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

ID or keywords:

Entry

Database: PDB / ID: 3byi

Title

Crystal structure of human Rho GTPase activating protein 15 (ARHGAP15)

Components

Rho GTPase activating protein 15

Keywords

SIGNALING PROTEIN / Rho GTPase / BM046 / ARHGAP15 / Structural Genomics Consortium / SGC

Function / homology

Function and homology information

regulation of small GTPase mediated signal transduction / small GTPase-mediated signal transduction / RAC3 GTPase cycle / RAC1 GTPase cycle / GTPase activator activity / regulation of cell shape / nucleoplasm / plasma membrane / cytosol / cytoplasm
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.25 Å

Authors

Shrestha, L. / Tickle, J. / Elkins, J. / Burgess-Brown, N. / Johansson, C. / Papagrigoriou, E. / Kavanagh, K. / Pike, A.C.W. / Ugochukwu, E. / Uppenberg, J. ...

Citation

Journal: 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. ...

History

Deposition	Jan 16, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 26, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Aug 30, 2023	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3byi.cif.gz	175.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3byi.ent.gz	140 KB	Display	PDB format
PDBx/mmJSON format	3byi.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3byi_validation.pdf.gz	448.6 KB	Display	wwPDB validaton report
Full document	3byi_full_validation.pdf.gz	456.1 KB	Display
Data in XML	3byi_validation.xml.gz	31.3 KB	Display
Data in CIF	3byi_validation.cif.gz	43.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/by/3byi ftp://data.pdbj.org/pub/pdb/validation_reports/by/3byi	HTTPS FTP

-
Related structure data

Related structure data	1am4S 1f7cS 1grnS 1ow3S 1rgpS 1tx4S 2ngrS S: Starting model for refinement
Similar structure data	6ni1-1 2ahs-1 4qua-d 2ooq-1 6bfk-1 1nq1-d 6mx2-6 6ni1-2 1nuo-d 3ra0-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

S: Starting model for refinement

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#148 - Apr 2012 Ras Protein similarity (3) #35 - Nov 2002 Ferritin and Transferrin similarity (2) #245 - May 2020 Spliceosomes similarity (1)

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

98 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Rho GTPase activating protein 15

defined by author
24.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Rho GTPase activating protein 15

defined by author
24.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Rho GTPase activating protein 15

defined by author
24.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Rho GTPase activating protein 15

defined by author
24.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

Idetical with deposited unit
defined by software

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 number	18
Space group name H-M	P2₁2₁2

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	PRO	PRO	THR	THR	4	A	A	263 - 293	4 - 34
2	1	PRO	PRO	THR	THR	4	B	B	263 - 293	4 - 34
3	1	PRO	PRO	THR	THR	4	C	C	263 - 293	4 - 34
4	1	PRO	PRO	THR	THR	4	D	D	263 - 293	4 - 34
5	2	VAL	VAL	PHE	PHE	2	A	A	294 - 330	35 - 71
6	2	VAL	VAL	PHE	PHE	2	B	B	294 - 330	35 - 71
7	2	VAL	VAL	PHE	PHE	2	C	C	294 - 330	35 - 71
8	2	VAL	VAL	PHE	PHE	2	D	D	294 - 330	35 - 71
9	3	ILE	ILE	LEU	LEU	1	A	A	331 - 338	72 - 79
10	3	ILE	ILE	LEU	LEU	1	B	B	331 - 338	72 - 79
11	3	ILE	ILE	LEU	LEU	1	C	C	331 - 338	72 - 79
12	3	ILE	ILE	LEU	LEU	1	D	D	331 - 338	72 - 79
13	4	ASN	ASN	PRO	PRO	2	A	A	339 - 368	80 - 109
14	4	ASN	ASN	PRO	PRO	2	B	B	339 - 368	80 - 109
15	4	ASN	ASN	PRO	PRO	2	C	C	339 - 368	80 - 109
16	4	ASN	ASN	PRO	PRO	2	D	D	339 - 368	80 - 109
17	5	TYR	TYR	ASP	ASP	4	A	A	369 - 404	110 - 145
18	5	TYR	TYR	ASP	ASP	4	B	B	369 - 404	110 - 145
19	5	TYR	TYR	ASP	ASP	4	C	C	369 - 404	110 - 145
20	5	TYR	TYR	ASP	ASP	4	D	D	369 - 404	110 - 145
21	6	THR	THR	LEU	LEU	2	A	A	405 - 439	146 - 180
22	6	THR	THR	LEU	LEU	2	B	B	405 - 439	146 - 180
23	6	THR	THR	LEU	LEU	2	C	C	405 - 439	146 - 180
24	6	THR	THR	LEU	LEU	2	D	D	405 - 439	146 - 180
25	7	ARG	ARG	HIS	HIS	4	A	A	440 - 451	181 - 192
26	7	ARG	ARG	HIS	HIS	4	B	B	440 - 451	181 - 192
27	7	ARG	ARG	HIS	HIS	4	C	C	440 - 451	181 - 192
28	7	ARG	ARG	HIS	HIS	4	D	D	440 - 451	181 - 192
29	8	MET	MET	PHE	PHE	2	A	A	452 - 470	193 - 211
30	8	MET	MET	PHE	PHE	2	B	B	452 - 470	193 - 211
31	8	MET	MET	PHE	PHE	2	C	C	452 - 470	193 - 211
32	8	MET	MET	PHE	PHE	2	D	D	452 - 470	193 - 211

