[English] 日本語
Yorodumi
- PDB-2r82: Pyruvate phosphate dikinase (PPDK) triple mutant R219E/E271R/S262... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2r82
TitlePyruvate phosphate dikinase (PPDK) triple mutant R219E/E271R/S262D adapts a second conformational state
ComponentsPyruvate, phosphate dikinase
KeywordsTRANSFERASE / phosphotransferase / conformational transition / swiveling domain / remote active sites / ATP-binding / Kinase / Magnesium / Metal-binding / Nucleotide-binding / Phosphorylation
Function / homology
Function and homology information


pyruvate, phosphate dikinase / pyruvate, phosphate dikinase activity / pyruvate metabolic process / kinase activity / phosphorylation / ATP binding / metal ion binding
Similarity search - Function
Pyruvate Phosphate di-kinase; domain 2 / Pyruvate Phosphate Dikinase, domain 2 / Acyl-CoA Binding Protein - #30 / Pyruvate, phosphate dikinase / Pyruvate phosphate dikinase, AMP/ATP-binding / Pyruvate phosphate dikinase, AMP/ATP-binding domain / Phosphohistidine domain / PEP-utilising enzyme, active site / PEP-utilizing enzymes phosphorylation site signature. / PEP-utilising enzyme, conserved site ...Pyruvate Phosphate di-kinase; domain 2 / Pyruvate Phosphate Dikinase, domain 2 / Acyl-CoA Binding Protein - #30 / Pyruvate, phosphate dikinase / Pyruvate phosphate dikinase, AMP/ATP-binding / Pyruvate phosphate dikinase, AMP/ATP-binding domain / Phosphohistidine domain / PEP-utilising enzyme, active site / PEP-utilizing enzymes phosphorylation site signature. / PEP-utilising enzyme, conserved site / PEP-utilizing enzymes signature 2. / PEP-utilising enzyme, C-terminal / PEP-utilising enzyme, PEP-binding domain / PEP-utilising enzyme, mobile domain / Phosphohistidine domain superfamily / PEP-utilising enzyme, mobile domain / Acyl-CoA Binding Protein / Phosphoenolpyruvate-binding domains / Glucose Oxidase; domain 1 / ATP-grasp fold, A domain / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / 3-Layer(bba) Sandwich / TIM Barrel / Alpha-Beta Barrel / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Pyruvate, phosphate dikinase
Similarity search - Component
Biological speciesClostridium symbiosum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsLim, K. / Read, R.J. / Chen, C.C. / Herzberg, O.
Citation
Journal: Biochemistry / Year: 2007
Title: Swiveling domain mechanism in pyruvate phosphate dikinase.
Authors: Lim, K. / Read, R.J. / Chen, C.C. / Tempczyk, A. / Wei, M. / Ye, D. / Wu, C. / Dunaway-Mariano, D. / Herzberg, O.
#1: Journal: Biochemistry / Year: 2002
Title: Pyruvate site of pyruvate phosphate dikinase: crystal structure of the enzyme-phosphonopyruvate complex, and mutant analysis
Authors: Herzberg, O. / Chen, C. / Liu, S. / Tempczyk, A. / Howard, A. / Wei, M. / Ye, D. / Dunaway-Mariano, D.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1996
Title: Swiveling-domain mechanism for enzymatic phosphotransfer between remote reaction sites
Authors: Herzberg, O. / Chen, C. / Kapadia, G. / Mcguire, M. / Carroll, L.J. / Noh, S.J. / Dunaway-Mariano, D.
#3: Journal: Biochemistry / Year: 1998
Title: Location of the phosphate binding site within Clostridium Symbiosum pyruvate phosphate dikinase
Authors: Mcguire, M. / Huang, K. / Kapadia, G. / Herzberg, O. / Dunaway-Mariano, D.
#4: Journal: J.Biol.Chem. / Year: 2000
Title: Identification of the domain-domain docking sites within Clostridium Symbiosum pyruvate phosphate dikinase by amino acid replacement
Authors: Wei, M. / Li, Z. / Ye, D. / Herzberg, O. / Dunaway-Mariano, D.
History
DepositionSep 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Aug 14, 2019Group: Data collection / Category: computing
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pyruvate, phosphate dikinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,9913
Polymers96,7991
Non-polymers1922
Water0
1
A: Pyruvate, phosphate dikinase
hetero molecules

A: Pyruvate, phosphate dikinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,9836
Polymers193,5992
Non-polymers3844
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area4950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.352, 125.096, 183.978
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Pyruvate, phosphate dikinase / / Pyruvate / orthophosphate dikinase


Mass: 96799.359 Da / Num. of mol.: 1 / Mutation: R219E, S262D, E271R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium symbiosum (bacteria) / Gene: ppdK / Plasmid: pACYC184 D12 / Production host: Escherichia coli (E. coli) / Strain (production host): JM101 / References: UniProt: P22983, pyruvate, phosphate dikinase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.19 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 50% saturated ammonium sulfate, 0.1 M Na Hepes, 28 mg/ml protein (in 20 mM imidazole (pH 6.5), 0.1 mM EDTA, 100 mM KCl, and 1mM DTT), pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 303K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE
RadiationMonochromator: Harvard mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. all: 11406 / Num. obs: 11406 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.155 / Net I/σ(I): 6.1
Reflection shellResolution: 3.6→3.76 Å / Redundancy: 2 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 2.5 / % possible all: 76.5

-
Processing

Software
NameClassification
REFMACrefinement
PHASERphasing
CNSrefinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1KBL

1kbl


Resolution: 3.6→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.325 982 -random
Rwork0.265 ---
all-11339 --
obs-11339 91.2 %-
Displacement parametersBiso mean: 68 Å2
Refinement stepCycle: LAST / Resolution: 3.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6754 0 10 0 6764
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.01
X-RAY DIFFRACTIONr_angle_refined_deg1.2
LS refinement shellResolution: 3.6→3.76 Å / Rfactor Rfree: 0.38 / Rfactor Rwork: 0.35

+
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