PDB-3ztq: Hexagonal crystal form P61 of the Aquifex aeolicus nucleoside dip...

ID or keywords:

Entry

Database: PDB / ID: 3ztq

Title

Hexagonal crystal form P61 of the Aquifex aeolicus nucleoside diphosphate kinase

Components

NUCLEOSIDE DIPHOSPHATE KINASE

Nucleoside-diphosphate kinase

Keywords

TRANSFERASE

Function / homology

Function and homology information

purine nucleotide metabolic process / pyrimidine nucleotide metabolic process /

nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / GTP biosynthetic process /

nucleoside diphosphate kinase activity /

phosphorylation /

ATP binding /

metal ion binding /

cytoplasm
Similarity search - Function

Biological species

AQUIFEX AEOLICUS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Boissier, F. / Georgescauld, F. / Moynie, L. / Dupuy, J.-W. / Sarger, C. / Podar, M. / Lascu, I. / Giraud, M.-F. / Dautant, A.

Citation

Journal: Proteins / Year: 2012
Title: An Inter-Subunit Disulphide Bridge Stabilizes the Tetrameric Nucleoside Diphosphate Kinase of Aquifex Aeolicus
Authors: Boissier, F. / Georgescauld, F. / Moynie, L. / Dupuy, J.-W. / Sarger, C. / Podar, M. / Lascu, L. / Giraud, M.-F. / Dautant, A.

History

Deposition	Jul 12, 2011	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 29, 2012	Provider: repository / Type: Initial release
Revision 1.1	Mar 14, 2012	Group: Other
Revision 1.2	May 23, 2012	Group: Other
Revision 1.3	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3ztq.cif.gz	470.8 KB	Display	PDBx/mmCIF format
PDB format	pdb3ztq.ent.gz	391.9 KB	Display	PDB format
PDBx/mmJSON format	3ztq.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zt/3ztq ftp://data.pdbj.org/pub/pdb/validation_reports/zt/3ztq	HTTPS FTP

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Related structure data

Related structure data	3ztoSC 3ztpC 3ztrC 3ztsC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3ztr-3 3ztr-2 3zts-2 3zts-1 3zto-1 3ztr-1 3zts-3 5ey9-1 2pyx-1 5icr-4 Search similar-shape structures by Omokage search (details) 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

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Links

PDB pages	PDBj / wwPDB / NCBI

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

128 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: NUCLEOSIDE DIPHOSPHATE KINASE

B: NUCLEOSIDE DIPHOSPHATE KINASE

C: NUCLEOSIDE DIPHOSPHATE KINASE

D: NUCLEOSIDE DIPHOSPHATE KINASE

defined by software
63.9 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

E: NUCLEOSIDE DIPHOSPHATE KINASE

F: NUCLEOSIDE DIPHOSPHATE KINASE

G: NUCLEOSIDE DIPHOSPHATE KINASE

H: NUCLEOSIDE DIPHOSPHATE KINASE

defined by software
63.9 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	116.360, 116.360, 247.320
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	169
Space group name H-M	P6₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details
1	1	1	CHAIN A AND RESSEQ 2:142 AND BACKBONE
2	1	1	CHAIN B AND RESSEQ 2:142 AND BACKBONE
3	1	1	CHAIN E AND RESSEQ 2:142 AND BACKBONE
4	1	1	CHAIN F AND RESSEQ 2:142 AND BACKBONE
1	1	2	CHAIN C AND RESSEQ 2:142 AND BACKBONE
2	1	2	CHAIN D AND RESSEQ 2:142 AND BACKBONE
3	1	2	CHAIN G AND RESSEQ 2:142 AND BACKBONE
4	1	2	CHAIN H AND RESSEQ 2:142 AND BACKBONE
1	1	3	CHAIN A AND RESSEQ 2:142 AND SIDECHAIN
2	1	3	CHAIN B AND RESSEQ 2:142 AND SIDECHAIN
3	1	3	CHAIN E AND RESSEQ 2:142 AND SIDECHAIN
4	1	3	CHAIN F AND RESSEQ 2:142 AND SIDECHAIN
1	1	4	CHAIN C AND RESSEQ 2:142 AND SIDECHAIN
2	1	4	CHAIN D AND RESSEQ 2:142 AND SIDECHAIN
3	1	4	CHAIN G AND RESSEQ 2:142 AND SIDECHAIN
4	1	4	CHAIN H AND RESSEQ 2:142 AND SIDECHAIN
1	1	5	CHAIN A AND RESSEQ 1:157
2	1	5	CHAIN B AND RESSEQ 1:157
3	1	5	CHAIN C AND RESSEQ 1:157
4	1	5	CHAIN D AND RESSEQ 1:157
5	1	5	CHAIN E AND RESSEQ 1:157
6	1	5	CHAIN F AND RESSEQ 1:157
7	1	5	CHAIN G AND RESSEQ 1:157
8	1	5	CHAIN H AND RESSEQ 1:157

NCS ensembles :

ID
1
2
3
4
5

#1: Protein	NUCLEOSIDE DIPHOSPHATE KINASE / Nucleoside-diphosphate kinase / NDK / NDP KINASE / NUCLEOSIDE-2-P KINASE Mass: 15963.325 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) AQUIFEX AEOLICUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O67528, nucleoside-diphosphate kinase
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1269 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

NUCLEOSIDE DIPHOSPHATE KINASE /

Nucleoside-diphosphate kinase / NDK / NDP KINASE / NUCLEOSIDE-2-P KINASE

Mass: 15963.325 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

AQUIFEX AEOLICUS (bacteria) / Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O67528,

nucleoside-diphosphate kinase

#2: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 1269 / 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: 3.77 Å³/Da / Density % sol: 67.4 % / Description: NONE
Crystal grow	pH: 9 / Details: 2 M MAGNESIUM CHLORIDE, 0.1 M BICINE PH 9

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 22, 2008 / Details: KIRKPATRICK BAEZ
Radiation	Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 2.1→38 Å / Num. obs: 107031 / % possible obs: 97.2 % / Observed criterion σ(I): 1 / Redundancy: 2.2 % / B_iso Wilson estimate: 17.58 Å² / R_merge(I) obs: 0.09 / Net I/σ(I): 6.3
Reflection shell	Resolution: 2.1→2.21 Å / Redundancy: 2.2 % / R_merge(I) obs: 0.23 / Mean I/σ(I) obs: 3.4 / % possible all: 98.9

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
MOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZTO

3zto

Resolution: 2.1→38.088 Å / SU ML: 0.23 / σ(F): 0 / Phase error: 23.54 / Stereochemistry target values: ML
Details: IN THE SSBOND CARDS: THE FIRST ATOM BELONGS TO THE ALTERNATE CONFORMER A (WITH OCCUPANCY Q1). THE SECOND ONE BELONGS TO THE ALTERNATE CONFORMER B (WITH OCCUPANCY Q2). ABS(Q1 - Q2)*100 IS THE ...

	R_factor	Num. reflection	% reflection
R_free	0.1993	5340	5 %
R_work	0.1696	-	-
obs	0.171	106917	97.23 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 46.358 Å² / k_sol: 0.352 e/Å³

Displacement parameters

B_iso mean: 22.7 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.4994 Å²	0 Å²	0 Å²
2-	-	-2.4994 Å²	0 Å²
3-	-	-	4.8512 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→38.088 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8920	0	0	1269	10189

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	9230
X-RAY DIFFRACTION	f_angle_d	1.103	12438
X-RAY DIFFRACTION	f_dihedral_angle_d	13.146	3542
X-RAY DIFFRACTION	f_chiral_restr	0.077	1342
X-RAY DIFFRACTION	f_plane_restr	0.005	1650

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	559	X-RAY DIFFRACTION	POSITIONAL
1	2	B	559	X-RAY DIFFRACTION	POSITIONAL	0.028
1	3	E	561	X-RAY DIFFRACTION	POSITIONAL	0.021
1	4	F	563	X-RAY DIFFRACTION	POSITIONAL	0.028
2	1	C	561	X-RAY DIFFRACTION	POSITIONAL
2	2	D	561	X-RAY DIFFRACTION	POSITIONAL	0.033
2	3	G	564	X-RAY DIFFRACTION	POSITIONAL	0.02
2	4	H	565	X-RAY DIFFRACTION	POSITIONAL	0.033
3	1	A	541	X-RAY DIFFRACTION	POSITIONAL
3	2	B	541	X-RAY DIFFRACTION	POSITIONAL	0.086
3	3	E	547	X-RAY DIFFRACTION	POSITIONAL	0.042
3	4	F	544	X-RAY DIFFRACTION	POSITIONAL	0.087
4	1	C	549	X-RAY DIFFRACTION	POSITIONAL
4	2	D	549	X-RAY DIFFRACTION	POSITIONAL	0.206
4	3	G	549	X-RAY DIFFRACTION	POSITIONAL	0.199
4	4	H	554	X-RAY DIFFRACTION	POSITIONAL	0.113
5	1	A	134	X-RAY DIFFRACTION	POSITIONAL
5	2	B	134	X-RAY DIFFRACTION	POSITIONAL	0.278
5	3	C	131	X-RAY DIFFRACTION	POSITIONAL	0.506
5	4	D	126	X-RAY DIFFRACTION	POSITIONAL	0.417
5	5	E	139	X-RAY DIFFRACTION	POSITIONAL	0.274
5	6	F	137	X-RAY DIFFRACTION	POSITIONAL	0.358
5	7	G	131	X-RAY DIFFRACTION	POSITIONAL	0.488
5	8	H	128	X-RAY DIFFRACTION	POSITIONAL	0.389

