PDB-4f36: Crystal structure of Nucleoside diphosphate kinase B from Trypano...

ID or keywords:

Entry

Database: PDB / ID: 4f36

Title

Crystal structure of Nucleoside diphosphate kinase B from Trypanosoma brucei, apo form

Components

Nucleoside diphosphate kinase

Keywords

TRANSFERASE / SSGCID / NIH / NIAID / SBRI / Emerald BioStructures / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

nucleoside-diphosphate kinase / ciliary plasm / CTP biosynthetic process / UTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / post-transcriptional regulation of gene expression / phosphorylation / ATP binding / nucleus / cytoplasm
Similarity search - Function

Biological species

Trypanosoma brucei brucei (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.3 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: To be Published
Title: Crystal structure of Nucleoside diphosphate kinase B from Trypanosoma brucei, apo form
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Gardberg, A.S. / Edwards, T.E. / Staker, B. / Stewart, L.

History

Deposition	May 8, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 16, 2012	Provider: repository / Type: Initial release
Revision 1.1	Sep 13, 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 / 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 / _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	4f36.cif.gz	331 KB	Display	PDBx/mmCIF format
PDB format	pdb4f36.ent.gz	269.7 KB	Display	PDB format
PDBx/mmJSON format	4f36.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4f36_validation.pdf.gz	477.3 KB	Display	wwPDB validaton report
Full document	4f36_full_validation.pdf.gz	478.9 KB	Display
Data in XML	4f36_validation.xml.gz	32.1 KB	Display
Data in CIF	4f36_validation.cif.gz	45.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f3/4f36 ftp://data.pdbj.org/pub/pdb/validation_reports/f3/4f36	HTTPS FTP

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Related structure data

Related structure data	3r9lS S: Starting model for refinement
Similar structure data	1avm-1 3u9f-6 1kbv-2 3u9b-3 3u9f-5 5osy-d 3bla-d 4l1k-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: SSGCID-TrbrA.00438.a

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#190 - Oct 2015 Two-component Systems similarity (1)

Deposited unit

A: Nucleoside diphosphate kinase

C: Nucleoside diphosphate kinase

B: Nucleoside diphosphate kinase

D: Nucleoside diphosphate kinase

E: Nucleoside diphosphate kinase

F: Nucleoside diphosphate kinase

hetero molecules

103 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	52.460, 123.670, 145.360
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Nucleoside diphosphate kinase / Nucleoside diphosphate kinase B Mass: 17177.566 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / Gene: Tb11.01.7800 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q381H3, nucleoside-diphosphate kinase
#2: Chemical	ChemComp-SCN / THIOCYANATE ION Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.34 Å³/Da / Density % sol: 47.36 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7 Details: EBS internal tracking number 233837B2: JCSG B2, protein: 20.2 mg/mL TrbrA.00438.a.B1 PS01459 in 25 mM HEPES, pH 7.0, 500 mM sodium chloride, 2 mM DTT, 0.025% sodium azide, 5% glycerol, ...Details: EBS internal tracking number 233837B2: JCSG B2, protein: 20.2 mg/mL TrbrA.00438.a.B1 PS01459 in 25 mM HEPES, pH 7.0, 500 mM sodium chloride, 2 mM DTT, 0.025% sodium azide, 5% glycerol, crystallant: 20% PEG3350, 200 mM sodium isothiocyanate, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal

Density Matthews: 2.34 Å³/Da / Density % sol: 47.36 %

Crystal grow

Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: EBS internal tracking number 233837B2: JCSG B2, protein: 20.2 mg/mL TrbrA.00438.a.B1 PS01459 in 25 mM HEPES, pH 7.0, 500 mM sodium chloride, 2 mM DTT, 0.025% sodium azide, 5% glycerol, ...

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL7-1 / Wavelength: 1.033171 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 26, 2012

Radiation

Monochromator: Side scattering I-beam bent single crystal, asymmetric cut 4.9650 degrees
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.033171 Å / Relative weight: 1

Reflection

Resolution: 2.3→50 Å / Num. obs: 42511 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.3 % / B_iso Wilson estimate: 44.419 Å² / R_merge(I) obs: 0.077 / Net I/σ(I): 12.47

