PDB-4rkf: Drosophila melanogaster Rab3 bound to GMPPNP

ID or keywords:

Entry

Database: PDB / ID: 4rkf

Title

Drosophila melanogaster Rab3 bound to GMPPNP

Components

Ras-related protein Rab-3

Keywords

HYDROLASE / GTP hydrolysis

Function / homology

Function and homology information

GABA synthesis, release, reuptake and degradation / RAB geranylgeranylation / Serotonin Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Glutamate Neurotransmitter Release Cycle / Dopamine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / cytoskeletal matrix organization at active zone / maintenance of presynaptic active zone structure / regulation of synaptic vesicle fusion to presynaptic active zone membrane ...
Similarity search - Function

Biological species

Drosophila melanogaster (fruit fly)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.5 Å

Authors

Lardong, J.A. / Driller, J.H. / Depner, H. / Weise, C. / Petzoldt, A. / Wahl, M.C. / Sigrist, S.J. / Loll, B.

Citation

Journal: Acta Crystallogr F Struct Biol Commun / Year: 2015
Title: Structures of Drosophila melanogaster Rab2 and Rab3 bound to GMPPNP.
Authors: Lardong, J.A. / Driller, J.H. / Depner, H. / Weise, C. / Petzoldt, A. / Wahl, M.C. / Sigrist, S.J. / Loll, B.

History

Deposition	Oct 13, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 10, 2014	Provider: repository / Type: Initial release
Revision 1.1	Jan 7, 2015	Group: Database references
Revision 1.2	Feb 4, 2015	Group: Database references
Revision 1.3	Sep 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4rkf.cif.gz	173.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4rkf.ent.gz	136.9 KB	Display	PDB format
PDBx/mmJSON format	4rkf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4rkf_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	4rkf_full_validation.pdf.gz	1 MB	Display
Data in XML	4rkf_validation.xml.gz	20.1 KB	Display
Data in CIF	4rkf_validation.cif.gz	29.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rk/4rkf ftp://data.pdbj.org/pub/pdb/validation_reports/rk/4rkf	HTTPS FTP

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Related structure data

Related structure data	4rkeC 3rabS 1zbd S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1x3s-d 2oin-1 1ftn-d 1n6o-d 5ejn-1 1vg8-2 4fgp-1 6y7g-2 5l9k-2 2gf9-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) 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	#174 - Jun 2014 GFP-like Proteins similarity (1) #44 - Aug 2003 Calmodulin similarity (1) #148 - Apr 2012 Ras Protein similarity (1) #81 - Sep 2006 Elongation Factors similarity (1) #245 - May 2020 Spliceosomes similarity (1)

Deposited unit

A: Ras-related protein Rab-3

B: Ras-related protein Rab-3

hetero molecules

45.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Ras-related protein Rab-3

hetero molecules

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

2

B: Ras-related protein Rab-3

hetero molecules

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

Unit cell

Length a, b, c (Å)	37.230, 80.470, 123.940
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Ras-related protein Rab-3 Mass: 21760.533 Da / Num. of mol.: 2 / Fragment: GTPase domain (UNP Residues 1-188) / Mutation: Q80L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Rab3, CG7576 / Plasmid: pET-MBP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P25228
#2: Chemical	ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₇N₆O₁₃P₃ Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical	ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 Mass: 238.278 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₂₂O₆ / Comment: precipitant*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 378 / 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: 2.13 Å³/Da / Density % sol: 42.33 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 28% (v/v) PEG 200, 5% (w/v) PEG 3000; 100 mM MES buffer at pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.3 / Wavelength: 0.895 Å
Detector	Type: RAYONIX MX-225 / Detector: CCD / Date: Apr 24, 2014 / Details: MIRROR
Radiation	Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.895 Å / Relative weight: 1
Reflection	Resolution: 1.5→50 Å / Num. obs: 60482 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / B_iso Wilson estimate: 19.7 Å²
Reflection shell	Resolution: 1.5→1.54 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

Software

Name	Version	Classification
MAR345dtb		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.9_1692)	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3RAB

