[English] 日本語
Yorodumi
- PDB-3qtg: Crystal structure of pyruvate kinase from Pyrobaculum aerophilum -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3qtg
TitleCrystal structure of pyruvate kinase from Pyrobaculum aerophilum
ComponentsPyruvate kinase
KeywordsTRANSFERASE / TIM barrel / Kinase / glycolysis
Function / homology
Function and homology information


pyruvate kinase / pyruvate kinase activity / potassium ion binding / glycolytic process / kinase activity / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
PK beta-barrel domain-like / M1 Pyruvate Kinase; Domain 3 / Pyruvate kinase, C-terminal domain / Pyruvate Kinase; Chain: A, domain 1 / Pyruvate kinase / Pyruvate kinase, barrel / Pyruvate kinase, insert domain superfamily / Pyruvate kinase, barrel domain / Pyruvate kinase, C-terminal / Pyruvate kinase, C-terminal domain superfamily ...PK beta-barrel domain-like / M1 Pyruvate Kinase; Domain 3 / Pyruvate kinase, C-terminal domain / Pyruvate Kinase; Chain: A, domain 1 / 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 / Phosphoenolpyruvate-binding domains / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesPyrobaculum aerophilum (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDavies, C. / Solomons, J.T.G.
CitationJournal: To be Published
Title: The crystal structure of pyruvate kinase from the hyperthermophilic archaeon Pyrobaculum aerophilum: insights into cooperative regulation
Authors: Solomons, J.T.G. / Johnson, U. / Schoenheit, P. / Davies, C.
History
DepositionFeb 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pyruvate kinase
B: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,9325
Polymers100,6432
Non-polymers2883
Water2,522140
1
A: Pyruvate kinase
B: Pyruvate kinase
hetero molecules

A: Pyruvate kinase
B: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,86310
Polymers201,2874
Non-polymers5766
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area9890 Å2
ΔGint-153 kcal/mol
Surface area68180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.300, 107.400, 105.000
Angle α, β, γ (deg.)90.00, 110.50, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Pyruvate kinase / PK


Mass: 50321.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrobaculum aerophilum (archaea) / Strain: ATCC 51768, IM2 / Gene: PAE0819, pyk / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8ZYE0, pyruvate kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 3.05 Å3/Da / Density % sol: 59.69 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 17% PEG 1500, 100mM Tris pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 24, 2006
RadiationMonochromator: SI(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→39 Å / Num. all: 60944 / Num. obs: 60944 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 47.6 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 33.3
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 3.5 / Num. unique all: 5983 / % possible all: 98.3

-
Processing

Software
NameVersionClassification
MAR345RESEARCHdata collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PKL

1pkl


Resolution: 2.2→39 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.937 / SU B: 11.636 / SU ML: 0.143 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.247 3110 5.1 %RANDOM
Rwork0.206 ---
all0.208 60943 --
obs0.208 60943 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20 Å2-0.78 Å2
2---0.07 Å20 Å2
3----1.06 Å2
Refinement stepCycle: LAST / Resolution: 2.2→39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6701 0 15 140 6856
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0226852
X-RAY DIFFRACTIONr_angle_refined_deg1.371.9849308
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9775868
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.7923.921278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.654151212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9211553
X-RAY DIFFRACTIONr_chiral_restr0.0910.21109
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025043
X-RAY DIFFRACTIONr_nbd_refined0.1980.22828
X-RAY DIFFRACTIONr_nbtor_refined0.30.24662
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2291
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.130.216
X-RAY DIFFRACTIONr_mcbond_it0.831.54472
X-RAY DIFFRACTIONr_mcangle_it1.37127054
X-RAY DIFFRACTIONr_scbond_it2.08932679
X-RAY DIFFRACTIONr_scangle_it3.2644.52254
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 235 -
Rwork0.282 3977 -
obs-3212 94.33 %

+
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