PDB-4ane: R80N MUTANT OF NUCLEOSIDE DIPHOSPHATE KINASE FROM MYCOBACTERIUM T...

ID or keywords:

Entry

Database: PDB / ID: 4ane

Title

R80N MUTANT OF NUCLEOSIDE DIPHOSPHATE KINASE FROM MYCOBACTERIUM TUBERCULOSIS

Components

NUCLEOSIDE DIPHOSPHATE KINASE

Keywords

TRANSFERASE

Function / homology

Function and homology information

symbiont-mediated perturbation of host Rab small GTPase signal transduction / purine nucleotide metabolic process / pyrimidine nucleotide metabolic process / symbiont-mediated killing of host cell / nuclease activity / nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / nucleoside diphosphate kinase activity / GTP biosynthetic process ...
Similarity search - Function

Biological species

MYCOBACTERIUM TUBERCULOSIS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Georgescauld, F. / Moynie, L. / Habersetzer, J. / Lascu, I. / Dautant, A.

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structure of Mycobacterium Tuberculosis Nucleoside Diphosphate Kinase R80N Mutant in Complex with Citrate
Authors: Georgescauld, F. / Moynie, L. / Habersetzer, J. / Dautant, A.

History

Deposition	Mar 16, 2012	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 13, 2013	Provider: repository / Type: Initial release
Revision 1.1	Apr 3, 2013	Group: Database references
Revision 1.2	Jan 15, 2014	Group: Database references
Revision 1.3	Jan 22, 2014	Group: Database references
Revision 1.4	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4ane.cif.gz	320.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4ane.ent.gz	264 KB	Display	PDB format
PDBx/mmJSON format	4ane.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4ane_validation.pdf.gz	488.8 KB	Display	wwPDB validaton report
Full document	4ane_full_validation.pdf.gz	501.6 KB	Display
Data in XML	4ane_validation.xml.gz	36 KB	Display
Data in CIF	4ane_validation.cif.gz	50.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/an/4ane ftp://data.pdbj.org/pub/pdb/validation_reports/an/4ane	HTTPS FTP

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Related structure data

Related structure data	1k44S 4anc 4and S: Starting model for refinement
Similar structure data	6qa2-d 4and-1 3emt-1 3dkd-1 3ddi-1 3eic-2 3g2x-1 3evw-2 3fbf-1 3fbe-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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#60 - Dec 2004 Ubiquitin similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1)

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

hetero molecules

87.5 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)	68.820, 113.340, 107.561
Angle α, β, γ (deg.)	90.00, 106.40, 90.00
Int Tables number	5
Space group name H-M	I121

Components on special symmetry positions

ID	Model	Components
1	1	F-2020- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1
3	1
4	1
5	1
6	1

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details
1	1	1	(CHAIN A AND (RESI 2:43 OR RESI 65:136) AND (NAME N OR NAME C OR NAME O OR NAME CA OR NAME CB) )
2	1	1	(CHAIN B AND (RESI 2:43 OR RESI 65:136) AND (NAME N OR NAME C OR NAME O OR NAME CA OR NAME CB) )
3	1	1	(CHAIN C AND (RESI 2:43 OR RESI 65:136) AND (NAME N OR NAME C OR NAME O OR NAME CA OR NAME CB) )
4	1	1	(CHAIN D AND (RESI 2:43 OR RESI 65:136) AND (NAME N OR NAME C OR NAME O OR NAME CA OR NAME CB) )
5	1	1	(CHAIN E AND (RESI 2:43 OR RESI 65:136) AND (NAME N OR NAME C OR NAME O OR NAME CA OR NAME CB) )
6	1	1	(CHAIN F AND (RESI 2:43 OR RESI 65:136) AND (NAME N OR NAME C OR NAME O OR NAME CA OR NAME CB) )

#1: Protein	NUCLEOSIDE DIPHOSPHATE KINASE / NDK / NDKA / NDP KINASE / NUCLEOSIDE-2-P KINASE Mass: 14479.378 Da / Num. of mol.: 6 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL References: UniProt: P84284, UniProt: P9WJH7*PLUS, nucleoside-diphosphate kinase
#2: Chemical	ChemComp-CIT / CITRIC ACID Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₆H₈O₇
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 448 / Source method: isolated from a natural source / Formula: H₂O
Compound details	ENGINEERED RESIDUE IN CHAIN A, ARG 80 TO ASN ENGINEERED RESIDUE IN CHAIN B, ARG 80 TO ASN ...ENGINEERED RESIDUE IN CHAIN A, ARG 80 TO ASN ENGINEERED RESIDUE IN CHAIN B, ARG 80 TO ASN ENGINEERED RESIDUE IN CHAIN C, ARG 80 TO ASN ENGINEERED RESIDUE IN CHAIN D, ARG 80 TO ASN ENGINEERED RESIDUE IN CHAIN E, ARG 80 TO ASN ENGINEERED RESIDUE IN CHAIN F, ARG 80 TO ASN

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.33 Å³/Da / Density % sol: 47.2 % / Description: NONE
Crystal grow	pH: 5.6 Details: 30% (W/V) PEG4000, 0.2 M AMMONIUM ACETATE, 0.1 M TRI-SODIUM CITRATE, PH 5.6

