[English] 日本語
Yorodumi
- PDB-11ko: Structure of Escherichia coli phosphoenolpyruvate carboxykinase w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 11ko
TitleStructure of Escherichia coli phosphoenolpyruvate carboxykinase with bound ATP, Mg2+, and Mn2+
ComponentsPhosphoenolpyruvate carboxykinase (ATP)
KeywordsLYASE / PEPCK / PCKA / adenyl nucleotide binding
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, ATP-utilising / Phosphoenolpyruvate carboxykinase (ATP), conserved site / Phosphoenolpyruvate carboxykinase / Phosphoenolpyruvate carboxykinase (ATP) signature. / Phosphoenolpyruvate carboxykinase, C-terminal / Phosphoenolpyruvate carboxykinase, N-terminal
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / : / Phosphoenolpyruvate carboxykinase (ATP)
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsLecomte, J.T.J. / Schlessman, J.L. / Schultz, T.D. / Siegler, M.A. / Johnson, E.A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of Escherichia coli phosphoenolpyruvate carboxykinase with bound ATP, Mg2+, and Mn2+
Authors: Johnson, E.A. / Lecomte, J.T.J. / Schlessman, J.L. / Schultz, T.D. / Siegler, M.A.
History
DepositionMar 2, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphoenolpyruvate carboxykinase (ATP)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3745
Polymers59,7321
Non-polymers6414
Water6,107339
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)125.170, 95.680, 46.560
Angle α, β, γ (deg.)90.000, 95.800, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-734-

HOH

21A-884-

HOH

31A-926-

HOH

41A-1004-

HOH

51A-1025-

HOH

-
Components

#1: Protein Phosphoenolpyruvate carboxykinase (ATP) / PCK / PEP carboxykinase / PEPCK


Mass: 59732.152 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: initial M replaced with GP / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: pckA, pck, b3403, JW3366 / Production host: Escherichia coli (E. coli)
References: UniProt: P22259, phosphoenolpyruvate carboxykinase (ATP)
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 4 ul drop with 4 mg/mL protein, 1 mM ADP, 1 mM phosphoenol pyruvate, 2.5 mM MgCl2, 2.5 mM MnCl2, 1 mM EDTA, 100 mM sodium acetate (pH 4.5), 200 mM ammonium acetate and 12% PEG 4000 was ...Details: 4 ul drop with 4 mg/mL protein, 1 mM ADP, 1 mM phosphoenol pyruvate, 2.5 mM MgCl2, 2.5 mM MnCl2, 1 mM EDTA, 100 mM sodium acetate (pH 4.5), 200 mM ammonium acetate and 12% PEG 4000 was allowed to equilibrate with a 1 mL reservoir of 100 mM sodium acetate, 200 mM ammonium acetate and 31% PEG 4000
Temp details: room temperature

-
Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU PhotonJet-R / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jul 25, 2025
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.58→21.97 Å / Num. obs: 74588 / % possible obs: 99.8 % / Redundancy: 10.8 % / Biso Wilson estimate: 10.99 Å2 / Rmerge(I) obs: 0.023 / Rsym value: 0.057 / Net I/σ(I): 37.2
Reflection shellResolution: 1.58→1.64 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.148 / Mean I/σ(I) obs: 6.71 / Num. unique obs: 7466 / Rsym value: 0.249 / % possible all: 99.2

-
Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
CrysalisPro1.171.43.144adata reduction
CrysalisPro1.171.43.144adata scaling
PHENIX1.21.2_5419phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.58→21.95 Å / SU ML: 0.1372 / Cross valid method: FREE R-VALUE / σ(F): 0.1 / Phase error: 17.3495
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1853 1961 2.69 %
Rwork0.1659 71039 -
obs0.1665 73000 97.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.77 Å2
Refinement stepCycle: LAST / Resolution: 1.58→21.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4129 0 34 339 4502
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00574372
X-RAY DIFFRACTIONf_angle_d0.83825969
X-RAY DIFFRACTIONf_chiral_restr0.0552653
X-RAY DIFFRACTIONf_plane_restr0.0073779
X-RAY DIFFRACTIONf_dihedral_angle_d14.86171646
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.620.20951380.15634875X-RAY DIFFRACTION94.78
1.62-1.660.17331390.15225073X-RAY DIFFRACTION96.88
1.66-1.710.17931400.14445026X-RAY DIFFRACTION97.4
1.71-1.770.16741360.1525011X-RAY DIFFRACTION97.35
1.77-1.830.20631380.15945072X-RAY DIFFRACTION97.8
1.83-1.90.21781390.17624845X-RAY DIFFRACTION93.79
1.9-1.990.1951420.17315102X-RAY DIFFRACTION98.28
1.99-2.090.18091410.17615056X-RAY DIFFRACTION97.4
2.09-2.220.19191350.17555071X-RAY DIFFRACTION97.53
2.22-2.40.22071420.17685075X-RAY DIFFRACTION97.73
2.4-2.640.18181420.17865161X-RAY DIFFRACTION99.51
2.64-3.020.19951430.18635197X-RAY DIFFRACTION99.61
3.02-3.80.17811410.17155217X-RAY DIFFRACTION99.8
3.8-21.950.15521450.13715258X-RAY DIFFRACTION99.56
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6607543556660.05357180776290.1222313543220.5998174304830.2281834706390.944045992578-0.0286290194067-0.0159577336759-0.0389096524738-0.007667526473840.0295551678236-0.06484841122530.03770264758860.116750713246-0.002293637888230.05946423461690.01252667674570.00897908808830.0763249188680.01165885455540.070824173072947.3032626881-8.080046457656.92356104754
20.929777611035-0.1850289568390.2319515683110.541072156884-0.07223785675110.675927427233-0.02271048757920.005689251744090.0519454440948-0.008068684716030.005963407505390.0868969596117-0.0759258418852-0.06687023390750.004638918807690.08059843368820.003002623353180.006568339687870.06960578474070.003162532290730.07865199532422.40240153113.7344659687410.8949038129
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 11 through 207 )11 - 2071 - 197
22chain 'A' and (resid 208 through 540 )208 - 540198 - 530

+
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