PDB-8qvy: Human NDPK-C unliganded

ID or keywords:

Entry

Database: PDB / ID: 8qvy

Title

Human NDPK-C unliganded

Components

Nucleoside diphosphate kinase 3

Keywords

TRANSFERASE / Kinase

Function / homology

Function and homology information

nucleoside triphosphate biosynthetic process / nucleoside-diphosphate kinase / Interconversion of nucleotide di- and triphosphates / UTP biosynthetic process / CTP biosynthetic process / GTP biosynthetic process / mitochondrial fusion / nucleoside diphosphate kinase activity / ciliary basal body / mitochondrial outer membrane ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 2.64 Å

Authors

Werten, S. / Amjadi, R. / Scheffzek, K.

Funding support

1items

Citation

Journal: Int J Mol Sci / Year: 2024
Title: Mechanistic Insights into Substrate Recognition of Human Nucleoside Diphosphate Kinase C Based on Nucleotide-Induced Structural Changes.
Authors: Amjadi, R. / Werten, S. / Lomada, S.K. / Baldin, C. / Scheffzek, K. / Dunzendorfer-Matt, T. / Wieland, T.

History

Deposition	Oct 18, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 18, 2024	Provider: repository / Type: Initial release
Revision 1.1	Oct 9, 2024	Group: Database references / Structure summary / Category: citation / pdbx_entry_details Item: _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8qvy.cif.gz	476.8 KB	Display	PDBx/mmCIF format
PDB format	pdb8qvy.ent.gz	305.6 KB	Display	PDB format
PDBx/mmJSON format	8qvy.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8qvy_validation.pdf.gz	2.2 MB	Display	wwPDB validaton report
Full document	8qvy_full_validation.pdf.gz	2.2 MB	Display
Data in XML	8qvy_validation.xml.gz	35.9 KB	Display
Data in CIF	8qvy_validation.cif.gz	45.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qv/8qvy ftp://data.pdbj.org/pub/pdb/validation_reports/qv/8qvy	HTTPS FTP

-
Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#233 - May 2019 S-Nitrosylated Hemoglobin similarity (1) #238 - Oct 2019 Ribonucleotide Reductase similarity (1)

Deposited unit

A: Nucleoside diphosphate kinase 3

B: Nucleoside diphosphate kinase 3

C: Nucleoside diphosphate kinase 3

D: Nucleoside diphosphate kinase 3

E: Nucleoside diphosphate kinase 3

F: Nucleoside diphosphate kinase 3

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	106.230, 115.510, 82.610
Angle α, β, γ (deg.)	90.000, 94.316, 90.000
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: GLU / End label comp-ID: GLU / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 18 - 169 / Label seq-ID: 4 - 155

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12
7	Local NCS retraints between domains: 13 14
8	Local NCS retraints between domains: 15 16
9	Local NCS retraints between domains: 17 18
10	Local NCS retraints between domains: 19 20
11	Local NCS retraints between domains: 21 22
12	Local NCS retraints between domains: 23 24
13	Local NCS retraints between domains: 25 26
14	Local NCS retraints between domains: 27 28
15	Local NCS retraints between domains: 29 30

#1: Protein	Nucleoside diphosphate kinase 3 Mass: 17545.137 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NME3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13232
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO₄ / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interest	Y
Has protein modification	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.4 Å³/Da / Density % sol: 48.9 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion / Details: 27% glycerol, 7% PEG 8000, 40 mM KH2PO4

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
Detector	Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 26, 2021 / Details: Vertical CRL / horizontal eliptical mirror
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9677 Å / Relative weight: 1
Reflection	Resolution: 2.64→47.335 Å / Num. obs: 28215 / % possible obs: 96.4 % / Redundancy: 7.3 % / B_iso Wilson estimate: 79.1 Å² / CC_1/2: 0.992 / R_merge(I) obs: 0.127 / R_rim(I) all: 0.137 / Net I/σ(I): 9.45
Reflection shell	Resolution: 2.64→2.71 Å / Redundancy: 7.4 % / R_merge(I) obs: 2.39 / Mean I/σ(I) obs: 0.92 / Num. unique obs: 2137 / CC_1/2: 0.48 / R_rim(I) all: 2.571 / % possible all: 98.2

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0419	refinement
XDS		data reduction
XSCALE		data scaling
REFMAC		phasing

Refinement

Method to determine structure:

