[English] 日本語
Yorodumi
- PDB-7rhv: Aspergillus fumigatus Enolase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7rhv
TitleAspergillus fumigatus Enolase
ComponentsEnolase
KeywordsLYASE / glycolysis
Function / homology
Function and homology information


phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / IgE binding / glycolytic process / magnesium ion binding
Similarity search - Function
Enolase / Enolase, conserved site / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Enolase signature. / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily
Similarity search - Domain/homology
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsNguyen, S. / Bruning, J.B.
CitationJournal: Proteins / Year: 2022
Title: A structural model of the human plasminogen and Aspergillus fumigatus enolase complex.
Authors: Nguyen, S. / Jovcevski, B. / Truong, J.Q. / Pukala, T.L. / Bruning, J.B.
History
DepositionJul 19, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 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: Enolase
B: Enolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,1244
Polymers97,0752
Non-polymers492
Water20,6451146
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, Native mass spectrometry confirms the presence of a dimeric species
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-25 kcal/mol
Surface area29280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.174, 83.969, 84.661
Angle α, β, γ (deg.)90.000, 97.560, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Enolase / 2-phospho-D-glycerate hydro-lyase / 2-phosphoglycerate dehydratase


Mass: 48537.484 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) (mold)
Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: enoA, AFUA_6G06770 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q96X30, phosphopyruvate hydratase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1146 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.55 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: 23% PEG 3350, 0.15 M Bis-Tris pH 5.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Sep 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2→42.393 Å / Num. obs: 63071 / % possible obs: 100 % / Redundancy: 7.2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.051 / Rrim(I) all: 0.138 / Net I/σ(I): 9.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.057.30.4123208144140.9570.1630.4443.4100
9.17-42.396.90.0747436910.9950.0290.07619.198.8

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.75 Å42.39 Å
Translation4.75 Å42.39 Å

-
Processing

Software
NameVersionClassification
PHENIX1.16-3549refinement
Aimless0.7.2data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.25data extraction
XDS20190315data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ONE

1one


Resolution: 2→42.39 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2136 3162 5.02 %
Rwork0.1603 59881 -
obs0.1629 63043 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.46 Å2 / Biso mean: 26.1137 Å2 / Biso min: 9.23 Å2
Refinement stepCycle: final / Resolution: 2→42.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6472 0 2 1146 7620
Biso mean--18.99 36.44 -
Num. residues----859
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2-2.02990.25841410.19712591
2.0299-2.06160.26741530.19152575
2.0616-2.09540.24781520.18622570
2.0954-2.13150.25431440.18542545
2.1315-2.17030.23721360.18092623
2.1703-2.2120.22971320.1872588
2.212-2.25720.24151180.17332615
2.2572-2.30620.24591320.1762597
2.3062-2.35990.26581320.17962590
2.3599-2.41890.27491250.18472618
2.4189-2.48430.25551370.18222612
2.4843-2.55740.26651310.17882583
2.5574-2.63990.23231300.172599
2.6399-2.73430.20111490.16572604
2.7343-2.84370.22991530.17232583
2.8437-2.97310.20861390.1642591
2.9731-3.12980.21541440.16062591
3.1298-3.32580.21131410.15532596
3.3258-3.58250.18121510.14972622
3.5825-3.94280.18671360.12952617
3.9428-4.51270.16481290.12832635
4.5127-5.68340.16941360.13892644
5.6834-42.390.19851210.16132692

+
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