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Highest resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. unique obs	% possible all
2.3-2.36		3.11	0.486	2.3	8886	2857	91.3
2.36-2.42			0.421	3.1	11429	2967	97.2
2.42-2.49			0.349	4.2	13545	2973	99.8
2.49-2.57			0.323	4.5	12858	2861	99.9
2.57-2.65			0.256	5.6	12670	2810	99.8
2.65-2.75			0.221	6.4	12311	2730	99.9
2.75-2.85			0.169	8	11619	2598	99.9
2.85-2.97			0.14	9.5	11387	2534	100
2.97-3.1			0.102	12.2	10927	2430	99.8
3.1-3.25			0.087	13.8	10455	2335	99.9
3.25-3.43			0.064	17.1	9710	2185	99.9
3.43-3.63			0.055	19.6	9465	2138	99.9
3.63-3.88			0.05	21.1	8687	1971	99.8
3.88-4.2			0.045	23.8	8169	1847	99.6
4.2-4.6			0.045	24.8	7517	1706	99.6
4.6-5.14			0.047	24.7	6825	1559	99.3
5.14-5.93			0.051	24.3	5945	1384	99.3
5.93-7.27			0.049	24.4	4863	1178	98.7
7.27-10.28			0.052	28.1	3792	927	97.6
	10.28		0.052	28.5	1935	521	92.5

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	2.5 Å	48.29 Å
Translation	2.5 Å	48.29 Å

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHASER		phasing
REFMAC	5.6.0117	refinement
PDB_EXTRACT	3.004	data extraction
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3R9l

3r9l

Resolution: 2.3→50 Å / Cor.coef. F_o:F_c: 0.947 / Cor.coef. F_o:F_c free: 0.92 / SU B: 13.043 / SU ML: 0.164 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.32 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.235	2144	5 %	RANDOM
R_work	0.198	-	-	-
obs	0.2	42483	98.92 %	-

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: 40.762 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.63 Å²	0 Å²	0 Å²
2-	-	-1.89 Å²	-0 Å²
3-	-	-	2.52 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6311	0	3	286	6600

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.019	6442
X-RAY DIFFRACTION	r_bond_other_d	0.008	0.02	4316
X-RAY DIFFRACTION	r_angle_refined_deg	1.411	1.946	8728
X-RAY DIFFRACTION	r_angle_other_deg	1.232	3	10478
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.082	5	830
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	28.429	23.384	263
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.369	15	1004
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	24.369	15	42
X-RAY DIFFRACTION	r_chiral_restr	0.078	0.2	976
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.021	7270
X-RAY DIFFRACTION	r_gen_planes_other	0.007	0.02	1364

LS refinement shell

Resolution: 2.3→2.36 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.323	131	-
R_work	0.262	2541	-
all	-	2672	-
obs	-	-	92.3 %

