PDB-2qor: Crystal structure of Plasmodium vivax guanylate kinase

ID or keywords:

Entry

Database: PDB / ID: 2qor

Title

Crystal structure of Plasmodium vivax guanylate kinase

Components

Guanylate kinase

Keywords

TRANSFERASE / phosphotransferase / purine metabolism / Structural Genomics / Structural Genomics of Pathogenic Protozoa Consortium / SGPP / PSI / Protein Structure Initiative / Kinase

Function / homology

Function and homology information

guanylate kinase / guanylate kinase activity / ATP binding
Similarity search - Function

Biological species

Plasmodium vivax (malaria parasite P. vivax)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.8 Å

Authors

Merritt, E.A. / Le Trong, I. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

Citation

Journal: To be Published
Title: Plasmodium vivax guanylate kinase.
Authors: Le Trong, I. / Merritt, E.A.

History

Deposition	Jul 20, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 7, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software

Remark 300

BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION ...

Remark 999

SEQUENCE THE SEQUENCE OF THIS PROTEIN IS ALSO AVAILABLE FROM PLASMODB UNDER THE ACCESION CODE PV099895.

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2qor.cif.gz	54.9 KB	Display	PDBx/mmCIF format
PDB format	pdb2qor.ent.gz	41.7 KB	Display	PDB format
PDBx/mmJSON format	2qor.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2qor_validation.pdf.gz	785.9 KB	Display	wwPDB validaton report
Full document	2qor_full_validation.pdf.gz	786.5 KB	Display
Data in XML	2qor_validation.xml.gz	10.1 KB	Display
Data in CIF	2qor_validation.cif.gz	13.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qo/2qor ftp://data.pdbj.org/pub/pdb/validation_reports/qo/2qor	HTTPS FTP

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Related structure data

Related structure data	1ex6 1ex7 1gky 1lvg 1s4q 1s96 1z6g 1z8f 1znw 1znx 1zny 1znz 2an9 2anb 2anc 2f3r 2f3t 2j41
Similar structure data	5aoi-1 4hoj-d 6ez3-3 3oqi-1 4ueb-2 4agn-2 2j1w-2 1y5u-d 4agq-1 5lap-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: Pviv008894AAASGPP target construct

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#151 - Jul 2012 Hypoxanthine-guanine phosphoribosyltransferase similarity (2) #104 - Aug 2008 Selenocysteine Synthase similarity (1) #106 - Oct 2008 Poly(A) Polymerase similarity (1) #116 - Aug 2009 Sulfotransferases similarity (1) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (1) #249 - Sep 2020 SARS-CoV-2 RNA-dependent RNA Polymerase similarity (1)

Deposited unit

A: Guanylate kinase

hetero molecules

24.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	43.535, 43.535, 342.800
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	179
Space group name H-M	P6₅22

Components on special symmetry positions

ID	Model	Components
1	1	A-264- HOH

#1: Protein	Guanylate kinase / GMP kinase / Guanosine monophosphate kinase Mass: 23946.582 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax) Gene: Pv099895, PVX_099895 / Plasmid: BG1861 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PlysS / References: UniProt: A5K709, guanylate kinase
#2: Chemical	ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE Mass: 363.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₅O₈P
#3: Chemical	ChemComp-POP / PYROPHOSPHATE 2- Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H₂O₇P₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 64 / 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: 1.96 Å³/Da / Density % sol: 37.18 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 ul Protein, 0.1 ul Crystallization buffer (65% PEG 400, 0.1M MOPS pH 7.5, 0.1M NaNO3, 5mM GMP), VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL9-2 / Wavelength: 0.97907, 0.97922, 0.91162

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 15, 2007

Radiation

Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97907	1
2	0.97922	1
3	0.91162	1

