PDB-3k7u: Structure of essential protein from Trypanosoma brucei

ID or keywords:

Entry

Database: PDB / ID: 3k7u

Title

Structure of essential protein from Trypanosoma brucei

Components

Antibody
MP18 RNA editing complex protein

Keywords

Immune System / RNA Binding Protein / RNA-editing / OB-fold / RNA-editing proteins / kinetoplastids

Function / homology

Function and homology information

RNA modification / mitochondrial mRNA editing complex / kinetoplast / single-stranded DNA binding / endonuclease activity / RNA binding / nucleus
Similarity search - Function

Biological species

Lama glama (llama)

Trypanosoma brucei (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Wu, M.

Citation

Journal: J.Struct.Biol. / Year: 2011
Title: Structures of a key interaction protein from the Trypanosoma brucei editosome in complex with single domain antibodies.
Authors: Wu, M. / Park, Y.J. / Pardon, E. / Turley, S. / Hayhurst, A. / Deng, J. / Steyaert, J. / Hol, W.G.

History

Deposition	Oct 13, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 17, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Sep 6, 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
Revision 1.3	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3k7u.cif.gz	60.1 KB	Display	PDBx/mmCIF format
PDB format	pdb3k7u.ent.gz	44 KB	Display	PDB format
PDBx/mmJSON format	3k7u.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3k7u_validation.pdf.gz	433.7 KB	Display	wwPDB validaton report
Full document	3k7u_full_validation.pdf.gz	439.8 KB	Display
Data in XML	3k7u_validation.xml.gz	11.3 KB	Display
Data in CIF	3k7u_validation.cif.gz	15 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/k7/3k7u ftp://data.pdbj.org/pub/pdb/validation_reports/k7/3k7u	HTTPS FTP

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Related structure data

Related structure data	3k80SC 3k81C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6sie-d 6f58-d 1dee-2 6w00-d 4uix-d 4lhb-d 4a1h-d 6wfw-d 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	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

A: Antibody

C: MP18 RNA editing complex protein

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

1

A: Antibody

C: MP18 RNA editing complex protein

A: Antibody

C: MP18 RNA editing complex protein

defined by author&software
60.3 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	123.362, 50.359, 44.150
Angle α, β, γ (deg.)	90.00, 108.97, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Antibody	Antibody Mass: 14037.454 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#2: Protein	MP18 RNA editing complex protein Mass: 16119.043 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: Tb10.70.2090 / Production host: Escherichia coli (E. coli) / References: UniProt: Q38B90
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.15 Å³/Da / Density % sol: 42.8 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 25% PEG2000, 0.1 M Bis-tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 77 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
Detector	Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 25, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.1→50 Å / Num. obs: 15229 / % possible obs: 96.4 % / Redundancy: 3.8 % / B_iso Wilson estimate: 40.4 Å² / R_sym value: 0.045 / Net I/σ(I): 30.6
Reflection shell	Resolution: 1.99→2.06 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 3.1 / Num. unique all: 15229 / R_sym value: 0.504 / % possible all: 76.2

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHASES		phasing
REFMAC	5.5.0095	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 3K80

3k80

Resolution: 2.1→29.69 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.929 / SU B: 13.041 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26459	752	5 %	RANDOM
R_work	0.20219	-	-	-
obs	0.20538	14154	98.62 %	-
all	-	14154	-	-

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: 25.722 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.06 Å²	0 Å²	-0.07 Å²
2-	-	0.18 Å²	0 Å²
3-	-	-	-0.29 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→29.69 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1668	0	0	70	1738

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.022	0.022	1717
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1137
X-RAY DIFFRACTION	r_angle_refined_deg	1.842	1.929	2333
X-RAY DIFFRACTION	r_angle_other_deg	1	3	2760
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.892	5	217
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.048	24.024	82
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.406	15	267
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.746	15	11
X-RAY DIFFRACTION	r_chiral_restr	0.12	0.2	259
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	1948
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	360
X-RAY DIFFRACTION	r_mcbond_it	1.107	1.5	1075
X-RAY DIFFRACTION	r_mcbond_other	0.279	1.5	447
X-RAY DIFFRACTION	r_mcangle_it	1.965	2	1729
X-RAY DIFFRACTION	r_scbond_it	2.729	3	642
X-RAY DIFFRACTION	r_scangle_it	4.152	4.5	602

LS refinement shell

Resolution: 2.1→2.155 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.384	52	-
R_work	0.26	1023	-
obs	-	-	97.64 %