#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 Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H₂O

#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

Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.5 Å³/Da / Density % sol: 50.83 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 2.4M Na malate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SLS

/ Beamline: X10SA / Wavelength: 0.95362 Å

Detector

Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 16, 2007

Radiation

Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.95362 Å / Relative weight: 1

Reflection

Redundancy: 7.1 % / Av σ(I) over netI: 6.8 / Number: 338056 / R_merge(I) obs: 0.086 / R_sym 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 (%)	ID	R_merge(I) obs	R_sym value	Redundancy
7.12	65.09	99.6	1	0.033	0.033	6.7
5.03	7.12	100	1	0.039	0.039	7.2
4.11	5.03	100	1	0.047	0.047	7.3
3.56	4.11	100	1	0.06	0.06	7.4
3.18	3.56	100	1	0.084	0.084	7.4
2.9	3.18	100	1	0.141	0.141	7.2
2.69	2.9	100	1	0.245	0.245	7.1
2.52	2.69	100	1	0.383	0.383	7
2.37	2.52	99.9	1	0.557	0.557	7
2.25	2.37	99.9	1	0.823	0.823	6.9

Reflection

Resolution: 2.25→50 Å / Num. all: 47518 / Num. obs: 47518 / % possible obs: 100 % / Redundancy: 7.1 % / R_merge(I) obs: 0.086 / R_sym value: 0.086 / Net I/σ(I): 15.4

Reflection shell

Resolution: 2.25→2.37 Å / Redundancy: 6.9 % / R_merge(I) obs: 0.823 / Mean I/σ(I) obs: 0.9 / Num. unique all: 6829 / R_sym value: 0.823 / % possible all: 99.9

-
Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	3 Å	60.31 Å
Translation	3 Å	60.31 Å

-
Processing

Software

Name	Version	Classification
SCALA		data scaling
PHASER		phasing
REFMAC		refinement
PDB_EXTRACT	3.004	data extraction
CrystalClear		data collection
MOSFLM		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: assembly of PDB entries 1TX4, 1OW3, 1RGP, 2NGR, 1GRN, 1F7C, 1AM4

Resolution: 2.25→50 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c 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

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.244	2418	5.1 %	RANDOM
R_work	0.188	-	-	-
all	0.191	47463	-	-
obs	0.191	47463	99.95 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 40.047 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.04 Å²	0 Å²	0 Å²
2-	-	3.01 Å²	0 Å²
3-	-	-	-1.97 Å²

Refinement step

Cycle: LAST / Resolution: 2.25→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6602	0	0	197	6799

