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- PDB-8zlf: Crystal structure of DH domain of FYVE Domain containing protein(... -

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Basic information

Entry
Database: PDB / ID: 8zlf
TitleCrystal structure of DH domain of FYVE Domain containing protein(FP10) from Entamoeba histolytica
ComponentsRho/RAC guanine nucleotide exchange factor, putative
KeywordsSIGNALING PROTEIN / DH domain / GTPase Activator / cytoskeleton Modulator
Function / homology
Function and homology information


guanyl-nucleotide exchange factor activity / cytoskeleton / intracellular signal transduction / zinc ion binding / cytoplasm
Similarity search - Function
: / FYVE zinc finger / FYVE zinc finger / Protein present in Fab1, YOTB, Vac1, and EEA1 / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Dbl homology (DH) domain superfamily / RhoGEF domain ...: / FYVE zinc finger / FYVE zinc finger / Protein present in Fab1, YOTB, Vac1, and EEA1 / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Zinc finger, FYVE/PHD-type / PH-like domain superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
CITRIC ACID / Rho/RAC guanine nucleotide exchange factor, putative
Similarity search - Component
Biological speciesEntamoeba histolytica HM-1:IMSS-A (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsGautam, A.K. / Umarao, P. / Gourinath, S.
Funding support India, 1items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB) India
CitationJournal: To Be Published
Title: crystal structure of DH domain of FYVE domain containing Protein(FP10) from Entamoeba histolytica
Authors: Gautam, A.K. / Umarao, P. / Gourinath, S.
History
DepositionMay 19, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 21, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rho/RAC guanine nucleotide exchange factor, putative
B: Rho/RAC guanine nucleotide exchange factor, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6223
Polymers48,4302
Non-polymers1921
Water1,40578
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.590, 69.337, 57.615
Angle α, β, γ (deg.)90.000, 118.275, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: GLU / End label comp-ID: GLU / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 1 - 192 / Label seq-ID: 1 - 192

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Rho/RAC guanine nucleotide exchange factor, putative


Mass: 24215.014 Da / Num. of mol.: 2
Fragment: DH domain of FYVE domain containing GEF(FP10) protein
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica HM-1:IMSS-A (eukaryote)
Gene: EHI7A_047060 / Production host: Escherichia coli (E. coli) / References: UniProt: N9UU15
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.12 Å3/Da / Density % sol: 41.9 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 1.5M Sodium Citrate tribasic dihydrate, 0.1M Sodium Citrate pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 2.48→50.741 Å / Num. obs: 16337 / % possible obs: 90.4 % / Redundancy: 7.1 % / CC1/2: 0.99 / Net I/σ(I): 2.6
Reflection shellResolution: 2.48→5.544 Å / Num. unique obs: 1780 / CC1/2: 0.93

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
autoPROCdata reduction
autoPROCdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.48→50.741 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.923 / SU B: 13.149 / SU ML: 0.283 / Cross valid method: FREE R-VALUE / ESU R Free: 0.386
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2893 697 5.493 %
Rwork0.2339 11993 -
all0.237 --
obs-12690 90.404 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 39.861 Å2
Baniso -1Baniso -2Baniso -3
1--4.04 Å20 Å2-1.922 Å2
2--6.717 Å2-0 Å2
3----0.386 Å2
Refinement stepCycle: LAST / Resolution: 2.48→50.741 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3037 0 13 78 3128
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0123100
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162937
X-RAY DIFFRACTIONr_angle_refined_deg1.4231.6394203
X-RAY DIFFRACTIONr_angle_other_deg0.4861.5666727
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.445394
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.925515
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.10210523
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.33110126
X-RAY DIFFRACTIONr_chiral_restr0.0670.2500
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023575
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02673
X-RAY DIFFRACTIONr_nbd_refined0.2470.2898
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2070.22937
X-RAY DIFFRACTIONr_nbtor_refined0.1910.21584
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21796
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2102
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.020.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2890.212
X-RAY DIFFRACTIONr_nbd_other0.3240.252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1580.26
X-RAY DIFFRACTIONr_mcbond_it4.4654.2321582
X-RAY DIFFRACTIONr_mcbond_other4.4654.2321582
X-RAY DIFFRACTIONr_mcangle_it6.7437.6051974
X-RAY DIFFRACTIONr_mcangle_other6.7437.6041975
X-RAY DIFFRACTIONr_scbond_it5.2634.581518
X-RAY DIFFRACTIONr_scbond_other5.2534.5831518
X-RAY DIFFRACTIONr_scangle_it8.1628.2372229
X-RAY DIFFRACTIONr_scangle_other8.1648.2362230
X-RAY DIFFRACTIONr_lrange_it11.51750.73213342
X-RAY DIFFRACTIONr_lrange_other11.51650.66913324
X-RAY DIFFRACTIONr_ncsr_local_group_10.1260.055945
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.126050.05008
12AX-RAY DIFFRACTIONLocal ncs0.126050.05008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.48-2.5440.36490.299740.29310270.9160.94599.61050.28
2.544-2.6140.368300.3487700.3499940.9110.93280.48290.324
2.614-2.68900.3120.319790.9440.20430.302
2.689-2.7720.393450.3537850.3559500.9120.9387.36840.323
2.772-2.8630.342480.2528630.2569120.930.96199.89040.246
2.863-2.9630.319510.2488410.2528930.950.96299.8880.242
2.963-3.0740.297590.2538060.2568650.9530.9651000.246
3.074-3.1990.322540.237750.2368320.9420.97199.63940.228
3.199-3.3410.269450.2277460.2297920.950.97399.87370.234
3.341-3.5030.328540.2486970.2537560.9390.96599.33860.253
3.503-3.6920.358190.2266850.237100.9410.97399.15490.239
3.692-3.9140.239290.2196640.227000.960.976990.241
3.914-4.1830.248480.215880.2136430.9690.97698.91140.237
4.183-4.5150.162190.1865850.1866090.9840.98199.1790.219
4.515-4.9420.417150.1815270.1855480.9770.98398.90510.224
4.942-5.5190.321350.2224670.2295040.9540.97799.60320.27
5.519-6.360.368520.2864010.2974560.9480.95999.34210.339
6.36-7.7590.184240.2413510.2373770.9830.97399.46950.31
7.759-10.8470.1470.192940.1883020.9970.98399.66890.283
10.847-50.7410.24140.2521680.2521840.9620.95698.9130.327

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