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	1.9653	-0.2031	0.1239	2.4545	0.2053	2.253	0.0705	-0.0321	-0.0488	0.2251	0.074	-0.2377	0.0662	0.241	-0.1445	0.2963	0.013	0.0411	0.3002	0.0335	0.3058	21.9075	-47.5693	8.3052
2	2.4967	-0.1305	-0.2983	3.3259	1.1907	2.4682	-0.0067	-0.0346	0.0251	0.1405	0.0158	-0.0127	0.1667	0.0208	-0.009	0.21	0.0004	-0.01	0.2185	0.0417	0.2453	25.9768	-41.0861	2.9623
3	7.6884	-1.4155	-5.292	9.0989	0.6825	3.8397	0.0367	-0.0926	-0.2068	0.103	-0.0379	-0.0379	0.1538	0.0295	0.0012	0.278	-0.008	-0.0213	0.236	0.0142	0.2753	31.1757	-43.035	-6.0552
4	2.8878	-0.5459	-1.0163	3.4675	0.8402	1.0138	0.0099	-0.0833	0.074	0.0803	-0.0042	0.0132	-0.0418	-0.0163	-0.0057	0.1526	-0.0038	-0.0034	0.1567	0.0132	0.1815	19.5581	-33.1213	3.9473
5	2.5681	0.156	-0.3504	2.3961	0.2164	2.532	0.0073	-0.0087	-0.0086	0.023	-0.0086	0.0052	0.0928	-0.0959	0.0013	0.1875	0.0072	0.0055	0.1798	0.0109	0.2461	15.6873	-39.2912	3.5769
6	3.2253	-0.4195	-0.3499	2.6496	0.3115	1.9333	0.0066	0.0043	0.0703	0.0142	-0.074	0.0927	-0.0511	-0.2033	0.0674	0.226	-0.0116	0.0091	0.1945	0.0344	0.2861	18.08	-46.1096	1.7935
7	2.9432	-0.6795	-0.7294	3.3639	-1.5087	2.3895	0.0233	-0.2427	0.1457	0.2664	-0.0085	-0.0868	-0.1329	0.0729	-0.0148	0.1964	-0.001	-0.0043	0.2131	-0.0035	0.1978	30.0308	-34.5801	4.5625
8	2.2625	2.1413	0.3034	6.0279	1.5728	0.9775	0.0829	-0.0708	-0.1489	0.158	-0.0382	-0.1361	0.1371	-0.071	-0.0446	0.2162	0.0172	0.0243	0.2401	0.016	0.2167	27.9294	-46.2128	3.8932
9	2.4474	-0.4968	-0.029	1.8309	0.87	1.7274	0.092	-0.1785	0.0524	0.0724	-0.0999	-0.1502	-0.2256	0.2296	0.0078	0.2232	0.024	-0.0278	0.2019	0.0092	0.1846	9.0772	-21.3104	-0.4151
10	1.9483	-0.6945	-2.9044	0.5479	1.2292	5.156	0.0976	-0.212	0.267	0.1959	0.0016	0.2213	-0.3215	-0.2311	-0.0992	0.5155	0.017	0.042	0.5151	-0.0369	0.5419	13.4544	-10.9691	14.5528
11	3.5384	0.7463	1.8821	4.3392	2.0261	8.2069	-0.1241	-0.0634	0.1237	-0.1673	-0.0942	0.1988	-0.1854	-0.3831	0.2183	0.1701	0.0078	0.0484	0.1755	0.0239	0.2472	10.1534	-18.4615	-4.0218
12	4.1749	-1.0771	2.1377	2.2356	-0.9979	3.208	-0.0414	-0.0671	0.1104	0.0747	0.0042	-0.0408	-0.1055	0.035	0.0373	0.1644	-0.0202	0.0196	0.1265	-0.0101	0.1782	14.9875	-19.3439	4.6877
13	4.7185	-0.4854	-0.3896	4.0541	0.0116	3.2488	0.0791	-0.289	0.1583	0.1446	-0.0094	0.144	-0.2051	-0.0154	-0.0696	0.2196	-0.0135	-0.0553	0.1644	0.0015	0.1567	9.4386	-22.0069	1.5748
14	0.4605	0.0599	0.0229	0.0142	-0.0484	0.4328	0.015	-0.2808	0.5342	0.067	-0.0146	0.0785	-0.5636	-0.1165	-0.0004	0.7548	0.0451	0.0102	0.5822	-0.1133	0.7314	1.1917	-3.4837	8.3665
15	3.4088	-1.3666	-0.8044	3.8164	-0.184	4.4536	-0.1476	-0.2478	-0.027	0.363	0.1398	0.3559	-0.1128	-0.2685	0.0078	0.1622	-0.0533	-0.0241	0.2033	-0.0171	0.2058	8.2661	-22.5866	5.9872
16	3.1749	0.4669	-5.3007	0.7997	-1.0991	11.8106	0.231	0.4143	0.4979	-0.5025	0.0047	-0.4849	-0.774	0.6317	-0.2357	0.6799	-0.1186	0.2299	0.7277	0.1694	0.6895	24.7459	-31.1455	-10.3334

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 29
2	X-RAY DIFFRACTION	2	A	30 - 42
3	X-RAY DIFFRACTION	3	A	43 - 46
4	X-RAY DIFFRACTION	4	A	47 - 62
5	X-RAY DIFFRACTION	5	A	63 - 75
6	X-RAY DIFFRACTION	6	A	76 - 94
7	X-RAY DIFFRACTION	7	A	95 - 108
8	X-RAY DIFFRACTION	8	A	109 - 121
9	X-RAY DIFFRACTION	9	C	2 - 16
10	X-RAY DIFFRACTION	10	C	17 - 23
11	X-RAY DIFFRACTION	11	C	24 - 47
12	X-RAY DIFFRACTION	12	C	48 - 68
13	X-RAY DIFFRACTION	13	C	69 - 82
14	X-RAY DIFFRACTION	14	C	83 - 95
15	X-RAY DIFFRACTION	15	C	96 - 111
16	X-RAY DIFFRACTION	16	C	112 - 115

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