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- PDB-7v67: Crystal Structure of Enolase1 from Candida albicans -

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Basic information

Entry
Database: PDB / ID: 7v67
TitleCrystal Structure of Enolase1 from Candida albicans
ComponentsEnolase 1
KeywordsMETAL BINDING PROTEIN / Enolase1 / Candida albicans
Function / homology
Function and homology information


high molecular weight kininogen binding / fungal-type cell wall organization or biogenesis / symbiont-mediated perturbation of host immune response / filamentous growth of a population of unicellular organisms in response to biotic stimulus / yeast-form cell wall / fungal biofilm matrix / hyphal cell wall / protein-glutamine gamma-glutamyltransferase activity / phosphopyruvate hydratase / phosphopyruvate hydratase complex ...high molecular weight kininogen binding / fungal-type cell wall organization or biogenesis / symbiont-mediated perturbation of host immune response / filamentous growth of a population of unicellular organisms in response to biotic stimulus / yeast-form cell wall / fungal biofilm matrix / hyphal cell wall / protein-glutamine gamma-glutamyltransferase activity / phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / fungal-type cell wall / symbiont entry into host / filamentous growth / fibrinolysis / gluconeogenesis / glycolytic process / extracellular vesicle / external side of plasma membrane / cell surface / magnesium ion binding / extracellular region / nucleus / membrane / plasma membrane / cytosol
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 speciesCandida albicans SC5314 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhang, M. / Zhang, X.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB37010105 China
CitationJournal: Microbiol Spectr / Year: 2022
Title: Baicalein Acts against Candida albicans by Targeting Eno1 and Inhibiting Glycolysis.
Authors: Li, L. / Lu, H. / Zhang, X. / Whiteway, M. / Wu, H. / Tan, S. / Zang, J. / Tian, S. / Zhen, C. / Meng, X. / Li, W. / Zhang, D. / Zhang, M. / Jiang, Y.
History
DepositionAug 19, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 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 1
B: Enolase 1
C: Enolase 1
D: Enolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,9459
Polymers192,4654
Non-polymers4805
Water7,170398
1
A: Enolase 1
B: Enolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,5215
Polymers96,2322
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-51 kcal/mol
Surface area29060 Å2
MethodPISA
2
C: Enolase 1
D: Enolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,4254
Polymers96,2322
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-39 kcal/mol
Surface area29400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)265.204, 62.183, 111.815
Angle α, β, γ (deg.)90.000, 109.920, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 48116.219 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans SC5314 (yeast) / Strain: SC5314 / Gene: ENO1 / Production host: Escherichia coli (E. coli) / References: UniProt: P30575, phosphopyruvate hydratase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / 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: 2.41 Å3/Da / Density % sol: 48.95 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Lithium sulfate monohydrate, 0.1 M BIS-TRIS pH 6.5, 25% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→33.114 Å / Num. obs: 116013 / % possible obs: 98.9 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.034 / Rpim(I) all: 0.034 / Rrim(I) all: 0.049 / Net I/σ(I): 12.79
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible allΧ2
2-2.0715.60.233115270.8530.330.23399.86
2.49-2.595.50.23465470.970.1060.25897.80.781
2.59-2.75.40.20866040.9680.0950.22998.10.979
2.7-2.855.30.16566310.9810.0780.18398.41.013
2.85-3.025.60.14466330.9850.0660.15998.91.043
3.02-3.265.40.12166780.9890.0560.13398.91.047
3.26-3.585.70.10267260.990.0470.11399.71.056
3.58-4.15.60.08567610.9930.0390.09499.71.064
4.1-5.175.40.07567990.9930.0360.08499.71.037
5.17-505.20.08469650.990.0410.09499.71.017

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AL2

2al2


Resolution: 2→33.114 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 23.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2179 5752 4.97 %
Rwork0.1768 110074 -
obs0.1789 115826 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.38 Å2 / Biso mean: 28.853 Å2 / Biso min: 12.92 Å2
Refinement stepCycle: final / Resolution: 2→33.114 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13156 0 25 398 13579
Biso mean--46.97 27.52 -
Num. residues----1745
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.02270.22381690.20763615100
2.0227-2.04650.27722180.20713613100
2.0465-2.07150.27911940.21563712100
2.0715-2.09770.23551950.20673622100
2.0977-2.12530.22941850.19043645100
2.1253-2.15440.2481710.1883673100
2.1544-2.18520.25461810.1783619100
2.1852-2.21780.22092210.18323683100
2.2178-2.25240.26871980.18623613100
2.2524-2.28940.23881820.19123707100
2.2894-2.32880.22261980.18213645100
2.3288-2.37120.22051870.18363663100
2.3712-2.41680.20882040.1853646100
2.4168-2.46610.2771920.18843643100
2.4661-2.51970.24771730.18833681100
2.5197-2.57830.22841820.19073672100
2.5783-2.64270.23341720.19223667100
2.6427-2.71410.24581960.19773683100
2.7141-2.7940.25192030.19563666100
2.794-2.88410.29511870.19873649100
2.8841-2.98710.21472000.20653673100
2.9871-3.10660.23632050.19953683100
3.1066-3.24790.23811940.20353669100
3.2479-3.4190.25871880.19793665100
3.419-3.63290.1962000.17813718100
3.6329-3.9130.20621970.15793676100
3.913-4.3060.18581860.14483705100
4.306-4.92740.15162000.13223720100
4.9274-6.20130.19851940.15873762100
6.2013-33.1140.15241800.145368696
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.70280.0040.05540.9139-0.30.70850.01670.0810.00440.06030.01390-0.0441-0.0163-0.02850.1837-0.00340.00460.1653-0.00730.169-20.081-48.142311.9957
20.8982-0.1495-0.48710.33580.10780.54870.01940.26880.0182-0.0266-0.0030.0745-0.0527-0.2146-0.01540.1690.0239-0.00840.2810.03280.1684-52.4026-45.090612.0562
30.4841-0.11720.2490.7302-0.14540.58080.02730.0185-0.00330.06140.0035-0.001-0.02210.032-0.03250.1669-0.00390.01610.1403-0.00360.1836-39.0087-17.132164.7447
40.6927-0.1534-0.20650.40440.2390.78740.0256-0.0419-0.0013-0.0028-0.03920.0674-0.0475-0.16460.01330.15670.0155-0.00830.19730.01730.1884-71.41-14.039562.9864
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 2 through 440)A2 - 440
2X-RAY DIFFRACTION2(chain 'B' and resid 3 through 440)B3 - 440
3X-RAY DIFFRACTION3(chain 'C' and resid 2 through 440)C2 - 440
4X-RAY DIFFRACTION4(chain 'D' and resid 2 through 440)D2 - 440

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