PDB-1xiq: Plasmodium falciparum Nucleoside diphosphate kinase B

ID or keywords:

Entry

Database: PDB / ID: 1xiq

Title

Plasmodium falciparum Nucleoside diphosphate kinase B

Components

Nucleoside diphosphate kinase B

Keywords

TRANSFERASE / Protein Structure Initiative / Structural Genomics / SGPP / PSI / Structural Genomics of Pathogenic Protozoa Consortium

Function / homology

Function and homology information

Ribavirin ADME / Azathioprine ADME / Interconversion of nucleotide di- and triphosphates / Neutrophil degranulation / nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / nucleoside diphosphate kinase activity / GTP biosynthetic process / magnesium ion binding / ATP binding
Similarity search - Function

Biological species

Plasmodium falciparum (malaria parasite P. falciparum)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 3.05 Å

Authors

Robien, M.A. / Bosch, J. / Hol, W.G.J. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

Citation

Journal: To be Published
Title: Crystal structure of Nucleoside diphosphate kinase B from Plasmodium falciparum
Authors: Robien, M.A. / Bosch, J. / Hol, W.G.J. / Structural Genomics of Pathogenic Protozoa Consortium

History

Deposition	Sep 21, 2004	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 12, 2004	Provider: repository / Type: Initial release
Revision 1.1	Apr 30, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Source and taxonomy / Version format compliance
Revision 1.3	Jan 31, 2018	Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4	Feb 14, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif 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.end_auth_comp_id / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	1xiq.cif.gz	181.6 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xi/1xiq ftp://data.pdbj.org/pub/pdb/validation_reports/xi/1xiq	HTTPS FTP

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Related structure data

Similar structure data	5iol-2 6joh-2 6joh-3 6k3h-1 3prv-d 6k3h-4 1nue-d 6k3h-3 1pku-1 3ngt-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
Other databases	TargetDB: Pfal006645AAA

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Nucleoside diphosphate kinase B

B: Nucleoside diphosphate kinase B

C: Nucleoside diphosphate kinase B

D: Nucleoside diphosphate kinase B

E: Nucleoside diphosphate kinase B

F: Nucleoside diphosphate kinase B

108 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)	68.593, 112.424, 68.590
Angle α, β, γ (deg.)	90.00, 119.05, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Refine code: 3

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	MET	MET	PRO	PRO	A	A	1 - 40	9 - 48
2	1	1	MET	MET	PRO	PRO	B	B	1 - 40	9 - 48
3	1	1	MET	MET	PRO	PRO	C	C	1 - 40	9 - 48
4	1	1	MET	MET	PRO	PRO	D	D	1 - 40	9 - 48
5	1	1	MET	MET	PRO	PRO	E	E	1 - 40	9 - 48
6	1	1	MET	MET	PRO	PRO	F	F	1 - 40	9 - 48
7	2	1	GLY	GLY	CYS	CYS	A	A	68 - 148	76 - 156
8	2	1	GLY	GLY	CYS	CYS	B	B	68 - 148	76 - 156
9	2	1	GLY	GLY	CYS	CYS	C	C	68 - 148	76 - 156
10	2	1	GLY	GLY	CYS	CYS	D	D	68 - 148	76 - 156
11	2	1	GLY	GLY	CYS	CYS	E	E	68 - 148	76 - 156
12	2	1	GLY	GLY	CYS	CYS	F	F	68 - 148	76 - 156
1	1	2	ASP	ASP	LYS	LYS	A	A	54 - 59	62 - 67
2	1	2	ASP	ASP	LYS	LYS	B	B	54 - 59	62 - 67
3	1	2	ASP	ASP	LYS	LYS	C	C	54 - 59	62 - 67
4	1	2	ASP	ASP	LYS	LYS	D	D	54 - 59	62 - 67
5	1	2	ASP	ASP	LYS	LYS	E	E	54 - 59	62 - 67
6	1	2	ASP	ASP	LYS	LYS	F	F	54 - 59	62 - 67

NCS ensembles :

ID
1
2

Details

asymmetric unit contains a hexamer, which is the biological unit

#1: Protein	Nucleoside diphosphate kinase B Mass: 18069.061 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Strain: 3D7 / Gene: PF13_0349 / Plasmid: pET14B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21star/DE3 / References: UniProt: Q8ID43, nucleoside-diphosphate kinase

#1: Protein

Nucleoside diphosphate kinase B

Mass: 18069.061 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: PF13_0349 / Plasmid: pET14B / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21star/DE3 / References: UniProt: Q8ID43, nucleoside-diphosphate kinase

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal	Density Matthews: 2.3 Å³/Da / Density % sol: 45.3 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: calcium acetate, PEG3350, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	SSRL	BL11-1	1	0.974609
SYNCHROTRON	ALS	8.2.1	2	0.9793

Detector

Type	ID	Detector	Date
ADSC QUANTUM 4	1	CCD	Jun 10, 2004
ADSC QUANTUM 210	2	CCD	Jun 20, 2004

