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- PDB-3pp2: Crystal structure of the pleckstrin homology domain of ArhGAP27 -

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Basic information

Entry
Database: PDB / ID: 3pp2
TitleCrystal structure of the pleckstrin homology domain of ArhGAP27
ComponentsRho GTPase-activating protein 27
KeywordsHYDROLASE ACTIVATOR / ph domain / GTPase activator / pleckstrin homology domain / structural genomics consortium / SGC
Function / homology
Function and homology information


regulation of small GTPase mediated signal transduction / Rho protein signal transduction / CDC42 GTPase cycle / RAC1 GTPase cycle / GTPase activator activity / receptor-mediated endocytosis / SH3 domain binding / membrane / cytosol / cytoplasm
Similarity search - Function
: / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Rho GTPase activation protein / WW domain / Quinoprotein alcohol dehydrogenase-like superfamily / WW domain superfamily / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) ...: / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Rho GTPase activation protein / WW domain / Quinoprotein alcohol dehydrogenase-like superfamily / WW domain superfamily / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
CITRIC ACID / Rho GTPase-activating protein 27
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 1.421 Å
AuthorsShen, L. / Tempel, W. / Tong, Y. / Nedyalkova, L. / Li, Y. / Wernimont, A.K. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. ...Shen, L. / Tempel, W. / Tong, Y. / Nedyalkova, L. / Li, Y. / Wernimont, A.K. / 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 pleckstrin homology domain of ArhGAP27
Authors: Shen, L. / Tempel, W. / Tong, Y. / Nedyalkova, L. / Li, Y. / Wernimont, A.K. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Park, H.
History
DepositionNov 23, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2010Provider: 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rho GTPase-activating protein 27
B: Rho GTPase-activating protein 27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,93434
Polymers27,7902
Non-polymers1,14532
Water2,306128
1
A: Rho GTPase-activating protein 27
B: Rho GTPase-activating protein 27
hetero molecules

A: Rho GTPase-activating protein 27
B: Rho GTPase-activating protein 27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,86968
Polymers55,5794
Non-polymers2,29064
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area9900 Å2
ΔGint-23 kcal/mol
Surface area20790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.243, 98.243, 66.909
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-998-

UNX

21A-101-

HOH

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Components

#1: Protein Rho GTPase-activating protein 27 / CIN85-associated multi-domain-containing Rho GTPase-activating protein 1 / Rho-type GTPase- ...CIN85-associated multi-domain-containing Rho GTPase-activating protein 1 / Rho-type GTPase-activating protein 27


Mass: 13894.833 Da / Num. of mol.: 2 / Fragment: UNP residues 491-613
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARHGAP27, CAMGAP1, SH3D20, PP905 / Plasmid: pNIC-CH / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: Q6ZUM4
#2: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 25 / Source method: obtained synthetically
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsEXPERIMENTAL CONSTRUCT SUBJECTED TO PROTEOLYSIS: ...EXPERIMENTAL CONSTRUCT SUBJECTED TO PROTEOLYSIS: MAVRTKTLDKAGVLHRTKTADKGKRLRKKHWSASWTVLEGGVLTFFKDSKTSAAGGLRQPSKFSTPEYTVELRGATLSWAPKDKSSRKNVLELRSRDGSEYLIQHDSEAIISTWHKAIAQGIQELSAELPPEESESSRVDFGSSERLGSWQEKEEDARPNAAAPALGPVGLESDLSKVRHKLRKFLQRRPTLQSLREKGYIKDQVFGCALAALCERERSRVPRFVQQCIRAVEARGLDIDGLYRISGNLATIQKLRYKVDHDERLDLDDGRWEDVHVITGALKLFFRELPEPLFPFSHFRQFIAAIKLQDQARRSRCVRDLVRSLPAPNHDTLRMLFQHLCRVIEHGEQNRMSVQSVAIVFGPTLLRPEVEETSMPMTMVFQNQVVELILQQCADIFPPHHHHHHH

