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- PDB-3qik: Crystal structure of the first PDZ domain of PREX1 -

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Basic information

Entry
Database: PDB / ID: 3qik
TitleCrystal structure of the first PDZ domain of PREX1
ComponentsPhosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein
KeywordsHYDROLASE REGULATOR / pdz domain / structural genomics consortium / SGC
Function / homology
Function and homology information


regulation of signaling / regulation of dendrite development / neutrophil activation / regulation of actin filament polymerization / regulation of small GTPase mediated signal transduction / RHOB GTPase cycle / NRAGE signals death through JNK / superoxide metabolic process / RHOJ GTPase cycle / RHOC GTPase cycle ...regulation of signaling / regulation of dendrite development / neutrophil activation / regulation of actin filament polymerization / regulation of small GTPase mediated signal transduction / RHOB GTPase cycle / NRAGE signals death through JNK / superoxide metabolic process / RHOJ GTPase cycle / RHOC GTPase cycle / RHOQ GTPase cycle / CDC42 GTPase cycle / RHOG GTPase cycle / T cell differentiation / RHOA GTPase cycle / RAC3 GTPase cycle / RAC2 GTPase cycle / positive regulation of substrate adhesion-dependent cell spreading / RAC1 GTPase cycle / actin filament polymerization / GTPase activator activity / guanyl-nucleotide exchange factor activity / neutrophil chemotaxis / 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
Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin / DEP domain / 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 ...Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin / DEP domain / 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. / PDZ domain / Pdz3 Domain / 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 / Winged helix DNA-binding domain superfamily / Roll / Winged helix-like DNA-binding domain superfamily / Mainly Beta
Similarity search - Domain/homology
Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.285 Å
AuthorsShen, L. / Tong, Y. / Tempel, W. / Li, Y. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal structure of the first PDZ domain of PREX1
Authors: Shen, L. / Tong, Y. / Tempel, W. / Li, Y. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Park, H.
History
DepositionJan 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)11,5199
Polymers11,5191
Non-polymers08
Water28816
1
A: Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein

A: Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein


Theoretical massNumber of molelcules
Total (without water)23,03918
Polymers23,0392
Non-polymers016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area2480 Å2
ΔGint-14 kcal/mol
Surface area10790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.135, 78.135, 54.691
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein / P-Rex1 / PtdIns(3 / 4 / 5)-dependent Rac exchanger 1


Mass: 11519.360 Da / Num. of mol.: 1 / Fragment: UNP Residues 607-706
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PREX1, KIAA1415 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: Q8TCU6
#2: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 8 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
14.270.4
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, sitting drop6.21.2M lithium sulfate, 0.5M ammonium sulfate, 0.1M sodium citrate, pH 6.2, vapor diffusion, sitting drop, temperature 293K
2932vapor diffusion, sitting drop5.61.2M lithium sulfate, 0.5M ammonium sulfate, 0.1M sodium citrate. Soaked for 6 hours in 0.01 M potassium hexaiodoplatin-(IV)-ate and mother liquor, pH 5.6, vapor diffusion, sitting drop, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceTypeIDWavelength (Å)
ROTATING ANODERIGAKU FR-E SUPERBRIGHT11.5418
ROTATING ANODERIGAKU FR-E SUPERBRIGHT21.5418
Detector
TypeIDDetectorDate
RIGAKU RAXIS1IMAGE PLATEJan 11, 2011
RIGAKU SATURN A2002CCDJan 17, 2011
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.27→25 Å / Num. obs: 8971 / % possible obs: 100 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.075 / Χ2: 1.919 / Net I/σ(I): 15.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.27-2.3510.40.6748700.965100
2.35-2.4510.50.5688700.94100
2.45-2.5610.50.4298991.02100
2.56-2.6910.60.38891.091100
2.69-2.8610.60.2128821.309100
2.86-3.0810.60.1498911.65100
3.08-3.3910.60.0938882.462100
3.39-3.8810.40.0718993.173100
3.88-4.8810.30.0549173.446100
4.88-259.90.049663.064100

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RESOLVEphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
StructureStudiodata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.285→20 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.923 / WRfactor Rfree: 0.264 / WRfactor Rwork: 0.231 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.796 / SU ML: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.221 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY. Programs phaser, dm, arp/warp were also used during density improvement and model refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.2691 422 4.74 %RANDOM
Rwork0.2424 ---
obs0.244 8903 98.944 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso max: 59.78 Å2 / Biso mean: 33.465 Å2 / Biso min: 26.08 Å2
Baniso -1Baniso -2Baniso -3
1-1.279 Å20.64 Å20 Å2
2--1.279 Å20 Å2
3----1.919 Å2
Refinement stepCycle: LAST / Resolution: 2.285→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms781 0 8 16 805
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022801
X-RAY DIFFRACTIONr_bond_other_d0.0040.02552
X-RAY DIFFRACTIONr_angle_refined_deg1.191.9921084
X-RAY DIFFRACTIONr_angle_other_deg0.8131355
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7165104
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.24724.57135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.42215149
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.913156
X-RAY DIFFRACTIONr_chiral_restr0.0720.2130
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02886
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02156
X-RAY DIFFRACTIONr_mcbond_it0.6611.5508
X-RAY DIFFRACTIONr_mcbond_other0.0991.5205
X-RAY DIFFRACTIONr_mcangle_it1.3072820
X-RAY DIFFRACTIONr_scbond_it1.7933293
X-RAY DIFFRACTIONr_scangle_it3.1774.5262
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.285-2.3440.417360.37854262991.892
2.344-2.4070.441360.33459863699.686
2.407-2.4760.307290.33459462599.68
2.476-2.5510.297320.33155058499.658
2.551-2.6330.304230.30357460299.169
2.633-2.7240.237150.30354155999.463
2.724-2.8250.398270.27849352698.859
2.825-2.9370.22250.26450553599.065
2.937-3.0650.319250.26148150899.606
3.065-3.2110.274180.28145647998.956
3.211-3.380.276200.23344847199.363
3.38-3.5780.261230.231400423100
3.578-3.8170.248250.23740142799.766
3.817-4.110.38100.21237538699.741
4.11-4.4830.207170.19934135999.721
4.483-4.9810.145140.18732333999.41
4.981-5.6940.248130.20927429098.966
5.694-6.8360.356160.25124726499.621
6.836-9.1480.277110.238199210100
9.148-200.18870.203139146100

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