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- PDB-5ow4: Crystal structure of a protease-resistant fragment of the Trypano... -

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Basic information

Entry
Database: PDB / ID: 5ow4
TitleCrystal structure of a protease-resistant fragment of the Trypanosoma cruzi gamete fusion protein HAP2 ectodomain
ComponentsUncharacterized protein
KeywordsMEMBRANE PROTEIN / Gamete fusion protein / class II fold / HAP2 / Membrane fusion
Function / homologyGenerative cell specific-1/HAP2 domain / Male gamete fusion factor / HAP2/GCS1 / single fertilization / lipid binding / plasma membrane / Generative cell specific-1/HAP2 domain-containing protein
Function and homology information
Biological speciesTrypanosoma cruzi strain CL Brener (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsFedry, J. / Rey, F.A. / Krey, T.
Funding support France, 1items
OrganizationGrant numberCountry
European Research Council340371 (CelCelFus) France
CitationJournal: PLoS Biol. / Year: 2018
Title: Evolutionary diversification of the HAP2 membrane insertion motifs to drive gamete fusion across eukaryotes.
Authors: Fedry, J. / Forcina, J. / Legrand, P. / Pehau-Arnaudet, G. / Haouz, A. / Johnson, M. / Rey, F.A. / Krey, T.
History
DepositionAug 30, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)64,5541
Polymers64,5541
Non-polymers00
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.090, 150.090, 123.780
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Uncharacterized protein


Mass: 64553.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi strain CL Brener (eukaryote)
Gene: Tc00.1047053509105.4 / Cell line (production host): Schneider 2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q4DKJ2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.12 Å3/Da / Density % sol: 60.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 100mM CHES pH9.0 200mM NaCl 10%w/v PEG 8K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 15453 / % possible obs: 97.7 % / Redundancy: 8.9 % / Biso Wilson estimate: 116.25 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.201 / Net I/σ(I): 11.4
Reflection shellResolution: 3.1→3.31 Å / Redundancy: 8.6 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2389 / CC1/2: 0.41 / Rrim(I) all: 2.493 / % possible all: 98.2

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MF1

5mf1


Resolution: 3.1→49.13 Å / Cor.coef. Fo:Fc: 0.8853 / Cor.coef. Fo:Fc free: 0.8521 / SU R Cruickshank DPI: 0.346 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.349 / SU Rfree Blow DPI: 0.277 / SU Rfree Cruickshank DPI: 0.278
RfactorNum. reflection% reflectionSelection details
Rfree0.26 780 5.06 %RANDOM
Rwork0.233 ---
obs0.2344 15430 99.95 %-
Displacement parametersBiso mean: 84.33 Å2
Baniso -1Baniso -2Baniso -3
1--2.6134 Å20 Å20 Å2
2---2.6134 Å20 Å2
3---5.2269 Å2
Refine analyzeLuzzati coordinate error obs: 0.659 Å
Refinement stepCycle: 1 / Resolution: 3.1→49.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1855 0 0 2 1857
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081903HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.992569HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d650SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes37HARMONIC2
X-RAY DIFFRACTIONt_gen_planes283HARMONIC5
X-RAY DIFFRACTIONt_it1903HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.65
X-RAY DIFFRACTIONt_other_torsion18.95
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion229SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2051SEMIHARMONIC4
LS refinement shellResolution: 3.1→3.31 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3092 144 5.3 %
Rwork0.2749 2574 -
all0.2767 2718 -
obs--99.95 %

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