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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: 3.35 Å3/Da / Density % sol: 63.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.4 M sodium citrate, 0.1 M HEPES, 1:100 w/w endoproteinase Glu-C V8, pH 7.5, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97625 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 7, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.42→30 Å / Num. obs: 136029 / % possible obs: 99.8 % / Redundancy: 8.5 % / Rmerge(I) obs: 0.059 / Χ2: 1.726 / Net I/σ(I): 12.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.42-1.443.70.87264991.25595.9
1.44-1.474.60.79268241.23899.7
1.47-1.55.20.67367761.269100
1.5-1.535.50.51168061.279100
1.53-1.565.60.43768941.272100
1.56-1.65.60.3467301.294100
1.6-1.645.60.30468231.283100
1.64-1.685.60.24368021.319100
1.68-1.736.80.31668602.035100
1.73-1.798.80.38868292.731100
1.79-1.8510.60.33668372.265100
1.85-1.9311.30.24868052.036100
1.93-2.0111.40.16368111.712100
2.01-2.1211.40.12568041.591100
2.12-2.2511.40.09368131.543100
2.25-2.4311.40.0868001.657100
2.43-2.6711.40.06768421.882100
2.67-3.0611.30.05268401.868100
3.06-3.8511.20.03868031.872100
3.85-3011.20.02868311.384100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
RefinementResolution: 1.421→30 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.959 / Matrix type: sparse / WRfactor Rfree: 0.197 / WRfactor Rwork: 0.177 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 1.607 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.05 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1919 3100 4.427 %THIN SHELLS (SFTOOLS)
Rwork0.1708 66920 --
obs0.172 70020 99.766 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso max: 125.24 Å2 / Biso mean: 19.239 Å2 / Biso min: 10.79 Å2
Baniso -1Baniso -2Baniso -3
1-0.419 Å20.209 Å20 Å2
2--0.419 Å20 Å2
3----0.628 Å2
Refinement stepCycle: LAST / Resolution: 1.421→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1717 0 102 128 1947
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0211908
X-RAY DIFFRACTIONr_bond_other_d0.0010.021318
X-RAY DIFFRACTIONr_angle_refined_deg1.6691.9782592
X-RAY DIFFRACTIONr_angle_other_deg0.92433222
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7985242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.60823.46775
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.72115336
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5281511
X-RAY DIFFRACTIONr_chiral_restr0.1020.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022091
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02372
X-RAY DIFFRACTIONr_mcbond_it1.9471.51135
X-RAY DIFFRACTIONr_mcbond_other0.5361.5465
X-RAY DIFFRACTIONr_mcangle_it3.1421828
X-RAY DIFFRACTIONr_scbond_it4.1563773
X-RAY DIFFRACTIONr_scangle_it6.1984.5751
X-RAY DIFFRACTIONr_rigid_bond_restr1.59333226
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection all% reflection obs (%)WRfactor Rwork
1.421-1.4580.252040.23648690.237510999.2950.211
1.458-1.4980.2042030.18547800.186499299.820.16
1.498-1.5410.2092180.16146690.164489699.8160.135
1.541-1.5890.1741970.14645350.148474399.7680.124
1.589-1.6410.171780.13843820.139457399.7160.114
1.641-1.6980.1772520.1442010.142446199.8210.118
1.698-1.7620.1681480.14241220.143428199.7430.119
1.762-1.8340.1541380.13939710.14412899.540.119
1.834-1.9150.1662100.14637640.147398999.6240.129
1.915-2.0080.1832180.14735670.149379299.8150.134
2.008-2.11600.1536090.15361699.8060.14
2.116-2.2440.1642080.15532280.155344499.7680.148
2.244-2.3970.2011650.17230720.173324199.8770.169
2.397-2.5880.1931390.17828610.179300599.8340.18
2.588-2.8330.1922400.19225490.192279199.9280.197
2.833-3.1640.182750.18624420.18625171000.202
3.164-3.6470.191720.17621860.17622581000.197
3.647-4.450.1781210.16218000.16319211000.192
4.45-6.2250.246680.17714490.1815171000.224
6.225-300.255460.2538640.2539101000.322

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