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- PDB-7rhw: Aspergillus fumigatus Enolase Bound to 2-Phosphoglycerate -

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Basic information

Entry
Database: PDB / ID: 7rhw
TitleAspergillus fumigatus Enolase Bound to 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 / Enolase
Similarity search - Component
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 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)97,4966
Polymers97,0752
Non-polymers4214
Water10,377576
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, Native mass spectrometry experiments show the presence of enolase as a dimeric species.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-30 kcal/mol
Surface area27460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.379, 83.290, 84.161
Angle α, β, γ (deg.)90.000, 97.450, 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-2PG / 2-PHOSPHOGLYCERIC ACID


Mass: 186.057 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7O7P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 576 / 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: 2.41 Å3/Da / Density % sol: 49.01 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: 23% PEG 3350, 0.1 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: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.9→42.32 Å / Num. obs: 72696 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.032 / Rrim(I) all: 0.083 / Net I/σ(I): 13.5 / Num. measured all: 490423 / Scaling rejects: 118
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
1.9-1.9470.8543141245040.7290.3470.9232.2100
9.31-42.326.90.02244866500.9990.0090.02452.698.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.87 Å41.73 Å

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Processing

Software
NameVersionClassification
PHENIX1.16-3549refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7RHV

7rhv


Resolution: 1.9→41.725 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2272 3714 5.11 %
Rwork0.1897 68907 -
obs0.1916 72621 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.97 Å2 / Biso mean: 39.3865 Å2 / Biso min: 24.39 Å2
Refinement stepCycle: final / Resolution: 1.9→41.725 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6433 0 24 576 7033
Biso mean--38.04 44.34 -
Num. residues----863
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.9-1.92410.55581220.46062587
1.9241-1.94940.41951410.36662515
1.9494-1.97610.36981410.31112555
1.9761-2.00430.29311340.27432547
2.0043-2.03420.29541150.272546
2.0342-2.0660.32841370.25372540
2.066-2.09990.27791340.24042565
2.0999-2.13610.28591330.22342544
2.1361-2.17490.24811490.22982530
2.1749-2.21680.28451400.23512521
2.2168-2.2620.33731380.29582531
2.262-2.31120.26641420.20262545
2.3112-2.36490.2371690.19752524
2.3649-2.42410.21651600.18282514
2.4241-2.48960.2331250.19562580
2.4896-2.56290.27791300.1972535
2.5629-2.64560.2321360.19112536
2.6456-2.74010.25451240.18782575
2.7401-2.84980.22761270.18832559
2.8498-2.97950.19081180.18132584
2.9795-3.13650.20391450.18742523
3.1365-3.33290.22031460.17872555
3.3329-3.59010.20181410.18622556
3.5901-3.95120.21471470.16292560
3.9512-4.52230.18121460.14822549
4.5223-5.69540.18521380.14682593
5.6954-41.7250.17741360.15572638

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