PDB-3js9: Crystal structure of nucleoside diphosphate kinase family protein...

ID or keywords:

Entry

Database: PDB / ID: 3js9

Title

Crystal structure of nucleoside diphosphate kinase family protein from Babesia bovis

Components

Nucleoside diphosphate kinase family protein

Keywords

TRANSFERASE / NIAID / SSGCID / Seattle Structural Genomics Center for Infectious Disease / babesiosis / parasitic protozoan / blood disease / hemolytic disease / piroplasmosis / Texas cattle fever / tick fever / Nantucket fever / redwater fever / Kinase

Function / homology

Function and homology information

CTP biosynthetic process / UTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity
Similarity search - Function

Biological species

Babesia bovis (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.5 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: To be Published
Title: Crystal structure of nucleoside diphosphate kinase family protein from Babesia bovis
Authors: Edwards, T.E. / Staker, B.L. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

History

Deposition	Sep 9, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 22, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2	Nov 1, 2017	Group: Refinement description / Category: software
Revision 1.3	Sep 6, 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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	3js9.cif.gz	106 KB	Display	PDBx/mmCIF format
PDB format	pdb3js9.ent.gz	82 KB	Display	PDB format
PDBx/mmJSON format	3js9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3js9_validation.pdf.gz	455.9 KB	Display	wwPDB validaton report
Full document	3js9_full_validation.pdf.gz	459.1 KB	Display
Data in XML	3js9_validation.xml.gz	19.2 KB	Display
Data in CIF	3js9_validation.cif.gz	26.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/js/3js9 ftp://data.pdbj.org/pub/pdb/validation_reports/js/3js9	HTTPS FTP

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Related structure data

Related structure data	2vu5S S: Starting model for refinement
Similar structure data	2vu5-1 3bbf-d 4o0n-1 1nue-d 1xiq-d 4fky-1 5iom-1 1ncl-1 1zs6-1 3ngs-1 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
Other databases	TargetDB: BaboA.00819.a

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Nucleoside diphosphate kinase family protein

B: Nucleoside diphosphate kinase family protein

C: Nucleoside diphosphate kinase family protein

hetero molecules

54.4 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Nucleoside diphosphate kinase family protein

B: Nucleoside diphosphate kinase family protein

C: Nucleoside diphosphate kinase family protein

hetero molecules

A: Nucleoside diphosphate kinase family protein

B: Nucleoside diphosphate kinase family protein

C: Nucleoside diphosphate kinase family protein

hetero molecules

defined by author&software
109 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	125.894, 125.894, 101.512
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	96
Space group name H-M	P4₃2₁2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: 5 / Auth seq-ID: 1 - 148 / Label seq-ID: 9 - 156

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B
3	C	C

#1: Protein	Nucleoside diphosphate kinase family protein Mass: 17713.447 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Babesia bovis (eukaryote) / Strain: T2Bo / Gene: BBOV_III005290 / Production host: Escherichia coli (E. coli) / References: UniProt: A7ANF8
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 161 / 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: 3.78 Å³/Da / Density % sol: 67.5 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: CSHT condition A4, 2.0 M ammonium sulfate, 0.1 M Tris pH 8.5; 0.4:0.4 uL drops; 31.2 mg/mL protein in 25 mM Hepes pH 7.0, 0.3 M NaCl, 10% glycerol, 2 mM DTT; crystal tracking ID 204382a4; ...Details: CSHT condition A4, 2.0 M ammonium sulfate, 0.1 M Tris pH 8.5; 0.4:0.4 uL drops; 31.2 mg/mL protein in 25 mM Hepes pH 7.0, 0.3 M NaCl, 10% glycerol, 2 mM DTT; crystal tracking ID 204382a4; non-cleavable expression tag, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal

Density Matthews: 3.78 Å³/Da / Density % sol: 67.5 %

Crystal grow

Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: CSHT condition A4, 2.0 M ammonium sulfate, 0.1 M Tris pH 8.5; 0.4:0.4 uL drops; 31.2 mg/mL protein in 25 mM Hepes pH 7.0, 0.3 M NaCl, 10% glycerol, 2 mM DTT; crystal tracking ID 204382a4; ...

