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- PDB-7vrd: Crystal structure of Enolase1 from Candida albicans complexed wit... -

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Basic information

Entry
Database: PDB / ID: 7vrd
TitleCrystal structure of Enolase1 from Candida albicans complexed with 2'-phosphoglyceric acid sodium
ComponentsEnolase 1Alpha-enolase
KeywordsMETAL BINDING PROTEIN
Function / homology
Function and homology information


fungal-type cell wall organization or biogenesis / high molecular weight kininogen binding / 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 ...fungal-type cell wall organization or biogenesis / high molecular weight kininogen binding / 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 / magnesium ion binding / cell surface / extracellular region / membrane / nucleus / 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
2-PHOSPHOGLYCERIC ACID / Enolase 1
Similarity search - Component
Biological speciesCandida albicans SC5314 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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
DepositionOct 22, 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

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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)189,14312
Polymers188,6254
Non-polymers5188
Water21,7081205
1
A: Enolase 1
B: Enolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,5716
Polymers94,3122
Non-polymers2594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-39 kcal/mol
Surface area29420 Å2
MethodPISA
2
C: Enolase 1
D: Enolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,5716
Polymers94,3122
Non-polymers2594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-39 kcal/mol
Surface area29610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)264.264, 61.848, 111.752
Angle α, β, γ (deg.)90.000, 109.800, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 47156.156 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-2PG / 2-PHOSPHOGLYCERIC ACID / 2-Phosphoglyceric acid


Mass: 186.057 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7O7P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1205 / 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: 2.39 Å3/Da / Density % sol: 48.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Magnesium acetate tetrahydrate, 0.1 M Sodium cacodylate trihydrate pH 6.5, 20% w/v Polyethlene glycol 8,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 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: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 185469 / % possible obs: 99.6 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.029 / Rrim(I) all: 0.075 / Χ2: 0.738 / Net I/σ(I): 7.7 / Num. measured all: 1237061
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.7-1.766.90.5183060.9210.2030.5410.46598.9
1.76-1.836.80.378183910.9580.1550.4090.49199.1
1.83-1.916.60.275183550.9480.1150.2980.59299.3
1.91-2.026.50.188184140.9850.0790.2040.57499.4
2.02-2.146.70.142184610.9660.0590.1540.73199.6
2.14-2.316.60.102185350.9930.0430.1110.79599.8
2.31-2.546.90.076185810.9970.0310.0820.75299.9
2.54-2.916.50.059186700.9980.0250.0640.904100
2.91-3.666.70.045187590.9990.0190.0481.046100
3.66-506.50.034189970.9990.0140.0371.03299.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AL2

2al2


Resolution: 1.7→38.06 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.781 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1966 9219 5 %RANDOM
Rwork0.172 ---
obs0.1732 176250 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 58.37 Å2 / Biso mean: 18.906 Å2 / Biso min: 7.74 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.7→38.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13278 0 28 1205 14511
Biso mean--12.88 26.22 -
Num. residues----1752
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01913541
X-RAY DIFFRACTIONr_bond_other_d0.0060.0213092
X-RAY DIFFRACTIONr_angle_refined_deg1.2121.96818331
X-RAY DIFFRACTIONr_angle_other_deg0.784330229
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.85451747
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.98725.461564
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.258152326
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8131548
X-RAY DIFFRACTIONr_chiral_restr0.0710.22066
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02115445
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022867
LS refinement shellResolution: 1.701→1.746 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 659 -
Rwork0.22 12675 -
all-13334 -
obs--97.01 %

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