PDB-6aes: Crystal structure of Nucleoside diphosphate kinase from Pseudomon...

Basic information

• Entry: Database: PDB / ID: 6aes
• Title: Crystal structure of Nucleoside diphosphate kinase from Pseudomonas aeruginosa at 3.55 A resolution.
• Components: Nucleoside diphosphate kinase
• Keywords: TRANSFERASE

Function / homology

Function:

nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / nucleoside diphosphate kinase activity / GTP biosynthetic process / ATP binding / metal ion binding / cytoplasm

Domain/homology:

Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta

Component:

Nucleoside diphosphate kinase

• Biological species: Pseudomonas aeruginosa (bacteria)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.55 Å
• Authors: Sikarwar, J. / Singh, P.K. / Sharma, S. / Singh, T.P.
• Citation: Journal: To Be Published; Title: Crystal structure of Nucleoside diphosphate kinase from Pseudomonas aeruginosa at 3.55 A resolution.; Authors: Sikarwar, J. / Singh, P.K. / Sharma, S. / Singh, T.P.

History

Deposition	Aug 6, 2018	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Sep 12, 2018	Provider: repository / Type: Initial release
Revision 1.1	Oct 24, 2018	Group: Data collection / Source and taxonomy / Category: entity_src_gen Item: _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.2	Nov 22, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _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

Assembly

Deposited unit

A: Nucleoside diphosphate kinase

B: Nucleoside diphosphate kinase

C: Nucleoside diphosphate kinase

D: Nucleoside diphosphate kinase

E: Nucleoside diphosphate kinase

F: Nucleoside diphosphate kinase

G: Nucleoside diphosphate kinase

H: Nucleoside diphosphate kinase

Summary:

• 125 kDa, 8 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	124,902	8
Polymers	124,902	8
Non-polymers	0	0
Water	126	7

1

A: Nucleoside diphosphate kinase

D: Nucleoside diphosphate kinase

G: Nucleoside diphosphate kinase

H: Nucleoside diphosphate kinase

Summary:

• defined by author&software
• 62.5 kDa, 4 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	62,451	4
Polymers	62,451	4
Non-polymers	0	0
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	5790 Å2
ΔGint	-43 kcal/mol
Surface area	25980 Å2
Method	PISA

2

B: Nucleoside diphosphate kinase

C: Nucleoside diphosphate kinase

E: Nucleoside diphosphate kinase

F: Nucleoside diphosphate kinase

Summary:

• defined by author&software
• 62.5 kDa, 4 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	62,451	4
Polymers	62,451	4
Non-polymers	0	0
Water	54	3

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	5660 Å2
ΔGint	-39 kcal/mol
Surface area	26210 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	68.566, 70.875, 71.097
Angle α, β, γ (deg.)	99.60, 109.12, 90.25
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	C
1	3	A
2	3	D
1	4	A
2	4	E
1	5	A
2	5	F
1	6	A
2	6	G
1	7	A
2	7	H
1	8	B
2	8	C
1	9	B
2	9	D
1	10	B
2	10	E
1	11	B
2	11	F
1	12	B
2	12	G
1	13	B
2	13	H
1	14	C
2	14	D
1	15	C
2	15	E
1	16	C
2	16	F
1	17	C
2	17	G
1	18	C
2	18	H
1	19	D
2	19	E
1	20	D
2	20	F
1	21	D
2	21	G
1	22	D
2	22	H
1	23	E
2	23	F
1	24	E
2	24	G
1	25	E
2	25	H
1	26	F
2	26	G
1	27	F
2	27	H
1	28	G
2	28	H

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 1 / Auth seq-ID: 1 - 143 / Label seq-ID: 1 - 143

Dom-ID	Ens-ID	Auth asym-ID	Label asym-ID
1	1	A	A
2	1	B	B
1	2	A	A
2	2	C	C
1	3	A	A
2	3	D	D
1	4	A	A
2	4	E	E
1	5	A	A
2	5	F	F
1	6	A	A
2	6	G	G
1	7	A	A
2	7	H	H
1	8	B	B
2	8	C	C
1	9	B	B
2	9	D	D
1	10	B	B
2	10	E	E
1	11	B	B
2	11	F	F
1	12	B	B
2	12	G	G
1	13	B	B
2	13	H	H
1	14	C	C
2	14	D	D
1	15	C	C
2	15	E	E
1	16	C	C
2	16	F	F
1	17	C	C
2	17	G	G
1	18	C	C
2	18	H	H
1	19	D	D
2	19	E	E
1	20	D	D
2	20	F	F
1	21	D	D
2	21	G	G
1	22	D	D
2	22	H	H
1	23	E	E
2	23	F	F
1	24	E	E
2	24	G	G
1	25	E	E
2	25	H	H
1	26	F	F
2	26	G	G
1	27	F	F
2	27	H	H
1	28	G	G
2	28	H	H

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28

Components

#1: Protein

A B C D E F G H
Nucleoside diphosphate kinase / NDP kinase / Nucleoside-2-P kinase

Details:

Mass: 15612.785 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: A0A1G5LIK5, nucleoside-diphosphate kinase

#2: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H₂O

Experimental details

Experiment

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

Sample preparation

• Crystal: Density Matthews: 2.6 ų/Da / Density % sol: 52.6 %
• Crystal grow: Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1M Sodium Malonate, 20% PEG 3350, PH-8.0. / PH range: 5-8

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.953 Å
• Detector: Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 13, 2018 / Details: mirror
• Radiation: Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.953 Å / Relative weight: 1
• Reflection: Resolution: 3.55→45.98 Å / Num. obs: 14065 / % possible obs: 97.5 % / Redundancy: 18.6 % / R_sym value: 0.2 / Net I/σ(I): 3.8
• Reflection shell: Resolution: 3.55→3.64 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1005 / R_sym value: 0.75 / % possible all: 98.8