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	6759
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	4585
X-RAY DIFFRACTION	r_angle_refined_deg	1.379	1.955	9147
X-RAY DIFFRACTION	r_angle_other_deg	1.006	3	11240
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.688	5	843
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.647	24.751	301
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.796	15	1205
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.527	15	32
X-RAY DIFFRACTION	r_chiral_restr	0.082	0.2	1044
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	7450
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	1322
X-RAY DIFFRACTION	r_nbd_refined	0.218	0.2	1607
X-RAY DIFFRACTION	r_nbd_other	0.177	0.2	4569
X-RAY DIFFRACTION	r_nbtor_refined	0.178	0.2	3315
X-RAY DIFFRACTION	r_nbtor_other	0.086	0.2	3378
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.164	0.2	216
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.279	0.2	13
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.236	0.2	41
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.18	0.2	5
X-RAY DIFFRACTION	r_mcbond_it	2.023	3	4327
X-RAY DIFFRACTION	r_mcbond_other	0.528	3	1695
X-RAY DIFFRACTION	r_mcangle_it	2.915	5	6801
X-RAY DIFFRACTION	r_scbond_it	5.269	8	2728
X-RAY DIFFRACTION	r_scangle_it	6.794	11	2343

Refine LS restraints NCS

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

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	807	TIGHT POSITIONAL	0.06	0.05
2	B	807	TIGHT POSITIONAL	0.05	0.05
3	C	807	TIGHT POSITIONAL	0.04	0.05
4	D	807	TIGHT POSITIONAL	0.04	0.05
1	A	1834	MEDIUM POSITIONAL	0.47	0.5
2	B	1834	MEDIUM POSITIONAL	0.52	0.5
3	C	1834	MEDIUM POSITIONAL	0.39	0.5
4	D	1834	MEDIUM POSITIONAL	0.34	0.5
1	A	807	TIGHT THERMAL	0.18	0.5
2	B	807	TIGHT THERMAL	0.18	0.5
3	C	807	TIGHT THERMAL	0.15	0.5
4	D	807	TIGHT THERMAL	0.16	0.5
1	A	1834	MEDIUM THERMAL	1.14	2
2	B	1834	MEDIUM THERMAL	1.08	2
3	C	1834	MEDIUM THERMAL	1	2
4	D	1834	MEDIUM THERMAL	1.06	2

LS refinement shell

Resolution: 2.25→2.308 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.35	172	-
R_work	0.25	3291	-
all	-	3463	-
obs	-	-	99.91 %

Refinement TLS params.

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

ID	L11 (°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)
1	1.7545	0.4178	0.0968	1.5351	0.5836	2.1854	0.0247	0.3293	-0.111	-0.002	-0.0278	-0.0695	-0.0647	0.1098	0.003	-0.1982	0.04	-0.0215	0.0264	-0.0776	-0.2307	18.3287	-37.2958	-32.7971
2	3.9844	0.9223	-0.5924	1.3778	0.3079	3.2272	0.1267	-0.0503	0.3588	0.0554	-0.0002	0.0366	-0.2338	0.243	-0.1265	-0.1066	-0.0193	0.0492	-0.1842	-0.0633	-0.1946	29.9814	-19.8642	1.177
3	2.3684	0.4389	-0.2265	1.6221	0.6004	2.983	0.1618	-0.0138	-0.054	0.1444	0.0828	-0.1407	-0.0078	0.3396	-0.2445	-0.2037	-0.0527	0.0125	0.0968	-0.1245	-0.1313	52.4813	-24.1043	-10.4774
4	2.1692	0.4661	0.2662	1.6239	0.7199	3.451	0.056	0.1448	-0.4584	0.168	0.0215	-0.1818	0.4361	0.1397	-0.0775	-0.0132	0.1051	-0.0291	-0.171	-0.1598	0.1143	32.0115	-55.8565	-21.8456

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	261 - 471	2 - 212
2	X-RAY DIFFRACTION	2	B	B	261 - 471	2 - 212
3	X-RAY DIFFRACTION	3	C	C	263 - 472	4 - 213
4	X-RAY DIFFRACTION	4	D	D	263 - 471	4 - 212

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Phasing

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi