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- PDB-7rhv: Aspergillus fumigatus Enolase -

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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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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 / Water


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

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Experimental details

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Experiment

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

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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

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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

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Phasing

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

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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

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