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.1-2.1751	0.2354	524	0.2079	10282	X-RAY DIFFRACTION	99
2.1751-2.2621	0.2378	542	0.1949	10333	X-RAY DIFFRACTION	99
2.2621-2.3651	0.235	570	0.1961	10317	X-RAY DIFFRACTION	99
2.3651-2.4897	0.2173	543	0.1865	10301	X-RAY DIFFRACTION	99
2.4897-2.6457	0.2136	547	0.1684	10281	X-RAY DIFFRACTION	98
2.6457-2.8499	0.2284	520	0.1725	10244	X-RAY DIFFRACTION	98
2.8499-3.1366	0.2004	554	0.1752	10148	X-RAY DIFFRACTION	97
3.1366-3.5902	0.1908	547	0.1637	10098	X-RAY DIFFRACTION	97
3.5902-4.5221	0.162	501	0.1407	9841	X-RAY DIFFRACTION	94
4.5221-38.0939	0.1687	492	0.1565	9732	X-RAY DIFFRACTION	92

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	0.5415	-0.0476	0.2819	0.8624	-0.028	0.884	-0.0584	0.1658	0.0326	-0.1307	0.0753	0.1923	-0.0649	-0.1688	-0.0176	0.0221	-0.0312	-0.0265	0.0807	0.0393	0.0979	-47.77	48.3536	15.026
2	0.2695	-0.2931	0.5859	0.5391	-1.1295	2.4869	0.1112	0.1786	0.108	-0.1246	0.0835	0.0736	0.2695	-0.0732	-0.1311	0.2787	0.0418	0.0082	0.4344	0.2101	0.2786	-44.8675	63.3838	6.4245
3	0.7138	0.7975	-0.17	1.1186	-0.3713	0.5053	0.073	-0.0463	0.0269	0.0852	-0.0801	-0.0545	0.0047	0.0432	0.0116	0.0416	-0.0165	-0.0036	0.0491	0.0129	0.0471	-40.1222	35.1587	35.5772
4	0.0566	-0.1446	0.2346	0.3751	-0.6077	0.9926	-0.0132	-0.1182	-0.0569	0.1514	0.1216	0.0008	-0.1148	-0.2753	-0.0772	0.5143	-0.0843	-0.242	0.2897	0.1713	0.2208	-25.7764	30.2796	44.1617
5	1.4291	0.2192	-0.5391	0.1666	-0.1698	0.4486	-0.0459	0.1978	0.0016	-0.0114	-0.0033	0.0192	0.033	0.043	0.0596	0.0196	-0.0301	0.0017	0.0736	0.0097	0.0224	-14.0509	51.531	14.4014
6	1.314	0.1296	-1.9678	0.2849	-0.8561	4.5725	0.2444	0.0846	-0.0649	-0.0587	0.0465	-0.1058	-0.9063	-0.1335	-0.2249	0.3564	-0.0398	-0.0137	0.4169	-0.113	0.0977	-17.3813	37.6369	4.5066
7	1.253	0.3199	0.1908	1.1553	0.4616	0.524	-0.0394	-0.2421	0.2074	0.2568	-0.0388	0.013	-0.1293	0.0315	0.0688	0.0946	-0.0362	-0.0206	0.0588	-0.0171	0.0653	-20.6945	62.7666	36.2887
8	0.1248	0.1408	0.1088	0.6448	1.2724	2.8583	0.1789	0.0405	0.0897	0.2323	0.0443	0.0027	0.0765	-0.1072	-0.1787	0.4589	-0.0573	0.1132	0.402	-0.0783	0.1828	-34.3807	67.0335	46.0014
9	0.4156	0.0811	0.434	0.5614	0.2673	0.5281	-0.069	-0.133	0.02	0.1957	0.0655	-0.1238	-0.0537	0.1623	-0.0283	0.2077	0.0269	-0.0331	0.2595	-0.0319	0.0045	-68.6344	48.4746	61.568
10	0.2495	0.322	1.1984	0.4167	1.5372	5.9123	0.1722	-0.1203	0.0297	0.3112	0.1001	-0.1144	0.6577	-0.165	-0.1936	0.4029	0.0267	-0.0394	0.5945	-0.2372	0.2104	-71.513	63.3898	70.0494
11	0.0981	-0.0644	-0.0781	0.238	0.3334	0.4617	0.0341	0.0668	0.0448	-0.0454	-0.053	0.0361	-0.009	-0.0386	0.0169	0.2117	0.0249	0.0057	0.2111	-0.0157	-0.0169	-76.2439	35.2312	40.9292
12	0.0549	0.1502	0.2998	0.4864	0.9285	1.8529	-0.0536	0.2541	-0.0924	-0.2321	0.2778	-0.0387	-0.2502	0.5989	-0.141	0.6116	0.0868	-0.2852	0.4023	-0.1754	0.2219	-90.5865	30.2841	32.3028
13	0.5525	-0.0199	-0.4867	0.0985	0.0994	0.5053	-0.0702	-0.1919	-0.033	0.0202	0.028	-0.0062	0.0647	-0.0411	0.044	0.2112	0.035	0.0008	0.2755	-0.02	0.0023	-102.2043	51.6459	62.0236
14	0.0468	-0.0442	0.0354	0.1953	-0.8392	4.2527	0.099	-0.1468	-0.0342	0.1623	0.0259	0.0455	-0.5206	0.0334	-0.0923	0.4686	0.0265	0.0525	0.5443	0.1855	0.0722	-98.9778	37.6413	71.9676
15	0.5696	-0.0445	0.0442	0.4625	-0.3724	0.321	-0.0431	0.2291	0.1825	-0.2339	-0.0103	0.0176	-0.1371	-0.0239	0.0432	0.2796	0.0317	-0.0369	0.2379	0.0079	-0.0324	-95.7214	62.8388	40.3039
16	0.1004	0.0271	-0.3482	0.2186	-0.5212	2.3033	0.0765	0.0941	0.0957	-0.237	0.0838	0.0022	0.1817	0.0041	-0.0788	0.5781	0.0544	0.1932	0.4648	0.1332	0.1172	-81.9779	67.0414	30.4617