Refln sys abs

Index l	I	I/σ(I)	σ(I)
8	9.15	1.6	5.68
9	9.16	2.3	3.94
10	6.38	1.7	3.79
11	18.16	4.9	3.73
13	12.86	2.2	5.75
14	17.85	3.5	5.07
15	7	1.6	4.27
16	13.37	2.3	5.92
17	66.33	10.1	6.57
19	33.2	3.6	9.15
20	10.64	1.7	6.1
21	5.55	1.4	3.9
22	6.08	1.4	4.26
23	90.48	17.7	5.12
25	41.11	3.3	12.35
26	6.92	1.4	4.96
27	5.44	1.4	3.98
28	12.6	1.6	7.79
29	22.75	3	7.53
31	17.72	2.1	8.24
32	9.87	1.5	6.38
33	8.55	1.5	5.83
34	14.47	1.8	8.12
35	97.87	19.3	5.06
37	34.69	3.9	8.92
38	14.01	1.6	8.67
39	11.94	1.6	7.64
40	17.66	2	9
41	12.6	1.6	7.99
43	8.4	1.4	5.93
44	10.04	1.5	6.87
45	8.11	1.4	5.83
46	14.11	1.6	8.75
47	13.93	1.6	8.82
49	19.92	1.5	12.96
50	23	2	11.32
51	10.35	1.4	7.15
52	16.61	1.7	9.92
53	14.77	1.6	9.39
55	18.2	1.6	11.41
56	11.48	1.5	7.79
57	10.42	1.4	7.39
58	13.82	1.5	9.23
59	126.71	21.3	5.95
61	26.52	2	13.05
62	6.99	1.3	5.22
63	13.19	1.5	8.71
64	12.6	1.5	8.34
65	25.79	1.8	14.01
67	10.98	1.4	7.83
68	10.85	1.4	7.81
69	22.69	1.8	12.84
70	16.84	1.4	12.02
71	46.55	4.1	11.43
73	14.71	1.5	9.72
74	12.94	1.5	8.76
75	11.28	1.4	8.08
76	9.7	1.4	7.18
77	154.95	17.9	8.64
79	34.56	2.2	16.01
80	35.8	2.1	16.98
81	9.5	1.4	6.99
82	9.72	1.4	7.14
83	65.17	8	8.19
85	11.03	1.4	7.96
86	14.28	1.4	9.92
88	17.87	1.4	13.02
91	84.94	4.9	17.32
92	9.98	1.4	7.39
93	25.49	1.8	14.04
94	13.15	1.4	9.26
95	64.95	7.4	8.75
97	20.6	1.6	12.81
98	18.84	1.5	12.34
99	15.67	1.5	10.72
100	26.48	1.5	17.52
101	21.94	1.6	13.73
103	16.27	1.5	10.76
104	11.6	1.4	8.31
105	17.18	1.6	11.06
106	15	1.4	10.52
107	29.58	1.8	16.01
109	17.43	1.5	11.38
110	15.65	1.5	10.62
111	14.63	1.5	9.87
113	105.88	14.4	7.37
116	15.11	1.4	10.64
122	8.23	1.3	6.15
123	9.93	1.4	7.29
125	155.09	8	19.49
128	11.79	1.4	8.53
129	21.15	1.6	13.58
130	8.65	1.3	6.48
131	81.94	2.9	27.88
134	10.22	1.4	7.48
135	19.12	1.6	12.06
136	29.12	1.5	19.61
137	69.28	3.5	20.01
139	26.28	1.4	18.44
140	29.96	1.5	20.22
141	37.22	1.8	21.05
142	27.88	1.5	18.37
143	24.82	1.5	16.71
145	17.29	1.4	12.7
147	30.97	1.6	18.91
148	31.83	1.5	21.37
149	29.89	1.5	20.55
151	23.64	1.4	16.96
152	37.81	2	19.19
153	29.13	1.5	19.3
154	27.36	1.5	18.25
155	22.71	1.4	15.8
157	36.54	1.7	21.01
158	30.25	1.5	20.69
159	33.15	1.7	20
160	27.37	1.4	19.14
161	49.76	2.3	21.89
163	33.2	1.6	20.82
164	23.05	1.6	14.86
165	25.53	1.6	15.77
166	58.17	1.8	32.34
167	48.21	2.2	21.97
169	30.69	1.5	21.16
170	40.82	1.9	21.79
171	30.34	1.5	20.06
172	26.12	1.5	18.01
173	26.52	1.5	17.87
175	18.48	1.4	13.03
176	32.68	1.5	21.51
177	24.39	1.5	16.69
178	37.16	1.7	21.89
179	33.54	1.6	20.43
181	27.09	1.6	16.69
182	25.62	1.6	16.45
183	22.53	1.5	14.96
184	27.69	1.6	17.75
185	19.92	1.4	13.85
187	24.65	1.4	17.08
188	27.83	1.5	18.74
189	21.76	1.4	15.54
190	27.08	1.5	17.95

Reflection

Resolution: 1.8→42.84 Å / Num. obs: 19333 / % possible obs: 99.7 % / Redundancy: 17.2 % / B_iso Wilson estimate: 29.40802 Å² / R_merge(I) obs: 0.099 / Χ²: 1.182 / Net I/σ(I): 12.1

