[English] 日本語
Yorodumi
- PDB-1ayl: PHOSPHOENOLPYRUVATE CARBOXYKINASE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ayl
TitlePHOSPHOENOLPYRUVATE CARBOXYKINASE
ComponentsPHOSPHOENOLPYRUVATE CARBOXYKINASE
KeywordsKINASE (TRANSPHOSPHORYLATING) / P-LOOP / PROTEIN-ATP COMPLEX / NUCLEOTIDE-TRIPHOSPHATE HYDROLASE
Function / homology
Function and homology information


phosphoenolpyruvate carboxykinase (ATP) / phosphoenolpyruvate carboxykinase (ATP) activity / gluconeogenesis / calcium ion binding / magnesium ion binding / ATP binding / cytosol
Similarity search - Function
Phosphoenolpyruvate carboxykinase / Phosphoenolpyruvate carboxykinase, ATP-utilising / Phosphoenolpyruvate carboxykinase (ATP) signature. / Phosphoenolpyruvate carboxykinase (ATP), conserved site / Phosphoenolpyruvate Carboxykinase; domain 3 - #20 / Phosphoenolpyruvate Carboxykinase; domain 1 / Phosphoenolpyruvate Carboxykinase, domain 1 / Phosphoenolpyruvate Carboxykinase, domain 2 / Phosphoenolpyruvate Carboxykinase; domain 2 / Phosphoenolpyruvate carboxykinase, C-terminal ...Phosphoenolpyruvate carboxykinase / Phosphoenolpyruvate carboxykinase, ATP-utilising / Phosphoenolpyruvate carboxykinase (ATP) signature. / Phosphoenolpyruvate carboxykinase (ATP), conserved site / Phosphoenolpyruvate Carboxykinase; domain 3 - #20 / Phosphoenolpyruvate Carboxykinase; domain 1 / Phosphoenolpyruvate Carboxykinase, domain 1 / Phosphoenolpyruvate Carboxykinase, domain 2 / Phosphoenolpyruvate Carboxykinase; domain 2 / Phosphoenolpyruvate carboxykinase, C-terminal / Phosphoenolpyruvate carboxykinase, N-terminal / Phosphoenolpyruvate Carboxykinase; domain 3 / Beta Complex / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / OXALATE ION / Phosphoenolpyruvate carboxykinase (ATP)
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsTari, L.W. / Pugazenthi, U. / Goldie, H. / Delbaere, L.T.J.
Citation
Journal: Nat.Struct.Biol. / Year: 1996
Title: Snapshot of an enzyme reaction intermediate in the structure of the ATP-Mg2+-oxalate ternary complex of Escherichia coli PEP carboxykinase.
Authors: Tari, L.W. / Matte, A. / Pugazhenthi, U. / Goldie, H. / Delbaere, L.T.
#1: Journal: To be Published
Title: Allosteric Control by Calcium and Mechanism of Desensitization of Phosphoenolpyruvate Carboxykinase of Escherichia Coli
Authors: Goldie, H. / Sanwal, B.D.
#2: Journal: J.Mol.Biol. / Year: 1996
Title: Crystal Structure of Escherichia Coli Phosphoenolpyruvate Carboxykinase: A New Structural Family with the P-Loop Nucleoside Triphosphate Hydrolase Fold
Authors: Matte, A. / Goldie, H. / Sweet, R.M. / Delbaere, L.T.
#3: Journal: J.Mol.Biol. / Year: 1991
Title: Crystallization of the Calcium-Activated Phosphoenolpyruvate Carboxykinase from Escherichia Coli K12
Authors: Delbaere, L.T. / Vandonselaar, M. / Glaeske, D. / Jabs, C. / Goldie, H.
#4: Journal: J.Bacteriol. / Year: 1990
Title: Sequence of the Pcka Gene of Escherichia Coli K-12: Relevance to Genetic and Allosteric Regulation and Homology of E. Coli Phosphoenolpyruvate Carboxykinase with the Enzymes from Trypanosoma ...Title: Sequence of the Pcka Gene of Escherichia Coli K-12: Relevance to Genetic and Allosteric Regulation and Homology of E. Coli Phosphoenolpyruvate Carboxykinase with the Enzymes from Trypanosoma Brucei and Saccharomyces Cerevisiae
Authors: Medina, V. / Pontarollo, R. / Glaeske, D. / Tabel, H. / Goldie, H.
History
DepositionDec 7, 1995Processing site: BNL
Revision 1.0Jan 11, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Mar 21, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.pdbx_collection_date

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PHOSPHOENOLPYRUVATE CARBOXYKINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4164
Polymers59,7961
Non-polymers6203
Water6,215345
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.510, 96.690, 46.960
Angle α, β, γ (deg.)90.00, 96.63, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein PHOSPHOENOLPYRUVATE CARBOXYKINASE / / ATP-OXALOACETATE CARBOXY-LYASE (ATP)


Mass: 59796.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ORDERED MAGNESIUM ION OBSERVED BOUND TO ATP / Source: (natural) Escherichia coli (E. coli) / Strain: K12
References: UniProt: P22259, phosphoenolpyruvate carboxykinase (ATP)
#2: Chemical ChemComp-OXL / OXALATE ION / Oxalate


Mass: 88.019 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2O4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 345 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 49 %
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 4.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 mg/mlPCK1drop
22 mMATP1drop
32 mMoxalate1drop
45 mM1dropMgCl2
51 mMEDTA1drop
6100 mMsodium acetate1drop
7200 mMammonium acetate1drop
812 %(w/v)PEG40001drop
9100 mMsodium acetate1reservoir
10200 mMammonium acetate1reservoir
1127 %(w/v)PEG40001reservoir

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1
DetectorType: FUJI / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionNum. obs: 40067 / % possible obs: 76.7 % / Observed criterion σ(I): 1 / Redundancy: 2.2 % / Rmerge(I) obs: 0.076
Reflection
*PLUS
Highest resolution: 1.8 Å

-
Processing

Software
NameClassification
X-PLORrefinement
WEISdata reduction
RefinementResolution: 1.8→6 Å / σ(F): 2
Details: MET 477 HAS DISALLOWED RAMACHANDRAN ANGLES; THE DEPOSITORS ACCOUNT FOR THIS AS IT IS THE SECOND RESIDUE WITHIN A GAMMA-TURN.
RfactorNum. reflection
Rfree0.234 -
Rwork0.195 -
obs0.195 35508
Displacement parametersBiso mean: 21.42 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4107 0 38 345 4490
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.23
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_deg24.4
X-RAY DIFFRACTIONx_improper_angle_deg1.1

+
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