. / Walkinshaw, M.D.
History
DepositionJun 8, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 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.mon_nstd_flag / _chem_comp.name ..._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 1.3Nov 1, 2023Group: 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: Pyruvate kinase
B: Pyruvate kinase
C: Pyruvate kinase
D: Pyruvate kinase
E: Pyruvate kinase
F: Pyruvate kinase
G: Pyruvate kinase
H: Pyruvate kinase
I: Pyruvate kinase
J: Pyruvate kinase
K: Pyruvate kinase
L: Pyruvate kinase
M: Pyruvate kinase
N: Pyruvate kinase
O: Pyruvate kinase
P: Pyruvate kinase
Q: Pyruvate kinase
R: Pyruvate kinase
S: Pyruvate kinase
T: Pyruvate kinase
U: Pyruvate kinase
V: Pyruvate kinase
W: Pyruvate kinase
X: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,315,39348
Polymers1,307,23024
Non-polymers8,16324
Water00
1
A: Pyruvate kinase
H: Pyruvate kinase
I: Pyruvate kinase
J: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,2328
Polymers217,8724
Non-polymers1,3604
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15210 Å2
ΔGint-98 kcal/mol
Surface area73940 Å2
MethodPISA
2
B: Pyruvate kinase
C: Pyruvate kinase
O: Pyruvate kinase
P: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,2328
Polymers217,8724
Non-polymers1,3604
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15190 Å2
ΔGint-99 kcal/mol
Surface area74030 Å2
MethodPISA
3
D: Pyruvate kinase
E: Pyruvate kinase
F: Pyruvate kinase
G: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,2328
Polymers217,8724
Non-polymers1,3604
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15280 Å2
ΔGint-98 kcal/mol
Surface area73910 Å2
MethodPISA
4
K: Pyruvate kinase
L: Pyruvate kinase
M: Pyruvate kinase
N: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,2328
Polymers217,8724
Non-polymers1,3604
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15410 Å2
ΔGint-99 kcal/mol
Surface area73780 Å2
MethodPISA
5
Q: Pyruvate kinase
R: Pyruvate kinase
S: Pyruvate kinase
T: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,2328
Polymers217,8724
Non-polymers1,3604
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15340 Å2
ΔGint-98 kcal/mol
Surface area73830 Å2
MethodPISA
6
U: Pyruvate kinase
V: Pyruvate kinase
W: Pyruvate kinase
X: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,2328
Polymers217,8724
Non-polymers1,3604
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15440 Å2
ΔGint-99 kcal/mol
Surface area73760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)243.840, 254.690, 892.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein ...
Pyruvate kinase / PK


Mass: 54467.934 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania mexicana (eukaryote) / Strain: NHOM/B2/84/BEL46 / Gene: PYK / Plasmid: pET3A_lmPYK / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q27686, pyruvate kinase
#2: Sugar...
ChemComp-FDP / 2,6-di-O-phosphono-beta-D-fructofuranose / FRUCTOSE-2,6-DIPHOSPHATE / 2,6-di-O-phosphono-beta-D-fructose / 2,6-di-O-phosphono-D-fructose / 2,6-di-O-phosphono-fructose


Type: D-saccharide, beta linking / Mass: 340.116 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Formula: C6H14O12P2
IdentifierTypeProgram
b-D-Fruf2PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Sequence detailsTHE SEQUENCE OF L. MEXICANA PYRUVATE KINASE HAS BEEN DETERMINED IN THE LABORATORY OF PROF. PAUL ...THE SEQUENCE OF L. MEXICANA PYRUVATE KINASE HAS BEEN DETERMINED IN THE LABORATORY OF PROF. PAUL MICHELS, PUBLISHED AND DEPOSITED IN GENBANK. HOWEVER, THE SEQUENCE AS APPEARED IN GENBANK CONTAINED ERRORS. THE CORRECTION HAS BEEN INFORMED TO GENBANK WITH THE ACCESSION CODE X74944 AND IT WILL BE FILTRATED TO UNIPROT AT A LATER TIME.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.33 Å3/Da / Density % sol: 76.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 10-16% PEG8000, 20mM triethanolamine-HCl, 50mM MgCl2, 100mM KCl, 10-15% glycerol, pH7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 10, 2008 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 5→39.81 Å / Num. obs: 112851 / % possible obs: 98.1 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 5 / Redundancy: 5 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.189 / Net I/σ(I): 6.4
Reflection shellResolution: 5→5.2 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 3.7 / Num. unique all: 7903 / % possible all: 93.5

-
Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.5.0066refinement
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PKL

1pkl


Resolution: 5.07→39.81 Å / Cor.coef. Fo:Fc: 0.732 / Cor.coef. Fo:Fc free: 0.709 / SU B: 0.001 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 1.683 / ESU R Free: 1.701 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.35664 5652 5 %RANDOM
Rwork0.35274 ---
obs0.35294 107127 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.813 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2---0.57 Å20 Å2
3---0.74 Å2
Refinement stepCycle: LAST / Resolution: 5.07→39.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms91176 0 480 0 91656
LS refinement shellResolution: 5.07→5.199 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 380 -
Rwork0.387 7375 -
obs--100 %

+
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