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	1.3902	-0.4413	0.1005	1.3394	-0.3089	0.548	0.0322	0.0803	-0.0713	-0.1244	0.056	-0.0159	-0.0546	-0.0195	-0.0882	0.1213	-0.0142	-0.0925	0.0884	0.0073	0.1509	-4.834	13.717	-31.964
2	7.4028	-1.6897	-2.7973	1.9782	-1.3931	9.5511	0.3817	0.23	0.6845	0.1313	0.3602	0.2143	-0.9947	-1.2989	-0.742	0.2512	0.1077	-0.0166	0.2142	0.1446	0.2748	-7.417	31.004	-32.628
3	1.4848	0.0627	-0.2104	1.422	-0.1652	1.3167	-0.0135	0.2269	0.1033	-0.2003	0.1184	0.2486	-0.0839	-0.089	-0.1049	0.1299	-0.0037	-0.135	0.1046	0.0248	0.1718	-10.518	13.107	-34.543
4	2.3091	-0.6298	-1.22	2.0441	0.725	3.7037	-0.009	-0.1022	-0.2182	0.1138	0.295	-0.1769	0.3899	-0.035	-0.2859	0.1421	0.0066	-0.1854	0.0637	-0.0494	0.3481	7.396	-13.866	-15.928
5	2.9227	-0.3464	-0.8463	1.8982	-0.3075	1.574	0.03	-0.2215	-0.4792	0.2192	0.0872	-0.1815	0.2108	0.2353	-0.1171	0.1407	0.0438	-0.1788	0.061	-0.0413	0.3496	8.396	-16.956	-16.71
6	1.3536	-0.3496	0.2889	2.1507	0.1741	1.186	0.0363	-0.014	-0.3445	0.1159	0.0876	-0.3426	0.0417	0.1464	-0.1239	0.0633	0.0277	-0.1313	0.0626	-0.0697	0.3585	12.201	-13.183	-19.435
7	1.9083	1.256	1.4568	2.9222	1.5771	2.5784	-0.0969	0.3942	-0.0155	-0.218	0.1006	-0.4128	-0.1543	0.3578	-0.0037	0.0959	-0.0158	-0.0498	0.141	-0.0079	0.2291	11.138	13.412	-32.875
8	0.7841	-0.6388	-0.2087	2.8866	-0.4064	1.9978	-0.009	0.1916	-0.0101	-0.0524	-0.0817	-0.5176	0.0377	0.4257	0.0907	0.0585	-0.0158	-0.0547	0.1912	-0.0202	0.3042	17.879	7.532	-29.377
9	2.138	-0.3554	-0.9461	0.7678	-0.0002	4.8625	-0.1186	0.2126	0.2776	-0.0709	0.0348	-0.2206	-0.4148	0.2602	0.0838	0.1697	-0.0841	-0.0915	0.0751	0.0131	0.2317	9.188	25.959	-27.807
10	2.8073	0.6691	-1.8256	1.8336	-0.378	3.8985	-0.1634	0.0988	-0.2173	-0.1137	0.1626	0.0768	0.1671	0.0337	0.0008	0.0883	0.0162	-0.1303	0.0458	-0.0272	0.3018	-7.103	-11.191	-23.933
11	0.8456	-0.4295	0.22	2.4769	-0.8822	1.1864	0.1231	0.0952	-0.295	-0.2161	0.0045	0.2203	0.1407	-0.0456	-0.1276	0.0906	-0.0153	-0.1461	0.0814	-0.0406	0.3037	-11.591	-12.289	-25.481
12	2.4544	0.2555	0.6531	4.1359	3.1806	3.4558	0.0345	-0.0253	-0.5546	0.277	0.0964	0.3629	0.1397	0.0564	-0.1309	0.161	-0.0458	-0.1184	0.0236	0.0838	0.4627	-10.86	-20.171	-12.881
13	1.8283	-1.48	1.2047	5.2078	-2.4326	1.8899	-0.0651	-0.2291	-0.1543	0.4998	0.1891	0.2375	-0.047	-0.2095	-0.124	0.1469	0.0283	-0.0341	0.1003	-0.0161	0.1122	-11.119	9.734	-3.542
14	2.6169	-1.1426	1.0427	3.2377	-1.3328	2.7056	-0.018	-0.5121	-0.3787	0.5147	0.2971	0.5596	0.025	-0.486	-0.2791	0.2114	0.0444	0.0048	0.1905	0.0188	0.2195	-14.332	9.258	0.958
15	1.2	0.1205	0.3993	2.1179	0.0359	1.2102	-0.0083	-0.2828	-0.0026	0.3225	0.0351	0.289	-0.0287	-0.2774	-0.0268	0.1296	0.0644	-0.0191	0.1303	-0.0323	0.1371	-15.209	12.158	-5.132
16	1.0329	-0.5908	0.8564	4.8749	-1.3521	2.235	0.021	0.0414	0.1039	0.2657	-0.0218	-0.1811	-0.0281	0.0993	0.0008	0.1404	0.0263	-0.1179	0.087	-0.0613	0.1587	4.744	13.308	-3.163
17	2.6171	2.2387	0.3609	2.7408	1.2205	1.0659	0.3062	-0.129	0.3922	0.2747	-0.1742	0.2043	0.0622	-0.0391	-0.132	0.3559	0.0175	-0.0987	0.0985	-0.0084	0.2146	5.593	15.254	4.646
18	1.313	0.4517	-0.0535	1.4039	-0.0146	0.6079	0.0411	-0.2272	0.0353	0.3356	0.0299	-0.2117	-0.0444	0.1241	-0.071	0.2221	0.0242	-0.184	0.1059	-0.0383	0.1829	9.672	9.932	0.615

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 39
2	X-RAY DIFFRACTION	2	A	40 - 73
3	X-RAY DIFFRACTION	3	A	74 - 151
4	X-RAY DIFFRACTION	4	B	2 - 22
5	X-RAY DIFFRACTION	5	B	23 - 87
6	X-RAY DIFFRACTION	6	B	88 - 152
7	X-RAY DIFFRACTION	7	C	3 - 87
8	X-RAY DIFFRACTION	8	C	88 - 128
9	X-RAY DIFFRACTION	9	C	129 - 153
10	X-RAY DIFFRACTION	10	D	3 - 26
11	X-RAY DIFFRACTION	11	D	27 - 125
12	X-RAY DIFFRACTION	12	D	126 - 152
13	X-RAY DIFFRACTION	13	E	0 - 25
14	X-RAY DIFFRACTION	14	E	26 - 87
15	X-RAY DIFFRACTION	15	E	88 - 153
16	X-RAY DIFFRACTION	16	F	3 - 25
17	X-RAY DIFFRACTION	17	F	26 - 53
18	X-RAY DIFFRACTION	18	F	54 - 151

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