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- PDB-3mpx: Crystal structure of the DH and PH-1 domains of human FGD5 -

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Basic information

Entry
Database: PDB / ID: 3mpx
TitleCrystal structure of the DH and PH-1 domains of human FGD5
ComponentsFYVE, RhoGEF and PH domain-containing protein 5
KeywordsLIPID BINDING PROTEIN / Structural Genomics Consortium / DH domain / PH domain / SGC
Function / homology
Function and homology information


guanyl-nucleotide exchange factor activity => GO:0005085 / filopodium assembly / regulation of GTPase activity / ruffle / cytoskeleton organization / guanyl-nucleotide exchange factor activity / small GTPase binding / ruffle membrane / lamellipodium / regulation of cell shape ...guanyl-nucleotide exchange factor activity => GO:0005085 / filopodium assembly / regulation of GTPase activity / ruffle / cytoskeleton organization / guanyl-nucleotide exchange factor activity / small GTPase binding / ruffle membrane / lamellipodium / regulation of cell shape / actin cytoskeleton organization / early endosome / cytoskeleton / Golgi apparatus / endoplasmic reticulum / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
FYVE zinc finger / FYVE zinc finger / Protein present in Fab1, YOTB, Vac1, and EEA1 / Dbl Homology Domain; Chain A / Dbl homology (DH) domain / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases ...FYVE zinc finger / FYVE zinc finger / Protein present in Fab1, YOTB, Vac1, and EEA1 / Dbl Homology Domain; Chain A / Dbl homology (DH) domain / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / 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. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Zinc finger, RING/FYVE/PHD-type / Roll / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
FYVE, RhoGEF and PH domain-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / mad / Resolution: 2.8 Å
AuthorsShen, Y. / Nedyalkova, L. / Tong, Y. / Tempel, W. / Crombet, L. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. ...Shen, Y. / Nedyalkova, L. / Tong, Y. / Tempel, W. / Crombet, L. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of the DH and PH-1 domains of human FGD5
Authors: Shen, Y. / Nedyalkova, L. / Tong, Y. / Tempel, W. / Crombet, L. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H.
History
DepositionApr 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FYVE, RhoGEF and PH domain-containing protein 5


Theoretical massNumber of molelcules
Total (without water)50,30312
Polymers50,3031
Non-polymers011
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.140, 70.645, 127.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein FYVE, RhoGEF and PH domain-containing protein 5 / Zinc finger FYVE domain-containing protein 23


Mass: 50303.230 Da / Num. of mol.: 1 / Fragment: UNP Residues 889-1304
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGD5, ZFYVE23 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pRARE2 / References: UniProt: Q6ZNL6
#2: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 11 / Source method: obtained synthetically
Sequence detailsTHE PROTEIN USED FOR CRYSTALLIZATION CONTAINED AMINO-ACIDS AS GIVEN IN DBREF. THIS PROTEIN LIKELY ...THE PROTEIN USED FOR CRYSTALLIZATION CONTAINED AMINO-ACIDS AS GIVEN IN DBREF. THIS PROTEIN LIKELY DEGRADED IN THE PRESENCE TRYPSIN TO A TRUNCATED SPECIES DURING THE CRYSTALLIZATION EXPERIMENT. THEREFORE, CALCULATED VM AND VS VALUES ARE BASED ON AN ESTIMATE. THE AUTHORS ASSUMED RESIDUES 890 TO 1205 TO BE PRESENT.

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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: 2.4 Å3/Da / Density % sol: 48.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% w/v PEG 3350, 0.2M lithium sulfate, 0.1M HEPES pH 7.5. 1:100 trypsin was also added. vapor diffusion, sitting drop, temperature 291K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97942, 0.97934
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 25, 2010
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979421
20.979341
ReflectionResolution: 2.8→30 Å / Num. obs: 9116 / % possible obs: 99.8 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.142 / Χ2: 1.237 / Net I/σ(I): 5.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.8-2.856.30.4694340.80796.9
2.85-2.97.30.4354410.784100
2.9-2.967.20.3424610.775100
2.96-3.027.30.3344290.791100
3.02-3.087.20.2954460.808100
3.08-3.157.20.254360.831100
3.15-3.237.10.2154660.867100
3.23-3.327.20.1974290.931100
3.32-3.427.20.1774500.878100
3.42-3.537.10.1534581.141100
3.53-3.657.10.144501.074100
3.65-3.87.10.1324491.175100
3.8-3.9770.1174501.335100
3.97-4.1870.1164581.51999.8
4.18-4.446.90.1114621.683100
4.44-4.786.90.0984631.794100
4.78-5.266.70.0984511.447100
5.26-6.026.50.1174711.308100
6.02-7.566.70.1024861.55100
7.56-306.10.0715263.287100

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Phasing

PhasingMethod: mad

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RESOLVEphasing
PDB_EXTRACT3.005data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
BUSTER2.8.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.8→29.71 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.842 / Cross valid method: THROUGHOUT / σ(F): 0
Details: Model was refined against inflection wavelength data
RfactorNum. reflection% reflectionSelection details
Rfree0.289 430 4.77 %RANDOM
Rwork0.218 ---
obs0.221 9013 --
Displacement parametersBiso mean: 29.79 Å2
Baniso -1Baniso -2Baniso -3
1--3.702 Å20 Å20 Å2
2--7.505 Å20 Å2
3----3.803 Å2
Refine analyzeLuzzati coordinate error obs: 0.376 Å
Refinement stepCycle: LAST / Resolution: 2.8→29.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2287 0 11 0 2298
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012326HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.123157HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d785SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes54HARMONIC2
X-RAY DIFFRACTIONt_gen_planes348HARMONIC5
X-RAY DIFFRACTIONt_it2326HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.72
X-RAY DIFFRACTIONt_other_torsion19.9
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion305SEMIHARMONIC5
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_contact2621SEMIHARMONIC4
LS refinement shellResolution: 2.8→3.13 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.354 142 5.69 %
Rwork0.228 2355 -
all0.235 2497 -

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