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- PDB-7ri0: Aspergillus fumigatus Enolase Bound to Phosphoenolpyruvate and 2-... -

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Basic information

Entry
Database: PDB / ID: 7ri0
TitleAspergillus fumigatus Enolase Bound to Phosphoenolpyruvate and 2-Phosphoglycerate
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
2-PHOSPHOGLYCERIC ACID / PHOSPHOENOLPYRUVATE / Enolase
Similarity search - Component
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 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

Downloads & links

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Assembly

Deposited unit
A: Enolase
B: Enolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,5027
Polymers97,0752
Non-polymers4275
Water13,781765
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, Native mass spectrometry shows the presence of a dimeric species
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-39 kcal/mol
Surface area27920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.858, 84.154, 84.909
Angle α, β, γ (deg.)90.000, 98.040, 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.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-2PG / 2-PHOSPHOGLYCERIC ACID


Mass: 186.057 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H7O7P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEP / PHOSPHOENOLPYRUVATE


Mass: 168.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5O6P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 765 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.47 Å3/Da / Density % sol: 50.26 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 21% PEG 3350, 0.05 M Bis-Tris

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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: 2.3→46.9 Å / Num. obs: 42138 / % possible obs: 99.9 % / Redundancy: 7.2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.044 / Rrim(I) all: 0.118 / Net I/σ(I): 13.3 / Num. measured all: 302573 / Scaling rejects: 64
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
2.3-2.387.30.3422999640900.9650.1360.3684.799.9
8.91-46.96.90.06352437640.9960.0260.06923.599.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7.09 Å46.9 Å

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Processing

Software
NameVersionClassification
PHENIX1.16-3549refinement
Aimless0.5.25data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.25data extraction
XDS20190315data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7RHV

7rhv


Resolution: 2.3→42.497 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.255 2066 4.92 %
Rwork0.2079 39967 -
obs0.2103 42033 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.27 Å2 / Biso mean: 24.1257 Å2 / Biso min: 7.26 Å2
Refinement stepCycle: final / Resolution: 2.3→42.497 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6406 0 24 765 7195
Biso mean--26.23 30.81 -
Num. residues----861
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3-2.35350.4011230.3093263898
2.3535-2.41240.35971420.25032629100
2.4124-2.47760.36311090.24422660100
2.4776-2.55050.35911370.273263999
2.5505-2.63280.28051470.23592670100
2.6328-2.72690.27271450.22232643100
2.7269-2.8360.30881600.22092650100
2.836-2.96510.26151330.2132662100
2.9651-3.12140.25681280.20542668100
3.1214-3.31690.26761520.21662644100
3.3169-3.57280.23241260.20542689100
3.5728-3.93220.23641360.19582650100
3.9322-4.50060.19461380.16832695100
4.5006-5.66820.18331520.16312701100
5.6682-42.4970.21321380.18742729100

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