PDB-2osa: The Rho-GAP domain of human N-chimaerin

ID or keywords:

Entry

Database: PDB / ID: 2osa

Title

The Rho-GAP domain of human N-chimaerin

Components

N-chimaerin

Keywords

SIGNALING PROTEIN / Rho-GAP / GTPASE ACTIVATION /

Structural Genomics /

Structural Genomics Consortium / SGC

Function / homology

Function and homology information

motor neuron axon guidance / regulation of small GTPase mediated signal transduction /

regulation of axonogenesis / CDC42 GTPase cycle / ephrin receptor signaling pathway / RAC1 GTPase cycle /

GTPase activator activity /

ephrin receptor binding /

metal ion binding /

cytosol
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Walker, J.R. / Hong, B.S. / Shen, L. / Arrowsmith, C.H. / Sundstrom, M. / Weigelt, J. / Edwards, A.M. / Bochkarev, A. / Park, H.W. / Structural Genomics Consortium (SGC)

Citation

Journal: To be Published
Title: Crystal structure of the Rho-GAP domain from human N-chimaerin
Authors: Walker, J.R. / Hong, B.S. / Shen, L. / Arrowsmith, C.H. / Sundstrom, M. / Weigelt, J. / Edwards, A.M. / Bochkarev, A. / Park, H.W.

History

Deposition	Feb 5, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 6, 2007	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Oct 18, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.4	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_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2osa.cif.gz	97 KB	Display	PDBx/mmCIF format
PDB format	pdb2osa.ent.gz	75.9 KB	Display	PDB format
PDBx/mmJSON format	2osa.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/os/2osa ftp://data.pdbj.org/pub/pdb/validation_reports/os/2osa	HTTPS FTP

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Related structure data

Related structure data	1xa6S S: Starting model for refinement
Similar structure data	6tg4-2 4li8-1 4tos-2 4chh-1 5c5r-1 4mis-d 3udd-1 4tkg-2 5uvp-1 5aeh-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#195 - Mar 2016 RAF Protein Kinases similarity (6) #196 - Apr 2016 Lead Poisoning similarity (6) #222 - Jun 2018 Proteins and Nanoparticles similarity (6) #148 - Apr 2012 Ras Protein similarity (2) #35 - Nov 2002 Ferritin and Transferrin similarity (2) #245 - May 2020 Spliceosomes similarity (1)

Deposited unit

A: N-chimaerin

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	92.490, 92.490, 47.095
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	169
Space group name H-M	P6₁

#1: Protein	N-chimaerin / NC / N-chimerin / Alpha chimerin / A-chimaerin / Rho GTPase-activating protein 2 Mass: 23144.918 Da / Num. of mol.: 1 / Fragment: Rho-GAP Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CHN1, ARHGAP2, CHN / Plasmid: pET28-LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P15882
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

N-chimaerin / NC / N-chimerin / Alpha chimerin / A-chimaerin / Rho GTPase-activating protein 2

Mass: 23144.918 Da / Num. of mol.: 1 / Fragment: Rho-GAP Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: CHN1, ARHGAP2, CHN / Plasmid: pET28-LIC / Species (production host): Escherichia coli / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P15882

#2: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.51 Å³/Da / Density % sol: 51.02 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 30% Jeffamine ED-2001, 0.1M HEPES pH 7.0, 0.1 M Adenosine-5-triphosphate disodium salt, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å
Detector	Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 24, 2006
Radiation	Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54178 Å / Relative weight: 1
Reflection	Resolution: 1.8→18.43 Å / Num. all: 21064 / Num. obs: 21064 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / R_sym value: 0.09 / Net I/σ(I): 13.8
Reflection shell	Resolution: 1.8→1.86 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.1 / Num. unique all: 1912 / R_sym value: 0.77 / % possible all: 90.4

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
SBC-Collect		data collection
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 1XA6

1xa6

Resolution: 1.8→18.43 Å / Cor.coef. F_o:F_c: 0.967 / Cor.coef. F_o:F_c free: 0.942 / SU B: 6.477 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25131	1082	5.1 %	RANDOM
R_work	0.18671	-	-	-
obs	0.18978	19956	98.02 %	-
all	-	19956	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 36.411 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.11 Å²	-0.56 Å²	0 Å²
2-	-	-1.11 Å²	0 Å²
3-	-	-	1.67 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→18.43 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1582	0	0	153	1735

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.022	1610
X-RAY DIFFRACTION	r_angle_refined_deg	1.498	1.998	2178
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.05	5	197
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.101	24.384	73
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.146	15	306
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.355	15	11
X-RAY DIFFRACTION	r_chiral_restr	0.104	0.2	253
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	1187
X-RAY DIFFRACTION	r_nbd_refined	0.224	0.2	833
X-RAY DIFFRACTION	r_nbtor_refined	0.304	0.2	1150
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.142	0.2	121
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.165	0.2	40
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.19	0.2	13
X-RAY DIFFRACTION	r_mcbond_it	1.848	3	1026
X-RAY DIFFRACTION	r_mcangle_it	2.427	4	1605
X-RAY DIFFRACTION	r_scbond_it	3.81	5	657
X-RAY DIFFRACTION	r_scangle_it	4.938	7	573

LS refinement shell

Resolution: 1.8→1.846 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.436	75	-
R_work	0.327	1278	-
obs	-	-	86.45 %

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	8.6385	1.5006	9.7956	4.4819	7.2105	18.2971	-0.012	-0.1979	-0.1721	0.4945	-0.3451	0.3511	0.2039	-0.2384	0.357	0.0903	-0.0299	0.0487	0.1129	-0.0398	0.0037	-2.3775	37.6787	13.7681
2	23.5527	-7.5618	-2.6591	2.4379	0.4153	19.2634	-0.2153	-0.1313	-0.306	0.359	0.3447	0.1897	1.6252	0.7171	-0.1294	0.2775	-0.0407	0.0071	0.1837	-0.0238	-0.1541	2.4703	32.5612	19.6182
3	2.4744	-0.3225	0.1247	3.4411	0.4688	8.1601	0.0331	-0.5239	-0.1919	0.3237	-0.0054	-0.2564	0.0377	0.1128	-0.0277	0.0682	0.0266	0.011	0.1084	0.0399	0.032	4.0122	28.9172	9.4923
4	17.6244	1.3494	-2.2795	18.7804	-3.8993	4.2003	-0.1021	-0.1229	-0.882	-0.002	0.2819	0.2057	0.6166	-0.1542	-0.1798	0.1314	0.0475	0.0218	0.0138	0.0202	0.0909	4.0919	22.2497	0.2863
5	9.4348	-3.3845	4.627	18.2976	-3.821	2.5426	-0.2165	0.261	-0.2906	-0.3862	0.3089	-0.0622	0.0023	0.1061	-0.0924	0.1002	-0.0396	0.0642	0.1291	-0.0651	-0.0152	5.1975	26.3465	-9.8895
6	7.7357	0.8838	-2.6588	0.1754	-0.7816	3.9819	-0.0036	0.6852	0.2114	-0.1882	0.176	0.159	0.0747	-0.2846	-0.1724	0.0838	-0.0226	0.0382	0.0605	0.0119	0.0952	-6.1736	31.4222	-6.1388
7	7.0307	1.269	3.6174	1.1561	3.8304	12.7523	-0.1208	-0.3416	0.7947	-0.1217	-0.106	0.0919	-0.1214	-0.6165	0.2268	0.0422	-0.0184	0.041	0.1043	0.0072	0.1836	-11.4256	30.0148	4.766
8	18.7516	-2.8053	-5.6435	11.3307	4.2636	2.77	0.1095	-1.2982	-1.2319	0.2527	-0.4362	0.164	0.3333	-0.0162	0.3266	0.0671	-0.051	0.0348	0.1561	0.1411	0.0473	-7.258	24.684	11.5714
9	16.9274	1.763	-5.0162	2.7109	-5.8642	12.7772	-0.4556	0.2953	-1.052	-0.9533	-0.0021	-0.1681	1.3255	-0.6984	0.4577	0.1693	-0.0535	0.0975	-0.051	-0.0024	0.2302	-6.6589	19.4237	-0.2041
10	3.2883	0.5214	-1.1934	4.3891	0.1629	2.0253	-0.1014	0.008	-0.0958	-0.1104	0.0473	-0.0097	0.0338	-0.0481	0.0541	0.0614	0.0019	0.0219	0.1145	0.0066	0.049	-2.2493	31.3534	-0.1996
11	3.6662	-2.0157	-4.7724	16.6391	8.3508	8.3242	0.3885	-0.0023	0.097	-0.3553	-0.3033	0.3412	-0.3949	-0.1915	-0.0853	0.0957	0.0432	0.0131	0.0767	-0.0634	0.096	-2.9457	42.0625	7.5246
12	3.5154	0.6319	-1.2286	3.1877	0.4504	4.5019	-0.2079	0.117	0.2137	-0.0916	-0.0101	-0.2247	-0.3866	0.2697	0.218	0.0917	-0.0077	-0.0462	0.094	-0.0023	0.0718	12.0077	50.9198	3.1464
13	4.7162	2.5191	-8.5316	6.3805	-2.1583	22.618	-0.383	-0.221	-0.5375	0.2445	-0.0787	-1.0473	-0.6896	1.4788	0.4616	-0.0072	-0.0802	-0.0876	0.1342	0.0016	0.188	21.591	48.2503	3.1197
14	1.165	0.0307	-0.6207	3.3993	1.8899	4.0672	-0.0693	-0.2604	-0.1412	0.1998	-0.0441	-0.2867	-0.0302	0.1392	0.1135	0.0622	0.0331	-0.0266	0.0978	0.0223	0.0887	11.6975	36.4875	5.8711
15	11.0972	-1.1195	-2.5838	3.5527	1.2728	2.8885	-0.3474	0.6491	-0.5111	-0.6801	0.0901	-0.1923	0.6173	-0.0033	0.2573	0.1434	-0.016	0.0957	0.0437	-0.0335	0.0693	12.1726	27.5015	-12.175
16	7.8355	3.8629	-2.6313	12.0032	6.9905	7.6852	-0.0114	0.475	0.2104	-0.752	0.163	-0.4058	-0.4099	-0.3067	-0.1516	0.1247	-0.0141	0.0273	0.0914	0.0079	0.0452	9.3386	36.3297	-11.8246
17	2.8214	0.989	1.226	3.0003	2.3989	2.9138	-0.1889	-0.1444	0.2863	-0.0741	-0.0772	0.097	-0.1481	-0.1086	0.2662	0.0792	0.0087	-0.0292	0.0825	-0.0097	0.0948	3.0691	45.4878	-1.1909
18	14.9092	-8.3367	2.2368	4.6637	-1.1269	7.6798	-0.3575	0.3121	2.3636	0.0067	-0.0756	-1.0878	-0.7116	-0.0894	0.4331	0.0598	-0.0432	-0.1173	-0.0344	0.0515	0.3511	4.2364	56.1385	-6.2849
19	7.2927	-4.1753	2.499	7.8055	-4.9838	4.3931	-0.0852	0.3416	0.0739	-0.2416	-0.028	-0.323	0.143	0.2535	0.1132	0.0516	-0.0136	0.0104	0.0835	-0.0136	0.078	12.8964	43.0507	-3.8759
20	25.5029	-5.9968	-7.7283	28.0235	1.8571	9.034	-0.1063	-0.5273	-0.8936	0.3069	0.2216	-0.6972	0.5837	0.5487	-0.1153	-0.0263	0.0427	-0.0899	0.0759	0.0885	0.1529	19.8927	37.3648	3.2436