Radiation

Monochromator: single crystal Si(111) bent monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.974609	1
2	0.9793	1

Reflection

Resolution: 3.05→52.705 Å / Num. all: 17424 / Num. obs: 17326 / % possible obs: 99.44 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / B_iso Wilson estimate: 80.965 Å² / R_merge(I) obs: 0.111 / R_sym value: 0.111 / Net I/σ(I): 7.1

Reflection shell

Resolution: 3.05→3.21 Å / Redundancy: 3.4 % / R_merge(I) obs: 0.574 / Mean I/σ(I) obs: 1.9 / Num. unique all: 2519 / R_sym value: 0.574 / % possible all: 99

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Processing

Software

Name	Version	Classification
REFMAC	5.1.24	refinement
MOSFLM		data reduction
CCP4	(SCALA)	data scaling
SHARP		phasing

Refinement

Method to determine structure:

SAD / Resolution: 3.05→52.7 Å / Cor.coef. F_o:F_c: 0.91 / Cor.coef. F_o:F_c free: 0.856 / SU B: 26.787 / SU ML: 0.478 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.587 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The electron density for residues 40-63 is weak, for residues 50-61 it is very weak.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.28608	876	5.1 %	RANDOM
R_work	0.22948	-	-	-
all	0.23238	17424	-	-
obs	0.23238	16447	99.47 %	-

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: 50.431 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.22 Å²	0 Å²	-0.17 Å²
2-	-	0.22 Å²	0 Å²
3-	-	-	-0.17 Å²

Refinement step

Cycle: LAST / Resolution: 3.05→52.7 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7164	0	0	0	7164

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	7314
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.156	1.948	9828
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.823	5	888
X-RAY DIFFRACTION	r_dihedral_angle_2_deg
X-RAY DIFFRACTION	r_dihedral_angle_3_deg
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.086	0.2	1080
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	5268
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.211	0.2	3519
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.16	0.2	185
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.205	0.2	61
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.102	0.2	1
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_mcbond_it	1.618	4	4428
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	3.002	6	7182
X-RAY DIFFRACTION	r_scbond_it	2.836	6	2886
X-RAY DIFFRACTION	r_scangle_it	4.515	10	2646
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	484	tight positional	0.04	0.05
1	2	B	484	tight positional	0.03	0.05
1	3	C	484	tight positional	0.03	0.05
1	4	D	484	tight positional	0.03	0.05
1	5	E	484	tight positional	0.04	0.05
1	6	F	484	tight positional	0.03	0.05
2	1	A	24	tight positional	0.03	0.05
2	2	B	24	tight positional	0.04	0.05
2	3	C	24	tight positional	0.03	0.05
2	4	D	24	tight positional	0.03	0.05
2	5	E	24	tight positional	0.04	0.05
2	6	F	24	tight positional	0.03	0.05
1	1	A	473	loose positional	0.71	5
1	2	B	473	loose positional	0.84	5
1	3	C	473	loose positional	0.78	5
1	4	D	473	loose positional	0.74	5
1	5	E	473	loose positional	0.69	5
1	6	F	473	loose positional	0.7	5
2	1	A	31	loose positional	1.26	5
2	2	B	31	loose positional	1.09	5
2	3	C	31	loose positional	1.45	5
2	4	D	31	loose positional	1.05	5
2	5	E	31	loose positional	1.09	5
2	6	F	31	loose positional	1.21	5
1	1	A	484	tight thermal	0.07	0.5
1	2	B	484	tight thermal	0.07	0.5
1	3	C	484	tight thermal	0.06	0.5
1	4	D	484	tight thermal	0.06	0.5
1	5	E	484	tight thermal	0.06	0.5
1	6	F	484	tight thermal	0.07	0.5
2	1	A	24	tight thermal	0.06	0.5
2	2	B	24	tight thermal	0.03	0.5
2	3	C	24	tight thermal	0.02	0.5
2	4	D	24	tight thermal	0.03	0.5
2	5	E	24	tight thermal	0.03	0.5
2	6	F	24	tight thermal	0.05	0.5
1	1	A	473	loose thermal	3.54	10
1	2	B	473	loose thermal	3.51	10
1	3	C	473	loose thermal	3.36	10
1	4	D	473	loose thermal	3.06	10
1	5	E	473	loose thermal	3.16	10
1	6	F	473	loose thermal	3.53	10
2	1	A	31	loose thermal	1.05	10
2	2	B	31	loose thermal	1.14	10
2	3	C	31	loose thermal	0.68	10
2	4	D	31	loose thermal	1.11	10
2	5	E	31	loose thermal	0.76	10
2	6	F	31	loose thermal	0.94	10

LS refinement shell

Resolution: 3.05→3.215 Å / Total num. of bins used: 10

	R_factor	Num. reflection
R_free	0.331	118
R_work	0.268	2388
obs	-	2388

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