3rab

Resolution: 1.5→38.269 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.19 / Stereochemistry target values: ML
Details: The authors observe a covalently attached modification at Cys183. The latter modification remains enigmatic and hence has not been modeled in the crystal structure.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1941	3025	5 %	RANDOM
R_work	0.1567	-	-	-
obs	0.1585	60467	99.73 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.5→38.269 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2800	0	109	378	3287

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	3157
X-RAY DIFFRACTION	f_angle_d	1.256	4300
X-RAY DIFFRACTION	f_dihedral_angle_d	14.785	1226
X-RAY DIFFRACTION	f_chiral_restr	0.054	466
X-RAY DIFFRACTION	f_plane_restr	0.005	539

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.5-1.5235	0.2501	136	0.2102	2575	X-RAY DIFFRACTION	100
1.5235-1.5484	0.214	136	0.2033	2591	X-RAY DIFFRACTION	100
1.5484-1.5751	0.2283	135	0.193	2555	X-RAY DIFFRACTION	100
1.5751-1.6038	0.2425	136	0.1922	2591	X-RAY DIFFRACTION	100
1.6038-1.6346	0.2114	135	0.1883	2567	X-RAY DIFFRACTION	100
1.6346-1.668	0.2143	136	0.1664	2572	X-RAY DIFFRACTION	100
1.668-1.7043	0.1907	137	0.1695	2611	X-RAY DIFFRACTION	100
1.7043-1.7439	0.1899	135	0.1623	2567	X-RAY DIFFRACTION	100
1.7439-1.7875	0.2089	136	0.155	2579	X-RAY DIFFRACTION	100
1.7875-1.8358	0.2196	136	0.1604	2593	X-RAY DIFFRACTION	100
1.8358-1.8899	0.2242	137	0.1646	2591	X-RAY DIFFRACTION	100
1.8899-1.9509	0.2	137	0.1501	2606	X-RAY DIFFRACTION	100
1.9509-2.0206	0.1878	136	0.1513	2588	X-RAY DIFFRACTION	100
2.0206-2.1015	0.1849	137	0.1448	2604	X-RAY DIFFRACTION	100
2.1015-2.1971	0.1836	138	0.1416	2621	X-RAY DIFFRACTION	100
2.1971-2.3129	0.1556	138	0.1404	2608	X-RAY DIFFRACTION	100
2.3129-2.4578	0.1965	138	0.1457	2630	X-RAY DIFFRACTION	100
2.4578-2.6476	0.2021	138	0.1503	2628	X-RAY DIFFRACTION	100
2.6476-2.9139	0.1818	139	0.1598	2627	X-RAY DIFFRACTION	100
2.9139-3.3353	0.1752	140	0.1515	2675	X-RAY DIFFRACTION	100
3.3353-4.2013	0.163	142	0.1363	2684	X-RAY DIFFRACTION	100
4.2013-38.2814	0.2226	147	0.1703	2779	X-RAY DIFFRACTION	98