FOURIER SYNTHESIS / Resolution: 2.64→47.335 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.936 / SU B: 53.052 / SU ML: 0.41 / Cross valid method: FREE R-VALUE / ESU R Free: 0.344
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2469	1263	4.476 %
R_work	0.1972	26952	-
all	0.199	-	-
obs	-	28215	96.382 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 98.163 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.433 Å²	0 Å²	5.525 Å²
2-	-	-3.702 Å²	-0 Å²
3-	-	-	4.252 Å²

Refinement step

Cycle: LAST / Resolution: 2.64→47.335 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7073	0	30	0	7103

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	7256
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	6851
X-RAY DIFFRACTION	r_angle_refined_deg	1.47	1.649	9850
X-RAY DIFFRACTION	r_angle_other_deg	0.503	1.579	15620
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.423	5	906
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	14.102	5	82
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.641	10	1149
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.8	10	326
X-RAY DIFFRACTION	r_chiral_restr	0.061	0.2	1083
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	8871
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1793
X-RAY DIFFRACTION	r_nbd_refined	0.22	0.2	1504
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.205	0.2	6418
X-RAY DIFFRACTION	r_nbtor_refined	0.187	0.2	3561
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.082	0.2	3980
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.153	0.2	123
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.111	0.2	8
X-RAY DIFFRACTION	r_nbd_other	0.207	0.2	66
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.316	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	6.231	6.516	3642
X-RAY DIFFRACTION	r_mcbond_other	6.231	6.516	3642
X-RAY DIFFRACTION	r_mcangle_it	9.322	11.702	4542
X-RAY DIFFRACTION	r_mcangle_other	9.321	11.702	4543
X-RAY DIFFRACTION	r_scbond_it	7.037	7.016	3614
X-RAY DIFFRACTION	r_scbond_other	7.015	7.013	3609
X-RAY DIFFRACTION	r_scangle_it	10.455	12.681	5308
X-RAY DIFFRACTION	r_scangle_other	10.434	12.676	5303
X-RAY DIFFRACTION	r_lrange_it	13.029	61.345	7949
X-RAY DIFFRACTION	r_lrange_other	13.028	61.346	7950
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.066	0.05	4722
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.067	0.05	4704
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.051	0.05	4709
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.063	0.05	4681
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.06	0.05	4682
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.054	0.05	4794
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.068	0.05	4797
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.065	0.05	4785
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.05	0.05	4822
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.061	0.05	4763
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.064	0.05	4781
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.062	0.05	4798
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.06	0.05	4820
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.067	0.05	4842
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.057	0.05	4831

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.06648	0.0501
1	2	A	X-RAY DIFFRACTION	Local ncs	0.06648	0.0501
2	3	A	X-RAY DIFFRACTION	Local ncs	0.06703	0.0501
2	4	A	X-RAY DIFFRACTION	Local ncs	0.06703	0.0501
3	5	A	X-RAY DIFFRACTION	Local ncs	0.05103	0.0501
3	6	A	X-RAY DIFFRACTION	Local ncs	0.05103	0.0501
4	7	A	X-RAY DIFFRACTION	Local ncs	0.06292	0.0501
4	8	A	X-RAY DIFFRACTION	Local ncs	0.06292	0.0501
5	9	A	X-RAY DIFFRACTION	Local ncs	0.05957	0.0501
5	10	A	X-RAY DIFFRACTION	Local ncs	0.05957	0.0501
6	11	A	X-RAY DIFFRACTION	Local ncs	0.05431	0.05011
6	12	A	X-RAY DIFFRACTION	Local ncs	0.05431	0.05011
7	13	A	X-RAY DIFFRACTION	Local ncs	0.06814	0.0501
7	14	A	X-RAY DIFFRACTION	Local ncs	0.06814	0.0501
8	15	A	X-RAY DIFFRACTION	Local ncs	0.06512	0.0501
8	16	A	X-RAY DIFFRACTION	Local ncs	0.06512	0.0501
9	17	A	X-RAY DIFFRACTION	Local ncs	0.04997	0.0501
9	18	A	X-RAY DIFFRACTION	Local ncs	0.04997	0.0501
10	19	A	X-RAY DIFFRACTION	Local ncs	0.06146	0.0501
10	20	A	X-RAY DIFFRACTION	Local ncs	0.06146	0.0501
11	21	A	X-RAY DIFFRACTION	Local ncs	0.06446	0.0501
11	22	A	X-RAY DIFFRACTION	Local ncs	0.06446	0.0501
12	23	A	X-RAY DIFFRACTION	Local ncs	0.0618	0.0501
12	24	A	X-RAY DIFFRACTION	Local ncs	0.0618	0.0501
13	25	A	X-RAY DIFFRACTION	Local ncs	0.05991	0.0501
13	26	A	X-RAY DIFFRACTION	Local ncs	0.05991	0.0501
14	27	A	X-RAY DIFFRACTION	Local ncs	0.06666	0.0501
14	28	A	X-RAY DIFFRACTION	Local ncs	0.06666	0.0501
15	29	A	X-RAY DIFFRACTION	Local ncs	0.05716	0.05011
15	30	A	X-RAY DIFFRACTION	Local ncs	0.05716	0.05011

