[English] 日本語
Yorodumi
- PDB-1s2u: Crystal structure of the D58A phosphoenolpyruvate mutase mutant p... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1s2u
TitleCrystal structure of the D58A phosphoenolpyruvate mutase mutant protein
ComponentsPhosphoenolpyruvate phosphomutase
KeywordsISOMERASE / phosphoenolpyruvate mutase / PEP mutase / phosphonopyruvate / phosphonate biosynthesis pathway
Function / homology
Function and homology information


phosphoenolpyruvate mutase / phosphoenolpyruvate mutase activity / organic phosphonate biosynthetic process / metal ion binding
Similarity search - Function
Phosphoenolpyruvate phosphomutase, core / Phosphoenolpyruvate phosphomutase / ICL/PEPM domain / Phosphoenolpyruvate-binding domains / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Phosphoenolpyruvate phosphomutase
Similarity search - Component
Biological speciesMytilus edulis (blue mussel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLiu, S. / Lu, Z. / Han, Y. / Jia, Y. / Howard, A. / Dunaway-Mariano, D. / Herzberg, O.
CitationJournal: Biochemistry / Year: 2004
Title: Conformational Flexibility of PEP Mutase
Authors: Liu, S. / Lu, Z. / Han, Y. / Jia, Y. / Howard, A. / Dunaway-Mariano, D. / Herzberg, O.
History
DepositionJan 11, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 27, 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 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999SEQUENCE THE AUTHORS INFORMED THAT THEIR SEQUENCE IS CORRECT AT THE POSITIONS WHERE IT CONFLICTS ...SEQUENCE THE AUTHORS INFORMED THAT THEIR SEQUENCE IS CORRECT AT THE POSITIONS WHERE IT CONFLICTS WITH THE SWISS PROT SEQUENCE.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphoenolpyruvate phosphomutase
B: Phosphoenolpyruvate phosphomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,0334
Polymers65,8212
Non-polymers2122
Water10,233568
1
A: Phosphoenolpyruvate phosphomutase
B: Phosphoenolpyruvate phosphomutase
hetero molecules

A: Phosphoenolpyruvate phosphomutase
B: Phosphoenolpyruvate phosphomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,0668
Polymers131,6414
Non-polymers4244
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area22810 Å2
ΔGint-76 kcal/mol
Surface area39120 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)108.537, 119.746, 88.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Detailsbiological assembly is a tetramer which can be generated from the dimer by the operation: -x+1, y, -z+1/2

-
Components

#1: Protein Phosphoenolpyruvate phosphomutase / Phosphoenolpyruvate mutase / PEP mutase / PEP phosphomutase


Mass: 32910.336 Da / Num. of mol.: 2 / Mutation: D58A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mytilus edulis (blue mussel) / Plasmid: PET3C / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P56839, phosphoenolpyruvate mutase
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 568 / 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: 2.18 Å3/Da / Density % sol: 43.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: PEG 4000, Glycerol, HEPES, MgCl2, pH 7.0-8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationMonochromator: Si(111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 36902 / % possible obs: 94.1 % / Observed criterion σ(I): 1 / Redundancy: 5.48 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 10.4
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.299 / % possible all: 84.5

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1pym

1pym


Resolution: 2→27.7 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.219 3317 -random
Rwork0.165 ---
obs0.171 33155 84.6 %-
all-39213 --
Refinement stepCycle: LAST / Resolution: 2→27.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4533 0 14 568 5115
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4

+
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