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- PDB-3eap: Crystal structure of the RhoGAP domain of ARHGAP11A -

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Basic information

Entry
Database: PDB / ID: 3eap
TitleCrystal structure of the RhoGAP domain of ARHGAP11A
ComponentsRho GTPase-activating protein 11A
Keywordshydrolase activator / gtpase activating protein / gap / structural genomics consortium / GTPase activation / Phosphoprotein / Polymorphism / SGC
Function / homology
Function and homology information


: / regulation of small GTPase mediated signal transduction / GTPase activator activity / signal transduction / cytosol
Similarity search - Function
Rho GTPase-activating protein 11 / Phosphatidylinositol 3-kinase; Chain A / Rho GTPase activation protein / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Rho GTPase activation protein / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Rho GTPase-activating protein 11A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsShen, Y. / Shen, L. / Tong, Y. / Tempel, W. / MacKenzie, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. ...Shen, Y. / Shen, L. / Tong, Y. / Tempel, W. / MacKenzie, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of the RhoGAP domain of ARHGAP11A
Authors: Shen, Y. / Shen, L. / Tong, Y. / Tempel, W. / MacKenzie, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H.
History
DepositionAug 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 14, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: phasing / refine ...phasing / refine / software / struct_ref_seq_dif / struct_site
Item: _refine.pdbx_starting_model / _struct_ref_seq_dif.details ..._refine.pdbx_starting_model / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 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

Downloads & links

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Assembly

Deposited unit
A: Rho GTPase-activating protein 11A
B: Rho GTPase-activating protein 11A
C: Rho GTPase-activating protein 11A
D: Rho GTPase-activating protein 11A


Theoretical massNumber of molelcules
Total (without water)121,88910
Polymers121,8894
Non-polymers06
Water1,04558
1
A: Rho GTPase-activating protein 11A


Theoretical massNumber of molelcules
Total (without water)30,4722
Polymers30,4721
Non-polymers01
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Rho GTPase-activating protein 11A


Theoretical massNumber of molelcules
Total (without water)30,4725
Polymers30,4721
Non-polymers04
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Rho GTPase-activating protein 11A


Theoretical massNumber of molelcules
Total (without water)30,4722
Polymers30,4721
Non-polymers01
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Rho GTPase-activating protein 11A


Theoretical massNumber of molelcules
Total (without water)30,4721
Polymers30,4721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.066, 106.150, 107.335
Angle α, β, γ (deg.)90.000, 97.160, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Rho GTPase-activating protein 11A / Rho-type GTPase-activating protein 11A


Mass: 30472.131 Da / Num. of mol.: 4 / Fragment: UNP residues 1-253
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARHGAP11A / Plasmid: pET28-mhl / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q6P4F7
#2: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 6 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.14 Å3/Da / Density % sol: 42.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 8
Details: 6% PEG 8000, 0.2M sodium chloride, 0.1M tris, pH 8.0. The protein stock solution was supplemented with 5% Ethylene Glycol, and 1:100 (m:m) Endoproteinase Glu-C. vapor diffusion, temperature 291K, VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.96863 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 14, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 49354 / % possible obs: 94.7 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.063 / Χ2: 1.526
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.2-2.281.90.54935330.98668.7
2.28-2.372.50.43446040.94888.7
2.37-2.483.10.35250500.99997.2
2.48-2.613.60.26851941.01999.7
2.61-2.773.80.19551831.14100
2.77-2.993.80.13652001.328100
2.99-3.293.80.09252331.67599.7
3.29-3.763.80.05951001.94298.3
3.76-4.743.80.05250812.66897
4.74-503.70.03151761.69297.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.4.0069refinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
tlsmdrefinement
FFAS03/SCWRLrefinement
Cootmodel building
MolProbitymodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RGP

1rgp


Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.906 / WRfactor Rfree: 0.275 / WRfactor Rwork: 0.226 / SU B: 18.394 / SU ML: 0.212 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.339 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Atomic B-factors are residuals from TLS refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.277 2233 5.01 %thin shells (sftools)
Rwork0.227 ---
obs0.23 44569 98.072 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 48.527 Å2
Baniso -1Baniso -2Baniso -3
1-1.469 Å20 Å2-0.986 Å2
2--0.262 Å20 Å2
3----1.976 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6461 0 6 58 6525
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0226595
X-RAY DIFFRACTIONr_bond_other_d0.0010.024230
X-RAY DIFFRACTIONr_angle_refined_deg1.2931.9728978
X-RAY DIFFRACTIONr_angle_other_deg1.752310384
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4455848
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.53624255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.96215991
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3421525
X-RAY DIFFRACTIONr_chiral_restr0.0740.21078
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217326
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021296
X-RAY DIFFRACTIONr_mcbond_it1.22624318
X-RAY DIFFRACTIONr_mcbond_other0.3121722
X-RAY DIFFRACTIONr_mcangle_it1.90336841
X-RAY DIFFRACTIONr_scbond_it1.32822277
X-RAY DIFFRACTIONr_scangle_it1.94732137
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 (%)
2.3-2.3590.34810.2642971326491.054
2.359-2.4230.3093450.2492792328295.582
2.423-2.49200.2473062310098.774
2.492-2.5670.3012800.2362791307999.74
2.567-2.6500.2412961296599.865
2.65-2.7410.32720.24825822854100
2.741-2.8430.264800.24826792759100
2.843-2.9560.331500.2382522267499.925
2.956-3.0850.3061950.2492377257899.767
3.085-3.2310.318320.2492384242499.67
3.231-3.4010.3181370.242201235099.489
3.401-3.6010.2741470.2222045223498.12
3.601-3.8410.2751260.1951924209697.805
3.841-4.1360.2451050.2091786194897.074
4.136-4.5110.215800.1881638178296.409
4.511-5.0120.204830.1911529165797.284
5.012-5.7280.284600.2321369146797.41
5.728-6.8760.386590.2831160125397.287
6.876-9.1950.255530.227957101899.214
9.195-200.242280.22260666195.915
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.4544-0.38881.11951.9891-0.50195.26510.09460.20450.2018-0.152-0.0873-0.0213-0.0697-0.1611-0.0073-0.13710.0284-0.0038-0.0813-0.0029-0.1159-2.518543.195231.6927
21.570.9905-0.65343.5219-0.88542.8549-0.00760.14930.1925-0.1230.01610.0848-0.5859-0.0968-0.0085-0.0303-0.02690.0122-0.16710.053-0.1598-3.59429.74481.1514
32.87430.3671-1.37611.8832-0.97155.21580.1254-0.2011-0.0190.2396-0.1477-0.0899-0.2350.45620.0223-0.1928-0.078-0.0144-0.15560.0178-0.21540.9916-6.87823.7179
44.3864-0.89161.07144.3933-1.20732.73290.1066-0.045-0.3692-0.16930.17420.49890.2652-0.1688-0.2808-0.1907-0.0268-0.0517-0.2022-0.0016-0.0435-9.159724.690351.0377
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-4 - 25214 - 270
2X-RAY DIFFRACTION2BB1 - 25119 - 269
3X-RAY DIFFRACTION3CC3 - 24821 - 266
4X-RAY DIFFRACTION4DD-4 - 24914 - 267

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