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.976484 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 22, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.976484 Å / Relative weight: 1
Reflection	Resolution: 2.5→50 Å / Num. obs: 28787 / % possible obs: 99.5 % / Redundancy: 9.2 % / R_merge(I) obs: 0.149 / Χ²: 1.035 / Net I/σ(I): 14.3
Reflection shell	Resolution: 2.5→2.59 Å / Redundancy: 7.6 % / R_merge(I) obs: 0.677 / Mean I/σ(I) obs: 2.4 / Num. unique all: 2742 / Χ²: 0.93 / % possible all: 97.2

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
MOLREP		phasing
REFMAC		refinement
PDB_EXTRACT	3.005	data extraction
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: trimer generate from 2VU5

2vu5

Resolution: 2.5→47.08 Å / Cor.coef. F_o:F_c: 0.954 / Cor.coef. F_o:F_c free: 0.937 / WR_factor R_free: 0.216 / WR_factor R_work: 0.168 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.862 / SU B: 13.291 / SU ML: 0.135 / SU R Cruickshank DPI: 0.247 / SU R_free: 0.208 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.247 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: RESIDUAL ONLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.221	1464	5.1 %	RANDOM
R_work	0.176	-	-	-
obs	0.179	28727	99.27 %	-

Solvent computation

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

Displacement parameters

B_iso max: 118.09 Å² / B_iso mean: 28.414 Å² / B_iso min: 4.63 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.3 Å²	0 Å²	0 Å²
2-	-	-2.3 Å²	0 Å²
3-	-	-	4.61 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→47.08 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3478	0	65	161	3704

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	3651
X-RAY DIFFRACTION	r_angle_refined_deg	1.466	1.957	4956
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.978	5	449
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.58	23.269	156
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.537	15	599
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.979	15	21
X-RAY DIFFRACTION	r_chiral_restr	0.097	0.2	523
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	2744
X-RAY DIFFRACTION	r_mcbond_it	0.65	1.5	2217
X-RAY DIFFRACTION	r_mcangle_it	1.253	2	3568
X-RAY DIFFRACTION	r_scbond_it	2.093	3	1434
X-RAY DIFFRACTION	r_scangle_it	3.301	4.5	1385

Refine LS restraints NCS

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

Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
A	589	MEDIUM POSITIONAL	0.1	0.5
B	589	MEDIUM POSITIONAL	0.12	0.5
C	589	MEDIUM POSITIONAL	0.09	0.5
A	560	LOOSE POSITIONAL	0.31	5
B	560	LOOSE POSITIONAL	0.31	5
C	560	LOOSE POSITIONAL	0.27	5
A	589	MEDIUM THERMAL	3.54	2
B	589	MEDIUM THERMAL	4.57	2
C	589	MEDIUM THERMAL	1.86	2
A	560	LOOSE THERMAL	3.74	10
B	560	LOOSE THERMAL	4.64	10
C	560	LOOSE THERMAL	2.15	10

LS refinement shell

Resolution: 2.496→2.561 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.265	121	-
R_work	0.26	1878	-
all	-	1999	-
obs	-	-	95.1 %

