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- PDB-5d3v: Crystal Structure of the P-Rex1 PH domain with Citrate Bound -

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Basic information

Entry
Database: PDB / ID: 5d3v
TitleCrystal Structure of the P-Rex1 PH domain with Citrate Bound
ComponentsPhosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein
KeywordsLIPID BINDING PROTEIN / pleckstrin homology domain / beta sandwich / phosphatidylinositol-binding
Function / homology
Function and homology information


regulation of dendrite development / regulation of actin filament polymerization / neutrophil activation / negative regulation of TOR signaling / regulation of small GTPase mediated signal transduction / RHOB GTPase cycle / NRAGE signals death through JNK / superoxide metabolic process / RHOC GTPase cycle / RHOJ GTPase cycle ...regulation of dendrite development / regulation of actin filament polymerization / neutrophil activation / negative regulation of TOR signaling / regulation of small GTPase mediated signal transduction / RHOB GTPase cycle / NRAGE signals death through JNK / superoxide metabolic process / RHOC GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / CDC42 GTPase cycle / T cell differentiation / RHOG GTPase cycle / protein serine/threonine kinase inhibitor activity / RHOA GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / actin filament polymerization / neutrophil chemotaxis / RAC1 GTPase cycle / positive regulation of substrate adhesion-dependent cell spreading / GTPase activator activity / guanyl-nucleotide exchange factor activity / dendritic shaft / phospholipid binding / G alpha (12/13) signalling events / growth cone / intracellular signal transduction / positive regulation of cell migration / G protein-coupled receptor signaling pathway / perinuclear region of cytoplasm / enzyme binding / plasma membrane / cytosol
Similarity search - Function
: / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin / DEP domain / : / SOS1/NGEF-like PH domain / Dbl homology (DH) domain superfamily ...: / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin / DEP domain / : / SOS1/NGEF-like PH domain / 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 profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / PH-like domain superfamily / Roll / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Mainly Beta
Similarity search - Domain/homology
CITRATE ANION / Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.852 Å
AuthorsCash, J.N. / Tesmer, J.J.G.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL086865 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL122416 United States
American Cancer SocietyPF-14-224-01-DMC United States
CitationJournal: Structure / Year: 2016
Title: Structural and Biochemical Characterization of the Catalytic Core of the Metastatic Factor P-Rex1 and Its Regulation by PtdIns(3,4,5)P3.
Authors: Cash, J.N. / Davis, E.M. / Tesmer, J.J.
History
DepositionAug 6, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1May 18, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization ..._citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein
B: Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7633
Polymers38,5742
Non-polymers1891
Water3,999222
1
A: Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4762
Polymers19,2871
Non-polymers1891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein


Theoretical massNumber of molelcules
Total (without water)19,2871
Polymers19,2871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.080, 72.424, 82.526
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 Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein / PtdIns(3 / 4 / 5)-dependent Rac exchanger 1


Mass: 19286.953 Da / Num. of mol.: 2 / Fragment: unp residues 245-408
Source method: isolated from a genetically manipulated source
Details: pleckstrin homology domain / Source: (gene. exp.) Homo sapiens (human) / Gene: PREX1, KIAA1415 / Plasmid: pMALc2H10T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8TCU6
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.09 Å3/Da / Density % sol: 41.29 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: Sodium citrate, PEG 8000

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.078 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.078 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 27997 / % possible obs: 99.5 % / Redundancy: 4 % / Biso Wilson estimate: 22.58 Å2 / Rmerge(I) obs: 0.054 / Χ2: 1.177 / Net I/av σ(I): 25.811 / Net I/σ(I): 11.9 / Num. measured all: 111287
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.85-1.883.70.35913320.61797.8
1.88-1.9240.27413930.653100
1.92-1.9540.24513790.694100
1.95-1.9940.19313940.749100
1.99-2.0440.16313550.792100
2.04-2.0840.13114010.805100
2.08-2.1440.11613850.846100
2.14-2.1940.10213910.92100
2.19-2.2640.09314050.988100
2.26-2.3340.08813821.034100
2.33-2.4140.08513831.195100
2.41-2.5140.08414001.441100
2.51-2.6340.07713831.521100
2.63-2.7640.06314221.426100
2.76-2.9440.05314021.40199.9
2.94-3.1640.04814241.52599.7
3.16-3.4840.05214161.70499.6
3.48-3.9940.04314161.87699.4
3.99-5.0240.03114451.76998.6
5.02-503.80.02814891.46996

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data scaling
HKL-2000data reduction
SCALEPACKdata scaling
PHASER2.5.1phasing
PHENIXrefinement
Cootmodel building
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PZ1

2pz1


Resolution: 1.852→36.192 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2155 1379 5.08 %RANDOM
Rwork0.1721 26551 --
obs0.1742 27171 94.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.14 Å2 / Biso mean: 33.8325 Å2 / Biso min: 9.05 Å2
Refinement stepCycle: final / Resolution: 1.852→36.192 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2347 0 13 222 2582
Biso mean--42.01 35.68 -
Num. residues----288
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072439
X-RAY DIFFRACTIONf_angle_d0.9783292
X-RAY DIFFRACTIONf_chiral_restr0.041361
X-RAY DIFFRACTIONf_plane_restr0.004420
X-RAY DIFFRACTIONf_dihedral_angle_d14.393919
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8552-1.92150.2721130.21212583269698
1.9215-1.99840.24811380.189926252763100
1.9984-2.08930.2051380.173326312769100
2.0893-2.19950.22961500.174526262776100
2.1995-2.33720.22451340.171926582792100
2.3372-2.51760.22561350.184426392774100
2.5176-2.77090.23571450.188726582803100
2.7709-3.17150.24461660.183826642830100
3.1715-3.99470.22581500.155926762826100
3.9947-32.80970.15811340.16232791292598

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