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
1.8-1.86	9.5	0.612	1806	0.56	1	98.2
1.86-1.94	12.7	0.489	1850	0.678	1	99.8
1.94-2.03	14.6	0.355	1869	0.884	1	100
2.03-2.13	16.2	0.267	1877	1.215	1	99.9
2.13-2.27	17.1	0.204	1910	1.36	1	99.9
2.27-2.44	17	0.162	1910	1.533	1	99.9
2.44-2.69	17.8	0.14	1920	1.373	1	99.9
2.69-3.08	20.5	0.124	1948	1.297	1	99.8
3.08-3.88	22.6	0.102	2008	1.183	1	100
3.88-50	22	0.075	2258	1.188	1	99.7

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Phasing

Phasing	Method: MAD

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Processing

Software

Name	Version	Classification
TRUNCATE	CCP4_5.99	data reduction
DENZO		data reduction
SCALEPACK		data scaling
PDB_EXTRACT	2	data extraction
MAR345	CCD	data collection
HKL-2000		data reduction
HKL-2000		data scaling
SOLVE		phasing
REFMAC	5.2.0019	refinement

Refinement

Method to determine structure:

MAD / Resolution: 1.8→37.48 Å / Cor.coef. F_o:F_c: 0.953 / Cor.coef. F_o:F_c free: 0.95 / SU B: 4.945 / SU ML: 0.08 / SU R Cruickshank DPI: 0.141 / SU R_free: 0.127 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.141 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.227	984	5.1 %	RANDOM
R_work	0.2	-	-	-
obs	0.201	19191	99.65 %	-

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: 20.737 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.21 Å²	0.1 Å²	0 Å²
2-	-	0.21 Å²	0 Å²
3-	-	-	-0.31 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→37.48 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1595	0	33	64	1692

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	1663
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	1187
X-RAY DIFFRACTION	r_angle_refined_deg	1.422	2.011	2239
X-RAY DIFFRACTION	r_angle_other_deg	0.847	3	2878
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.854	5	195
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.375	24.024	82
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.563	15	310
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.554	15	13
X-RAY DIFFRACTION	r_chiral_restr	0.079	0.2	233
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	1808
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	345
X-RAY DIFFRACTION	r_nbd_refined	0.215	0.2	288
X-RAY DIFFRACTION	r_nbd_other	0.19	0.2	1211
X-RAY DIFFRACTION	r_nbtor_refined	0.186	0.2	788
X-RAY DIFFRACTION	r_nbtor_other	0.084	0.2	884
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.149	0.2	60
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.201	0.2	11
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.276	0.2	48
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.132	0.2	6
X-RAY DIFFRACTION	r_mcbond_it	1.335	2	1207
X-RAY DIFFRACTION	r_mcbond_other	0.279	2	399
X-RAY DIFFRACTION	r_mcangle_it	1.652	3	1577
X-RAY DIFFRACTION	r_scbond_it	2.707	4	801
X-RAY DIFFRACTION	r_scangle_it	3.865	6	662

LS refinement shell

Resolution: 1.8→1.85 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.265	66	-
R_work	0.208	1234	-
all	-	1300	-
obs	-	-	97.16 %

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	1.3341	0.3536	-0.5204	1.4313	-0.5517	1.7606	-0.0796	-0.0963	-0.1232	-0.0054	0.0109	0.0134	0.1998	0.0052	0.0687	0.0448	0.0077	0.0197	0.111	0.0364	0.0725	13.9203	0.0457	184.7113
2	2.5196	1.0478	-1.1058	4.1045	-1.2485	3.0998	0.026	-0.4633	-0.2059	0.5763	-0.1945	-0.243	-0.0119	0.4398	0.1685	0.0435	0.0009	-0.0203	0.1757	0.0478	0.0228	16.4594	9.0172	192.9553
3	3.7308	1.0111	-0.3438	2.8418	-0.5516	1.8629	-0.0217	-0.0754	-0.1831	-0.0506	0.1046	0.1135	0.0616	-0.1491	-0.0829	0.0003	0.0308	0.0074	0.133	0.0543	0.112	-2.6408	11.9089	181.5688
4	2.9717	-0.2135	0.0487	1.5865	-0.1666	1.7564	-0.0236	-0.1632	0.1797	0.1123	-0.0551	0.027	-0.0372	0.0366	0.0787	0.0311	-0.0279	-0.0051	0.0969	0.0298	0.0815	18.2272	17.6136	181.017

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	1 - 100	9 - 108
2	X-RAY DIFFRACTION	2	A	A	101 - 124	109 - 132
3	X-RAY DIFFRACTION	3	A	A	125 - 157	133 - 165
4	X-RAY DIFFRACTION	4	A	A	158 - 196	166 - 204

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