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	0.2434	0.0706	0.0757	0.4614	-0.043	0.8543	0.0232	0.0304	-0.0826	0.0047	-0.0122	0.0386	0.002	0.0196	-0.011	0.1175	0.0062	-0.0076	0.1006	-0.0082	0.1617	-27.0427	-37.6476	-2.7561
2	4.9701	0.1177	1.8781	6.6238	4.0072	7.0191	0.349	0.2234	-0.9355	0.3752	0.2989	-0.7564	0.5192	0.2305	-0.6478	0.0523	0.0317	-0.0924	0.0263	-0.0521	0.4442	-20.6358	-53.6352	1.6689
3	0.7029	-0.0168	0.3791	0.4668	0.1902	0.3978	0.0007	0.0165	-0.116	-0.0473	-0.0071	0.0131	0.0608	0.0499	0.0064	0.1305	0.0075	-0.0079	0.0858	-0.0142	0.1643	-22.5265	-39.2232	-6.852
4	1.6915	2.9743	-0.6219	5.231	-1.0829	2.9012	-0.1416	0.1197	0.0281	-0.2865	0.2321	0.0412	0.2103	-0.2018	-0.0904	0.1568	0.0283	-0.05	0.1352	-0.0019	0.1044	-32.1782	-23.808	-18.8801
5	1.4922	0.3043	0.32	0.4933	-0.1958	0.4007	0.0522	0.0659	0.0952	-0.0629	-0.0791	-0.0862	0.0217	0.0073	0.0269	0.1139	0.0136	0.0083	0.1214	0.0363	0.1607	-13.9685	-11.8439	-15.2376
6	2.8637	0.6626	0.0849	3.8145	2.3989	4.9904	0.0063	0.4839	-0.0437	-0.571	-0.0751	-0.2054	0.0113	-0.0427	0.0687	0.2172	0.0361	0.0527	0.1909	0.0777	0.0741	-19.7535	-11.5408	-32.6935
7	3.7252	0.5178	2.0203	1.0607	-0.6458	1.9802	-0.0243	0.3191	0.1716	-0.1547	-0.1104	-0.0477	0.093	0.2847	0.1346	0.1418	0.0599	0.0535	0.155	0.0438	0.1139	-12.3388	-11.7225	-20.6539
8	0.568	-0.0896	-0.1434	0.7073	-0.2548	0.9005	-0.0148	0.2685	0.0576	-0.1764	-0.07	-0.156	0.0837	0.0574	0.0848	0.0896	0.0046	0.0208	0.1687	0.0578	0.134	-10.5588	-13.6686	-18.8993
9	0.6504	-0.3389	0.4261	0.1891	-0.2223	0.2964	-0.0358	0.045	0.079	0.04	-0.0326	-0.0885	-0.0102	0.0392	0.0684	0.0965	-0.0125	-0.047	0.1315	0.0411	0.2153	0.6642	-21.4126	8.4978
10	10.0811	-1.8766	-1.7755	2.8333	-0.3553	5.0165	-0.0298	0.6478	0.4827	-0.0165	-0.4391	-0.3321	-0.128	0.5432	0.4689	0.0269	-0.0241	-0.0572	0.2213	0.1514	0.1846	14.3071	-16.368	2.9836
11	0.8361	-0.1999	-0.0884	0.707	-0.7046	0.8676	-0.012	0.0866	0.0405	-0.0457	-0.0821	-0.1894	0.0507	0.0811	0.0941	0.0808	-0.0006	0.0023	0.1498	0.0239	0.2231	0.0281	-24.6869	-1.7021
12	1.4803	-0.326	0.207	0.7049	0.1402	0.4521	-0.0827	-0.0811	-0.1037	0.073	0.0055	-0.1047	0.0303	0.0549	0.0772	0.0929	0.0084	-0.0561	0.1167	0.0543	0.1511	0.7396	-31.2371	13.7862

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 47
2	X-RAY DIFFRACTION	2	A	48 - 67
3	X-RAY DIFFRACTION	3	A	68 - 139
4	X-RAY DIFFRACTION	4	A	140 - 148
5	X-RAY DIFFRACTION	5	B	1 - 33
6	X-RAY DIFFRACTION	6	B	34 - 63
7	X-RAY DIFFRACTION	7	B	64 - 85
8	X-RAY DIFFRACTION	8	B	86 - 148
9	X-RAY DIFFRACTION	9	C	1 - 47
10	X-RAY DIFFRACTION	10	C	48 - 71
11	X-RAY DIFFRACTION	11	C	72 - 116
12	X-RAY DIFFRACTION	12	C	117 - 148

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