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND (RESSEQ 2:51 OR RESSEQ 58:142) AND NOT ELEMENT H)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESSEQ 52:57 AND NOT ELEMENT H)
3	X-RAY DIFFRACTION	3	(CHAIN B AND (RESSEQ 2:51 OR RESSEQ 58:142) AND NOT ELEMENT H)
4	X-RAY DIFFRACTION	4	(CHAIN B AND RESSEQ 52:57 AND NOT ELEMENT H)
5	X-RAY DIFFRACTION	5	(CHAIN C AND (RESSEQ 2:51 OR RESSEQ 58:142) AND NOT ELEMENT H)
6	X-RAY DIFFRACTION	6	(CHAIN C AND RESSEQ 52:57 AND NOT ELEMENT H)
7	X-RAY DIFFRACTION	7	(CHAIN D AND (RESSEQ 2:51 OR RESSEQ 58:142) AND NOT ELEMENT H)
8	X-RAY DIFFRACTION	8	(CHAIN D AND RESSEQ 52:57 AND NOT ELEMENT H)
9	X-RAY DIFFRACTION	9	(CHAIN E AND (RESSEQ 2:51 OR RESSEQ 58:142) AND NOT ELEMENT H)
10	X-RAY DIFFRACTION	10	(CHAIN E AND RESSEQ 52:57 AND NOT ELEMENT H)
11	X-RAY DIFFRACTION	11	(CHAIN F AND (RESSEQ 2:51 OR RESSEQ 58:142) AND NOT ELEMENT H)
12	X-RAY DIFFRACTION	12	(CHAIN F AND RESSEQ 52:57 AND NOT ELEMENT H)
13	X-RAY DIFFRACTION	13	(CHAIN G AND (RESSEQ 2:51 OR RESSEQ 58:142) AND NOT ELEMENT H)
14	X-RAY DIFFRACTION	14	(CHAIN G AND RESSEQ 52:57 AND NOT ELEMENT H)
15	X-RAY DIFFRACTION	15	(CHAIN H AND (RESSEQ 2:51 OR RESSEQ 58:142) AND NOT ELEMENT H)
16	X-RAY DIFFRACTION	16	(CHAIN H AND RESSEQ 52:57 AND NOT ELEMENT H)

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