Processing

Software

Name	Version	Classification
REFMAC	5.8.0230	refinement
XDS		data reduction
autoPROC		data scaling
MOLREP		phasing

Refinement

Method to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YOL

5yol

Resolution: 3.55→45.98 Å / Cor.coef. F_o:F_c: 0.843 / Cor.coef. F_o:F_c free: 0.8 / SU B: 42 / SU ML: 0.6 / Cross valid method: THROUGHOUT / ESU R Free: 0.7 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.33174	741	5 %	RANDOM
Rwork	0.28622	-	-	-
obs	0.28852	14065	98.63 %	-

• Solvent computation: Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 70 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	2.44 Å2	3.41 Å2	0.61 Å2
2-	-	-0.93 Å2	-0.47 Å2
3-	-	-	-1.37 Å2

Refinement step

Cycle: 1 / Resolution: 3.55→45.98 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8752	0	0	7	8759

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.014	8872
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.017	8250
X-RAY DIFFRACTION	r_angle_refined_deg	1.729	1.652	11936
X-RAY DIFFRACTION	r_angle_other_deg	0.929	1.639	19292
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.702	5	1136
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.806	21.333	480
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.314	15	1584
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.269	15	80
X-RAY DIFFRACTION	r_chiral_restr	0.063	0.2	1192
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	10112
X-RAY DIFFRACTION	r_gen_planes_other	0.01	0.02	1602
X-RAY DIFFRACTION	r_nbd_refined
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
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
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	5.833	11.125	4568
X-RAY DIFFRACTION	r_mcbond_other	5.832	11.124	4567
X-RAY DIFFRACTION	r_mcangle_it	9.962	16.661	5696
X-RAY DIFFRACTION	r_mcangle_other	9.961	16.663	5697
X-RAY DIFFRACTION	r_scbond_it	5.369	11.865	4304
X-RAY DIFFRACTION	r_scbond_other	5.361	11.862	4302
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	9.412	17.551	6240
X-RAY DIFFRACTION	r_long_range_B_refined	19.594		35436
X-RAY DIFFRACTION	r_long_range_B_other	19.594		35436
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

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

Ens-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	1086	TIGHT POSITIONAL	0.52	0.13
1	A	1092	TIGHT POSITIONAL	0.48	0.13
1	A	1092	TIGHT POSITIONAL	0.4	0.13
1	A	1092	TIGHT POSITIONAL	0.46	0.13
1	A	1089	TIGHT POSITIONAL	0.81	0.13
1	A	1083	TIGHT POSITIONAL	0.87	0.13
1	A	1089	TIGHT POSITIONAL	0.83	0.13
1	A	1089	TIGHT POSITIONAL	0.77	0.13
1	A	1089	TIGHT POSITIONAL	0.77	0.13
1	A	1088	TIGHT POSITIONAL	0.55	0.13
1	A	1092	TIGHT THERMAL	8.66	1.32
2	A	1094	TIGHT POSITIONAL	0.55	0.13
2	A	1094	TIGHT POSITIONAL	0.44	0.13
2	A	1094	TIGHT POSITIONAL	0.48	0.13
2	A	1088	TIGHT POSITIONAL	0.61	0.13
2	A	1088	TIGHT POSITIONAL	0.57	0.13
2	A	1088	TIGHT POSITIONAL	0.56	0.13
2	A	1094	TIGHT POSITIONAL	0.52	0.13
2	A	1094	TIGHT POSITIONAL	0.56	0.13
2	A	1094	TIGHT POSITIONAL	0.41	0.13
2	A	1089	TIGHT THERMAL	10.19	1.32
3	A	1094	TIGHT THERMAL	11.66	1.32
4	A	1088	TIGHT THERMAL	10.46	1.32
5	A	1094	TIGHT THERMAL	13.72	1.32
6	A	1094	TIGHT THERMAL	10.6	1.32
7	A	1094	TIGHT THERMAL	10.27	1.32
8	B	1087	TIGHT THERMAL	9.16	1.32
9	B	1092	TIGHT THERMAL	9.77	1.32
10	B	1086	TIGHT THERMAL	9.76	1.32
11	B	1092	TIGHT THERMAL	12.32	1.32
12	B	1092	TIGHT THERMAL	10.57	1.32
13	B	1092	TIGHT THERMAL	9.68	1.32
14	C	1089	TIGHT THERMAL	9.43	1.32
15	C	1083	TIGHT THERMAL	10.6	1.32
16	C	1089	TIGHT THERMAL	12.39	1.32
17	C	1089	TIGHT THERMAL	10.89	1.32
18	C	1089	TIGHT THERMAL	11.25	1.32
19	D	1088	TIGHT THERMAL	10	1.32
20	D	1094	TIGHT THERMAL	9.28	1.32
21	D	1094	TIGHT THERMAL	9.63	1.32
22	D	1094	TIGHT THERMAL	10.51	1.32
23	E	1088	TIGHT THERMAL	12.29	1.32
24	E	1088	TIGHT THERMAL	9.93	1.32
25	E	1088	TIGHT THERMAL	7.6	1.32
26	F	1094	TIGHT THERMAL	11.85	1.32
27	F	1094	TIGHT THERMAL	13.12	1.32
28	G	1094	TIGHT THERMAL	9.14	1.32

LS refinement shell

Resolution: 3.55→3.642 Å

	Rfactor	Num. reflection	% reflection
Rfree	0.372	53	-
Rwork	0.35	1005	-
obs	-	-	98.88 %