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- PDB-3byi: Crystal structure of human Rho GTPase activating protein 15 (ARHGAP15) -

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Basic information

Entry
Database: PDB / ID: 3byi
TitleCrystal structure of human Rho GTPase activating protein 15 (ARHGAP15)
ComponentsRho GTPase activating protein 15
KeywordsSIGNALING PROTEIN / Rho GTPase / BM046 / ARHGAP15 / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


: / regulation of small GTPase mediated signal transduction / regulation of GTPase activity / GTPase activator activity / regulation of cell shape / signal transduction / membrane / cytosol / cytoplasm
Similarity search - Function
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 / PH domain / PH domain profile. / Pleckstrin homology domain. ...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 / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Rho GTPase-activating protein 15 / Rho GTPase-activating protein 15
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å
AuthorsShrestha, L. / Tickle, J. / Elkins, J. / Burgess-Brown, N. / Johansson, C. / Papagrigoriou, E. / Kavanagh, K. / Pike, A.C.W. / Ugochukwu, E. / Uppenberg, J. ...Shrestha, L. / Tickle, J. / Elkins, J. / Burgess-Brown, N. / Johansson, C. / Papagrigoriou, E. / Kavanagh, K. / Pike, A.C.W. / Ugochukwu, E. / Uppenberg, J. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Doyle, D. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structure of Human Rho GTPase Activating Protein 15 (ARHGAP15).
Authors: Shrestha, L. / Tickle, J. / Elkins, J. / Burgess-Brown, N. / Johansson, C. / Papagrigoriou, E. / Kavanagh, K. / Pike, A.C.W. / Ugochukwu, E. / Uppenberg, J. / von Delft, F. / Arrowsmith, C.H. ...Authors: Shrestha, L. / Tickle, J. / Elkins, J. / Burgess-Brown, N. / Johansson, C. / Papagrigoriou, E. / Kavanagh, K. / Pike, A.C.W. / Ugochukwu, E. / Uppenberg, J. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Doyle, D.
History
DepositionJan 16, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 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 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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: Rho GTPase activating protein 15
B: Rho GTPase activating protein 15
C: Rho GTPase activating protein 15
D: Rho GTPase activating protein 15


Theoretical massNumber of molelcules
Total (without water)98,0174
Polymers98,0174
Non-polymers00
Water3,549197
1
A: Rho GTPase activating protein 15


Theoretical massNumber of molelcules
Total (without water)24,5041
Polymers24,5041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Rho GTPase activating protein 15


Theoretical massNumber of molelcules
Total (without water)24,5041
Polymers24,5041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Rho GTPase activating protein 15


Theoretical massNumber of molelcules
Total (without water)24,5041
Polymers24,5041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Rho GTPase activating protein 15


Theoretical massNumber of molelcules
Total (without water)24,5041
Polymers24,5041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.618, 130.142, 62.477
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51A
61B
71C
81D
91A
101B
111C
121D
131A
141B
151C
161D
171A
181B
191C
201D
211A
221B
231C
241D
251A
261B
271C
281D
291A
301B
311C
321D

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROTHRTHR4AA263 - 2934 - 34
21PROPROTHRTHR4BB263 - 2934 - 34
31PROPROTHRTHR4CC263 - 2934 - 34
41PROPROTHRTHR4DD263 - 2934 - 34
52VALVALPHEPHE2AA294 - 33035 - 71
62VALVALPHEPHE2BB294 - 33035 - 71
72VALVALPHEPHE2CC294 - 33035 - 71
82VALVALPHEPHE2DD294 - 33035 - 71
93ILEILELEULEU1AA331 - 33872 - 79
103ILEILELEULEU1BB331 - 33872 - 79
113ILEILELEULEU1CC331 - 33872 - 79
123ILEILELEULEU1DD331 - 33872 - 79
134ASNASNPROPRO2AA339 - 36880 - 109
144ASNASNPROPRO2BB339 - 36880 - 109
154ASNASNPROPRO2CC339 - 36880 - 109
164ASNASNPROPRO2DD339 - 36880 - 109
175TYRTYRASPASP4AA369 - 404110 - 145
185TYRTYRASPASP4BB369 - 404110 - 145
195TYRTYRASPASP4CC369 - 404110 - 145
205TYRTYRASPASP4DD369 - 404110 - 145
216THRTHRLEULEU2AA405 - 439146 - 180
226THRTHRLEULEU2BB405 - 439146 - 180
236THRTHRLEULEU2CC405 - 439146 - 180
246THRTHRLEULEU2DD405 - 439146 - 180
257ARGARGHISHIS4AA440 - 451181 - 192
267ARGARGHISHIS4BB440 - 451181 - 192
277ARGARGHISHIS4CC440 - 451181 - 192
287ARGARGHISHIS4DD440 - 451181 - 192
298METMETPHEPHE2AA452 - 470193 - 211
308METMETPHEPHE2BB452 - 470193 - 211
318METMETPHEPHE2CC452 - 470193 - 211
328METMETPHEPHE2DD452 - 470193 - 211

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Components

#1: Protein
Rho GTPase activating protein 15 / Rho GTPase activating protein 15 / isoform CRA_d