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	1.2463	-0.1248	0.1923	1.2143	-0.695	2.1796	-0.0193	0.0805	0.2237	0.0095	-0.0001	-0.0687	-0.2331	0.1326	0.0188	0.0799	-0.0101	0.0083	0.0745	0.0102	0.095	18.6262	13.403	134.2057
2	2.8383	-0.9151	-0.4735	1.249	0.4363	2.1135	0.0226	-0.1315	0.3042	0.0978	0.0594	-0.1601	0.0078	0.2111	-0.0904	0.1013	0.0095	0.0021	0.1327	-0.0126	0.1076	26.0695	9.0203	145.2645
3	2.7668	1.0447	-1.6577	2.1504	-1.3551	8.2102	0.1174	0.0862	0.0953	0.1141	-0.2136	-0.1207	-0.4339	0.6751	0.0376	0.1445	0.0013	0.0303	0.198	0.0423	0.1774	19.5829	17.825	130.6778
4	1.5066	0.315	0.0064	3.2557	-3.5501	7.5062	0.0441	0.2816	0.1795	-0.0764	0.045	0.1145	-0.2251	0.2493	-0.066	0.0977	-0.0011	0.003	0.1293	0.0298	0.1364	16.3797	17.9353	128.3663
5	3.7482	-0.5098	2.3309	0.4106	0.6329	5.3777	-0.0247	-0.1497	0.1271	0.0515	-0.0021	0.0795	-0.1831	-0.2202	0.006	0.107	0.0022	0.0149	0.108	0.0019	0.1083	8.5942	8.5477	146.7305
6	2.9904	-1.2261	0.5029	2.7641	-0.06	2.0816	0.0442	0.105	0.0889	-0.0441	-0.0114	0.2369	-0.1254	-0.1648	0.0159	0.0612	0.0092	0.0042	0.0785	0.0098	0.0886	12.1079	6.4935	134.5452
7	4.3499	-2.3696	-0.2811	2.4918	0.3024	1.1044	-0.0579	0.0142	-0.3124	0.1315	0.0208	0.2854	0.1073	-0.1318	0.008	0.0778	-0.0177	0.0185	0.0951	0.0023	0.0974	9.7031	-2.9756	139.4283
8	1.0748	-0.8966	-0.5594	2.0305	0.2811	0.9527	0.1117	0.0661	-0.0731	-0.1641	-0.016	0.282	-0.1342	-0.2796	-0.0636	0.0752	0.0314	-0.0166	0.1089	0.0277	0.1119	9.1926	5.5471	130.4782
9	2.0415	0.8603	-0.469	2.6843	0.4749	0.7412	0.0325	-0.1175	-0.2892	0.0462	0.0415	-0.4355	0.1985	0.244	-0.0774	0.1236	0.0392	-0.0285	0.131	0.0115	0.1604	27.8238	-7.9206	138.5809
10	5.5726	0.138	0.8328	2.7896	-1.4649	3.6123	0.0012	0.185	-0.5228	0.0573	-0.0156	0.1123	0.4714	0.0726	0.0014	0.133	0.0104	0.0003	0.0507	-0.0138	0.0929	14.6277	-9.0666	128.7701
11	5.2474	2.237	0.9606	2.2237	1.1837	1.9954	-0.0809	0.2269	0.0973	-0.1332	0.0852	-0.0308	-0.0427	0.2173	-0.006	0.0797	0.0101	0.003	0.0813	0.0067	0.0698	23.8234	0.6446	130.4879
12	5.9476	-1.3526	2.7657	3.6537	-0.0792	4.2229	0.0443	0.4688	0.1873	-0.3045	-0.0806	0.1332	0.0401	0.0977	0.0376	0.1389	-0.0236	0.0094	0.1334	0.0271	0.0923	16.2291	9.5799	123.5941
13	1.011	0.1049	0.1265	1.3788	0.194	1.1644	-0.0176	0.1244	0.1413	-0.1474	0.0153	-0.0226	-0.2049	-0.0317	-0.01	0.1172	0.0031	0.0062	0.0714	0.0138	0.0785	12.9628	-4.2701	98.6949
14	1.7422	-0.1898	-0.3113	1.6608	0.184	2.2816	0.0434	0.0103	0.1427	-0.1617	0.0003	-0.1993	-0.2094	0.1991	-0.0002	0.1052	-0.0167	0.0123	0.084	0.0005	0.0981	21.2741	-5.9569	102.9244
15	2.3981	0.4394	0.5535	1.5275	0.2284	2.218	0.0054	-0.1077	0.0414	0.1008	0.0089	0.0178	-0.0282	-0.0409	-0.0198	0.083	0.001	0.0156	0.0688	-0.0139	0.0498	13.3001	-7.2858	113.2758

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 16 through 43 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 44 through 55 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 56 through 65 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 66 through 77 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 78 through 91 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 92 through 102 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 103 through 122 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 123 through 134 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 135 through 145 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 146 through 156 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 157 through 170 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 171 through 186 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 16 through 55 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 56 through 134 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 135 through 187 )

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