[English] 日本語
Yorodumi
- PDB-7n3s: Human bisphosphoglycerate mutase complex with 2-phosphoglycolate -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7n3s
TitleHuman bisphosphoglycerate mutase complex with 2-phosphoglycolate
ComponentsBisphosphoglycerate mutase
KeywordsISOMERASE / BPGM / Bisphosphoglycerate mutase / 2 / 3-bisphosphoglycerate phosphatase / 2-phosphoglycolate / activation / erythrocyte
Function / homology
Function and homology information


carbohydrate derivative catabolic process / bisphosphoglycerate mutase / bisphosphoglycerate mutase activity / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / phosphoglycerate mutase activity / neuroinflammatory response / respiratory gaseous exchange by respiratory system / establishment of blood-brain barrier / Glycolysis / defense response to protozoan ...carbohydrate derivative catabolic process / bisphosphoglycerate mutase / bisphosphoglycerate mutase activity / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / phosphoglycerate mutase activity / neuroinflammatory response / respiratory gaseous exchange by respiratory system / establishment of blood-brain barrier / Glycolysis / defense response to protozoan / cellular response to stress / erythrocyte development / oxygen transport / glycolytic process / carbohydrate metabolic process / hydrolase activity / extracellular exosome / cytosol
Similarity search - Function
Phosphoglycerate mutase 1 / Phosphoglycerate/bisphosphoglycerate mutase, active site / Phosphoglycerate mutase family phosphohistidine signature. / Phosphoglycerate mutase family / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Histidine phosphatase superfamily
Similarity search - Domain/homology
2-PHOSPHOGLYCOLIC ACID / Bisphosphoglycerate mutase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsAljahdali, A.S. / Musayev, F.N. / Safo, M.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Minority Health and Health Disparities (NIH/NIMHD)R01MD009124 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Molecular insight into 2-phosphoglycolate activation of the phosphatase activity of bisphosphoglycerate mutase.
Authors: Aljahdali, A.S. / Musayev, F.N. / Burgner 2nd, J.W. / Ghatge, M.S. / Shekar, V. / Zhang, Y. / Omar, A.M. / Safo, M.K.
History
DepositionJun 1, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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: Bisphosphoglycerate mutase
B: Bisphosphoglycerate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7055
Polymers62,2372
Non-polymers4683
Water2,126118
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.643, 70.808, 158.933
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Bisphosphoglycerate mutase / BPGM / 2 / 3-bisphosphoglycerate mutase / erythrocyte / 3-bisphosphoglycerate synthase / 3- ...BPGM / 2 / 3-bisphosphoglycerate mutase / erythrocyte / 3-bisphosphoglycerate synthase / 3-diphosphoglycerate mutase / DPGM / BPG-dependent PGAM


Mass: 31118.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BPGM / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL
References: UniProt: P07738, bisphosphoglycerate mutase, phosphoglycerate mutase (2,3-diphosphoglycerate-dependent)
#2: Chemical ChemComp-PGA / 2-PHOSPHOGLYCOLIC ACID


Mass: 156.031 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H5O6P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density meas: 49.3 Mg/m3 / Density % sol: 48.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1 M BIS TRIS propane, 18% polyethylene glycol 8000, 10% polyethylene glycol 200

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54056 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Mar 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54056 Å / Relative weight: 1
ReflectionResolution: 2.48→29 Å / Num. obs: 21810 / % possible obs: 99.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 45.78 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.047 / Rrim(I) all: 0.12 / Net I/σ(I): 9.7 / Num. measured all: 140609 / Scaling rejects: 69
Reflection shellResolution: 2.48→2.58 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.71 / Num. unique obs: 2412 / CC1/2: 0.881 / Rpim(I) all: 0.3 / Rrim(I) all: 0.772 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.27data extraction
CrysalisPro41_64_69adata reduction
PHENIX1.9-1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2H4Z

2h4z


Resolution: 2.48→28.999 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2843 1093 5.03 %
Rwork0.2098 20627 -
obs0.2135 21720 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.97 Å2 / Biso mean: 53.1307 Å2 / Biso min: 23.15 Å2
Refinement stepCycle: final / Resolution: 2.48→28.999 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4056 0 27 118 4201
Biso mean--60.95 47.25 -
Num. residues----497
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.4801-2.59290.36911350.25552527
2.5929-2.72950.32791520.25732514
2.7295-2.90040.38051270.26422531
2.9004-3.12410.32341440.25632551
3.1241-3.4380.34071310.23632560
3.438-3.93440.26861310.2072595
3.9344-4.9530.21511360.17062602
4.953-28.9990.26591370.18682747

+
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