Mass: 24504.322 Da / Num. of mol.: 4 / Fragment: Residues 262-473
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARHGAP15 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)(R3)(pRARE2) / References: UniProt: Q8IXX1, UniProt: Q53QZ3*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.5 Å3/Da / Density % sol: 50.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 2.4M Na malate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.95362 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 16, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95362 Å / Relative weight: 1
ReflectionRedundancy: 7.1 % / Av σ(I) over netI: 6.8 / Number: 338056 / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / D res high: 1.525 Å / D res low: 65.094 Å / Num. obs: 47518 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
7.1265.0999.610.0330.0336.7
5.037.1210010.0390.0397.2
4.115.0310010.0470.0477.3
3.564.1110010.060.067.4
3.183.5610010.0840.0847.4
2.93.1810010.1410.1417.2
2.692.910010.2450.2457.1
2.522.6910010.3830.3837
2.372.5299.910.5570.5577
2.252.3799.910.8230.8236.9
ReflectionResolution: 2.25→50 Å / Num. all: 47518 / Num. obs: 47518 / % possible obs: 100 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 15.4
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.823 / Mean I/σ(I) obs: 0.9 / Num. unique all: 6829 / Rsym value: 0.823 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å60.31 Å
Translation3 Å60.31 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
CrystalCleardata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: assembly of PDB entries 1TX4, 1OW3, 1RGP, 2NGR, 1GRN, 1F7C, 1AM4

1tx4

1ow3

1rgp

2ngr

1grn

1f7c

1am4


Resolution: 2.25→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.936 / SU B: 13.993 / SU ML: 0.171 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.266 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.244 2418 5.1 %RANDOM
Rwork0.188 ---
all0.191 47463 --
obs0.191 47463 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.047 Å2
Baniso -1Baniso -2Baniso -3
1--1.04 Å20 Å20 Å2
2--3.01 Å20 Å2
3----1.97 Å2
Refinement stepCycle: LAST / Resolution: 2.25→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6602 0 0 197 6799
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0226759
X-RAY DIFFRACTIONr_bond_other_d0.0020.024585
X-RAY DIFFRACTIONr_angle_refined_deg1.3791.9559147
X-RAY DIFFRACTIONr_angle_other_deg1.006311240
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6885843
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.64724.751301
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.796151205
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5271532
X-RAY DIFFRACTIONr_chiral_restr0.0820.21044
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027450
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021322
X-RAY DIFFRACTIONr_nbd_refined0.2180.21607
X-RAY DIFFRACTIONr_nbd_other0.1770.24569
X-RAY DIFFRACTIONr_nbtor_refined0.1780.23315
X-RAY DIFFRACTIONr_nbtor_other0.0860.23378
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2216
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2790.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2360.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.25
X-RAY DIFFRACTIONr_mcbond_it2.02334327
X-RAY DIFFRACTIONr_mcbond_other0.52831695
X-RAY DIFFRACTIONr_mcangle_it2.91556801
X-RAY DIFFRACTIONr_scbond_it5.26982728
X-RAY DIFFRACTIONr_scangle_it6.794112343
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A807TIGHT POSITIONAL0.060.05
2B807TIGHT POSITIONAL0.050.05
3C807TIGHT POSITIONAL0.040.05
4D807TIGHT POSITIONAL0.040.05
1A1834MEDIUM POSITIONAL0.470.5
2B1834MEDIUM POSITIONAL0.520.5
3C1834MEDIUM POSITIONAL0.390.5
4D1834MEDIUM POSITIONAL0.340.5
1A807TIGHT THERMAL0.180.5
2B807TIGHT THERMAL0.180.5
3C807TIGHT THERMAL0.150.5
4D807TIGHT THERMAL0.160.5
1A1834MEDIUM THERMAL1.142
2B1834MEDIUM THERMAL1.082
3C1834MEDIUM THERMAL12
4D1834MEDIUM THERMAL1.062
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 172 -
Rwork0.25 3291 -
all-3463 -
obs--99.91 %
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)
11.75450.41780.09681.53510.58362.18540.02470.3293-0.111-0.002-0.0278-0.0695-0.06470.10980.003-0.19820.04-0.02150.0264-0.0776-0.230718.3287-37.2958-32.7971
23.98440.9223-0.59241.37780.30793.22720.1267-0.05030.35880.0554-0.00020.0366-0.23380.243-0.1265-0.1066-0.01930.0492-0.1842-0.0633-0.194629.9814-19.86421.177
32.36840.4389-0.22651.62210.60042.9830.1618-0.0138-0.0540.14440.0828-0.1407-0.00780.3396-0.2445-0.2037-0.05270.01250.0968-0.1245-0.131352.4813-24.1043-10.4774
42.16920.46610.26621.62390.71993.4510.0560.1448-0.45840.1680.0215-0.18180.43610.1397-0.0775-0.01320.1051-0.0291-0.171-0.15980.114332.0115-55.8565-21.8456
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA261 - 4712 - 212
2X-RAY DIFFRACTION2BB261 - 4712 - 212
3X-RAY DIFFRACTION3CC263 - 4724 - 213
4X-RAY DIFFRACTION4DD263 - 4714 - 212

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