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- PDB-1rj2: Crystal structure of the DH/PH fragment of Dbs without bound GTPase -

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Basic information

Entry
Database: PDB / ID: 1rj2
TitleCrystal structure of the DH/PH fragment of Dbs without bound GTPase
ComponentsGuanine nucleotide exchange factor DBS [Fragment]
KeywordsSIGNALING PROTEIN / Dbl homology / Pleckstrin homology / Guanine nucleotide exchange factor / Rho GTPase
Function / homology
Function and homology information


: / guanyl-nucleotide exchange factor activity => GO:0005085 / RHOB GTPase cycle / NRAGE signals death through JNK / RHOC GTPase cycle / G alpha (12/13) signalling events / RHOA GTPase cycle / CDC42 GTPase cycle / RHOG GTPase cycle / 1-phosphatidylinositol binding ...: / guanyl-nucleotide exchange factor activity => GO:0005085 / RHOB GTPase cycle / NRAGE signals death through JNK / RHOC GTPase cycle / G alpha (12/13) signalling events / RHOA GTPase cycle / CDC42 GTPase cycle / RHOG GTPase cycle / 1-phosphatidylinositol binding / NRAGE signals death through JNK / RAC1 GTPase cycle / G alpha (12/13) signalling events / positive regulation of Rho protein signal transduction / Rho protein signal transduction / endomembrane system / extrinsic component of membrane / phosphatidylinositol binding / guanyl-nucleotide exchange factor activity / extrinsic component of cytoplasmic side of plasma membrane / lamellipodium / positive regulation of transcription by RNA polymerase II / membrane / cytoplasm
Similarity search - Function
DBS, PH domain / DBS, SH3 domain / Dbl homology (DH) domain / Dbl Homology Domain; Chain A / Divergent CRAL/TRIO domain / CRAL-TRIO lipid binding domain profile. / Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) / CRAL-TRIO lipid binding domain / CRAL-TRIO lipid binding domain superfamily / Dbl homology (DH) domain signature. ...DBS, PH domain / DBS, SH3 domain / Dbl homology (DH) domain / Dbl Homology Domain; Chain A / Divergent CRAL/TRIO domain / CRAL-TRIO lipid binding domain profile. / Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) / CRAL-TRIO lipid binding domain / CRAL-TRIO lipid binding domain superfamily / Dbl homology (DH) domain signature. / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Spectrin repeat / Spectrin repeat / Spectrin repeats / Spectrin/alpha-actinin / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain superfamily / RhoGEF domain / Dbl homology (DH) domain profile. / Dbl homology (DH) domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / Roll / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Guanine nucleotide exchange factor DBS / Guanine nucleotide exchange factor DBS
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsWorthylake, D.K. / Rossman, K.L. / Sondek, J.
CitationJournal: Structure / Year: 2004
Title: Crystal structure of the DH/PH fragment of Dbs without bound GTPase.
Authors: Worthylake, D.K. / Rossman, K.L. / Sondek, J.
History
DepositionNov 18, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Guanine nucleotide exchange factor DBS [Fragment]
D: Guanine nucleotide exchange factor DBS [Fragment]
G: Guanine nucleotide exchange factor DBS [Fragment]
J: Guanine nucleotide exchange factor DBS [Fragment]


Theoretical massNumber of molelcules
Total (without water)164,8814
Polymers164,8814
Non-polymers00
Water27015
1
A: Guanine nucleotide exchange factor DBS [Fragment]


Theoretical massNumber of molelcules
Total (without water)41,2201
Polymers41,2201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Guanine nucleotide exchange factor DBS [Fragment]


Theoretical massNumber of molelcules
Total (without water)41,2201
Polymers41,2201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: Guanine nucleotide exchange factor DBS [Fragment]


Theoretical massNumber of molelcules
Total (without water)41,2201
Polymers41,2201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
J: Guanine nucleotide exchange factor DBS [Fragment]


Theoretical massNumber of molelcules
Total (without water)41,2201
Polymers41,2201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.989, 82.824, 127.257
Angle α, β, γ (deg.)90.00, 90.80, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: Protein
Guanine nucleotide exchange factor DBS [Fragment] / DBL's big sister / MCF2 transforming sequence-like protein / OST oncogene


Mass: 41220.332 Da / Num. of mol.: 4 / Fragment: DH/PH fragment (residues 498-842)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: MCF2L, OST / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (unknown) / Strain (production host): BL21(DE3) / References: UniProt: Q63406, UniProt: Q64096*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 3.56 Å3/Da / Density % sol: 65.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Na HEPES, PEG 20K, ethylene glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 22, 2002 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. all: 40298 / Num. obs: 40298 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 92.1 Å2 / Rsym value: 0.115 / Net I/σ(I): 13.3
Reflection shellResolution: 3→3.11 Å / Mean I/σ(I) obs: 1.5 / Num. unique all: 3645 / Rsym value: 0.821 / % possible all: 88.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
BEASTmodel building
CNS1.1refinement
BEASTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KZ7 (DH and PH domains)
Resolution: 3→30 Å / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2957 2007 5 %random
Rwork0.2391 ---
all-41093 --
obs-40099 97.6 %-
Displacement parametersBiso mean: 89.6 Å2
Baniso -1Baniso -2Baniso -3
1-13.53 Å20 Å29.399 Å2
2---1.082 Å20 Å2
3----12.449 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.58 Å0.45 Å
Luzzati d res low-30 Å
Luzzati sigma a0.6 Å0.51 Å
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10355 0 0 15 10370
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0076
X-RAY DIFFRACTIONc_angle_deg1.26742

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