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.64-2.708	0.631	112	0.569	2019	0.572	2169	0.454	0.487	98.248	0.559
2.708-2.782	0.48	97	0.505	1970	0.503	2109	0.82	0.768	98.0085	0.49
2.782-2.863	0.446	61	0.411	1899	0.412	2001	0.779	0.843	97.951	0.38
2.863-2.951	0.346	79	0.367	1864	0.366	1984	0.888	0.885	97.9335	0.334
2.951-3.047	0.313	89	0.283	1785	0.284	1920	0.909	0.925	97.6042	0.242
3.047-3.153	0.303	75	0.255	1737	0.257	1865	0.922	0.946	97.1582	0.22
3.153-3.272	0.32	65	0.231	1659	0.234	1801	0.922	0.957	95.7246	0.2
3.272-3.405	0.251	68	0.211	1566	0.213	1727	0.956	0.969	94.6149	0.184
3.405-3.555	0.28	54	0.211	1391	0.214	1650	0.949	0.971	87.5758	0.192
3.555-3.728	0.238	58	0.191	1186	0.193	1592	0.969	0.981	78.1407	0.179
3.728-3.928	0.236	71	0.164	1402	0.168	1496	0.964	0.985	98.4626	0.155
3.928-4.165	0.181	74	0.152	1347	0.154	1426	0.982	0.987	99.6494	0.149
4.165-4.45	0.163	74	0.145	1271	0.146	1351	0.981	0.987	99.5559	0.149
4.45-4.803	0.211	53	0.137	1193	0.14	1252	0.973	0.989	99.5208	0.147
4.803-5.256	0.226	67	0.164	1086	0.168	1158	0.977	0.986	99.5682	0.173
5.256-5.867	0.219	57	0.174	993	0.176	1054	0.971	0.984	99.6205	0.187
5.867-6.757	0.186	40	0.169	876	0.17	922	0.983	0.986	99.3492	0.186
6.757-8.234	0.194	34	0.146	755	0.147	792	0.979	0.987	99.6212	0.169
8.234-11.473	0.254	12	0.139	607	0.141	624	0.949	0.989	99.1987	0.178
11.473-47.335	0.337	23	0.269	346	0.274	375	0.943	0.945	98.4	0.341

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	2.8856	-0.1023	0.9339	3.3657	-0.703	3.0801	-0.0787	0.1905	0.4363	-0.1585	-0.088	0.7287	-0.4228	-0.5699	0.1667	0.284	0.0718	0.0639	0.218	-0.0183	0.7713	6.0557	7.6218	17.6407
2	3.5852	0.7081	0.5537	3.3309	-0.5032	2.4458	0.1226	0.1769	-0.1047	-0.0271	-0.1782	0.5368	0.2682	-0.3752	0.0556	0.1944	-0.1553	0.1396	0.2267	-0.0819	0.4841	4.3144	-25.6346	20.356
3	2.0774	-0.1335	0.2021	1.5059	1.0049	3.4944	0.107	0.6304	0.1015	-0.573	-0.0886	0.2202	-0.102	-0.1044	-0.0185	0.433	-0.06	0.0012	0.4988	0.0421	0.3525	21.9024	-11.8963	-4.2983
4	2.316	0.0757	0.6879	2.7821	0.7721	3.4835	-0.0868	0.0012	0.378	0.0745	-0.1087	0.2172	-0.234	-0.0266	0.1955	0.1957	-0.0462	0.1523	0.0155	-0.0378	0.3975	26.8129	8.7198	28.9119
5	3.5015	0.1068	0.0233	3.8169	-1.3172	2.0883	0.1104	-0.3676	-0.1098	0.4884	-0.0062	0.0121	0.1379	-0.1402	-0.1042	0.3381	-0.1275	0.1208	0.1056	0.0153	0.2763	22.1117	-23.5927	35.3671
6	3.7334	0.6257	-0.8068	1.711	0.9328	3.3864	0.0072	0.3649	-0.1048	-0.1311	0.0822	-0.1632	0.1731	0.2509	-0.0894	0.168	-0.0319	0.183	0.1904	-0.0665	0.2598	40.5832	-14.4295	9.5503

Refinement TLS group

Selection: ALL

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi