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- PDB-1txu: Crystal Structure of the Vps9 Domain of Rabex-5 -

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Basic information

Entry
Database: PDB / ID: 1txu
TitleCrystal Structure of the Vps9 Domain of Rabex-5
ComponentsRab5 GDP/GTP exchange factor
KeywordsPROTEIN TRANSPORT / VPS9 DOMAIN / RAB5 GUANINE-NUCLEOTIDE EXCHANGE FACTOR / GEF
Function / homology
Function and homology information


dendritic transport / negative regulation of Kit signaling pathway / mast cell migration / regulation of Fc receptor mediated stimulatory signaling pathway / Kit signaling pathway / negative regulation of mast cell degranulation / negative regulation of mast cell activation / negative regulation of leukocyte migration / negative regulation of receptor-mediated endocytosis / negative regulation of mast cell cytokine production ...dendritic transport / negative regulation of Kit signaling pathway / mast cell migration / regulation of Fc receptor mediated stimulatory signaling pathway / Kit signaling pathway / negative regulation of mast cell degranulation / negative regulation of mast cell activation / negative regulation of leukocyte migration / negative regulation of receptor-mediated endocytosis / negative regulation of mast cell cytokine production / negative regulation of Ras protein signal transduction / RAB GEFs exchange GTP for GDP on RABs / TBC/RABGAPs / protein targeting to membrane / mast cell degranulation / negative regulation of interleukin-6 production / endocytic vesicle / receptor-mediated endocytosis / guanyl-nucleotide exchange factor activity / negative regulation of protein phosphorylation / recycling endosome / small GTPase binding / negative regulation of inflammatory response / ubiquitin protein ligase activity / protein transport / early endosome membrane / Ras protein signal transduction / early endosome / dendrite / nucleolus / DNA binding / zinc ion binding / cytosol
Similarity search - Function
Serum Albumin; Chain A, Domain 1 - #120 / VPS9 domain / RABX5, catalytic core helical domain / Domain of unknown function (DUF5601) / Vacuolar protein sorting-associated protein 9-like / VPS9 domain / VPS9 domain superfamily / Vacuolar sorting protein 9 (VPS9) domain / VPS9 domain profile. / Domain present in VPS9 ...Serum Albumin; Chain A, Domain 1 - #120 / VPS9 domain / RABX5, catalytic core helical domain / Domain of unknown function (DUF5601) / Vacuolar protein sorting-associated protein 9-like / VPS9 domain / VPS9 domain superfamily / Vacuolar sorting protein 9 (VPS9) domain / VPS9 domain profile. / Domain present in VPS9 / Zinc finger, A20-type / A20-like zinc finger / Zinc finger A20-type profile. / A20-like zinc fingers / Serum Albumin; Chain A, Domain 1 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Rab5 GDP/GTP exchange factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.35 Å
AuthorsDelprato, A. / Merithew, E. / Lambright, D.G.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2004
Title: Structure, exchange determinants, and family-wide rab specificity of the tandem helical bundle and Vps9 domains of Rabex-5
Authors: Delprato, A. / Merithew, E. / Lambright, D.G.
History
DepositionJul 6, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Advisory / Experimental preparation / Category: exptl_crystal_grow / pdbx_unobs_or_zero_occ_atoms / Item: _exptl_crystal_grow.temp

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rab5 GDP/GTP exchange factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3882
Polymers32,3641
Non-polymers241
Water1,47782
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.047, 88.329, 47.299
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Rab5 GDP/GTP exchange factor / Rabex-5


Mass: 32363.783 Da / Num. of mol.: 1 / Fragment: VPS9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RABGEF1 / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UJ41
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O

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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: 2.28 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 8000, MgCl, TRIS, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 4K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.97956,0.97944,0.96805,0.97954,0.97948,0.99530
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 23, 2003 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979561
20.979441
30.968051
40.979541
50.979481
60.99531
ReflectionResolution: 2.35→20 Å / Num. all: 11599 / Num. obs: 11599 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 48 Å2 / Rsym value: 0.059 / Net I/σ(I): 23.3
Reflection shellResolution: 2.35→2.42 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2 / Rsym value: 0.372 / % possible all: 74.5

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNSrefinement
RefinementMethod to determine structure: MAD / Resolution: 2.35→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.269 586 -RANDOM
Rwork0.227 ---
all0.229 11599 --
obs0.229 11599 93.7 %-
Solvent computationBsol: 39.2366 Å2 / ksol: 0.323924 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.726 Å20 Å20 Å2
2---5.148 Å20 Å2
3---1.421 Å2
Refinement stepCycle: LAST / Resolution: 2.35→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2080 0 1 82 2163
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.5181.5
X-RAY DIFFRACTIONc_scbond_it2.3452
X-RAY DIFFRACTIONc_mcangle_it2.5942
X-RAY DIFFRACTIONc_scangle_it3.5732.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param

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