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	264 - 272	7 - 15
2	X-RAY DIFFRACTION	2	A	A	273 - 279	16 - 22
3	X-RAY DIFFRACTION	3	A	A	280 - 289	23 - 32
4	X-RAY DIFFRACTION	4	A	A	290 - 295	33 - 38
5	X-RAY DIFFRACTION	5	A	A	296 - 302	39 - 45
6	X-RAY DIFFRACTION	6	A	A	303 - 312	46 - 55
7	X-RAY DIFFRACTION	7	A	A	313 - 317	56 - 60
8	X-RAY DIFFRACTION	8	A	A	318 - 327	61 - 70
9	X-RAY DIFFRACTION	9	A	A	328 - 334	71 - 77
10	X-RAY DIFFRACTION	10	A	A	335 - 347	78 - 90
11	X-RAY DIFFRACTION	11	A	A	348 - 352	91 - 95
12	X-RAY DIFFRACTION	12	A	A	353 - 372	96 - 115
13	X-RAY DIFFRACTION	13	A	A	373 - 382	116 - 125
14	X-RAY DIFFRACTION	14	A	A	383 - 405	126 - 148
15	X-RAY DIFFRACTION	15	A	A	406 - 411	149 - 154
16	X-RAY DIFFRACTION	16	A	A	412 - 417	155 - 160
17	X-RAY DIFFRACTION	17	A	A	418 - 431	161 - 174
18	X-RAY DIFFRACTION	18	A	A	432 - 443	175 - 186
19	X-RAY DIFFRACTION	19	A	A	444 - 454	187 - 197
20	X-RAY DIFFRACTION	20	A	A	455 - 459	198 - 202

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