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Data collection

Diffraction	Mean temperature: 107 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625
Detector	Type: ADSC CCD / Detector: CCD / Date: Jun 25, 2007
Radiation	Monochromator: SINGLE CRYSTAL, SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97625 Å / Relative weight: 1
Reflection	Resolution: 1.9→32.9 Å / Num. obs: 57601 / % possible obs: 92.9 % / Observed criterion σ(I): 1 / Redundancy: 1.9 % / B_iso Wilson estimate: 21.02 Å² / R_merge(I) obs: 0.06 / Net I/σ(I): 7.8
Reflection shell	Resolution: 1.9→1.93 Å / Redundancy: 1.8 % / R_merge(I) obs: 0.14 / Mean I/σ(I) obs: 3.6 / % possible all: 83.7

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K44

1k44

Resolution: 1.9→29.651 Å / SU ML: 0.25 / σ(F): 0 / Phase error: 23 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2348	2927	5.1 %
R_work	0.1843	-	-
obs	0.1869	57601	92.62 %

Solvent computation

Shrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 63.576 Å² / k_sol: 0.418 e/Å³

Displacement parameters

B_iso mean: 32.22 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.4623 Å²	0 Å²	3.679 Å²
2-	-	0.0634 Å²	0 Å²
3-	-	-	-1.5257 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→29.651 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5933	0	39	448	6420

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	6172
X-RAY DIFFRACTION	f_angle_d	1.078	8405
X-RAY DIFFRACTION	f_dihedral_angle_d	13.83	2294
X-RAY DIFFRACTION	f_chiral_restr	0.07	993
X-RAY DIFFRACTION	f_plane_restr	0.004	1111

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	551	X-RAY DIFFRACTION	POSITIONAL
1	2	B	551	X-RAY DIFFRACTION	POSITIONAL	0.185
1	3	C	563	X-RAY DIFFRACTION	POSITIONAL	0.094
1	4	D	547	X-RAY DIFFRACTION	POSITIONAL	0.16
1	5	E	555	X-RAY DIFFRACTION	POSITIONAL	0.137
1	6	F	555	X-RAY DIFFRACTION	POSITIONAL	0.189

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 (%)
1.9-1.9328	0.3295	102	0.2395	2141	X-RAY DIFFRACTION	73
1.9328-1.9679	0.2764	135	0.2166	2443	X-RAY DIFFRACTION	83
1.9679-2.0057	0.2548	156	0.2077	2794	X-RAY DIFFRACTION	96
2.0057-2.0467	0.2739	139	0.2001	2886	X-RAY DIFFRACTION	97
2.0467-2.0912	0.2455	157	0.1968	2848	X-RAY DIFFRACTION	97
2.0912-2.1398	0.2533	175	0.1891	2863	X-RAY DIFFRACTION	97
2.1398-2.1933	0.2388	159	0.1757	2846	X-RAY DIFFRACTION	97
2.1933-2.2526	0.2426	144	0.1766	2889	X-RAY DIFFRACTION	97
2.2526-2.3188	0.2488	156	0.179	2846	X-RAY DIFFRACTION	97
2.3188-2.3936	0.2374	132	0.1877	2900	X-RAY DIFFRACTION	97
2.3936-2.4791	0.2326	166	0.1812	2809	X-RAY DIFFRACTION	96
2.4791-2.5784	0.2415	154	0.1925	2817	X-RAY DIFFRACTION	96
2.5784-2.6956	0.2437	143	0.1889	2853	X-RAY DIFFRACTION	96
2.6956-2.8376	0.2374	164	0.1908	2815	X-RAY DIFFRACTION	95
2.8376-3.0153	0.2301	151	0.1797	2806	X-RAY DIFFRACTION	95
3.0153-3.2478	0.2297	154	0.1796	2792	X-RAY DIFFRACTION	94
3.2478-3.5742	0.2094	131	0.1689	2775	X-RAY DIFFRACTION	94
3.5742-4.0902	0.2177	139	0.1675	2744	X-RAY DIFFRACTION	92
4.0902-5.1488	0.1873	150	0.1631	2600	X-RAY DIFFRACTION	88
5.1488-29.6542	0.2901	120	0.2286	2207	X-RAY DIFFRACTION	73

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	1.1316	-1.2341	-0.7192	1.2635	-0.3669	3.4477	0.0033	-0.1432	0.0225	0.0143	0.1108	-0.1121	0.1971	0.1636	-0.1065	0.0121	0.0227	-0.0398	0.0416	-0.035	0.0659	5.0768	-17.0686	24.4803
2	3.3837	-0.6243	-2.5191	2.9747	-1.2684	2.9619	0.0684	-0.3935	0.337	-0.4468	-0.1151	-0.4908	0.4959	0.8374	0.0904	0.1397	0.0716	0.0302	0.2347	-0.0332	0.2431	22.267	-16.963	15.0413
3	1.6629	-1.032	-0.2752	1.6334	-0.2881	1.7948	0.0401	0.0306	0.1409	-0.2159	0.0546	-0.1943	0.1321	0.1711	-0.0913	0.0688	0.0297	-0.0061	0.0877	-0.0527	0.1169	8.1869	-15.3003	17.057
4	3.6548	-0.4756	-0.8405	0.6787	0.7729	3.2427	-0.083	-0.2071	-0.4983	0.129	0.115	-0.0861	0.2968	0.0897	-0.0384	0.0907	0.042	-0.037	0.0176	0.0104	0.1091	-0.0702	-20.0345	38.3538
5	2.9073	1.3229	1.4082	1.5921	0.3747	2.8413	0.2332	-0.5145	0.0385	0.643	0.3257	-0.1347	0.7525	-0.686	-0.3242	1.2458	-0.2736	-0.3676	0.7143	0.0738	0.8499	-6.493	-30.8469	53.1559
6	2.6002	-0.482	-0.1004	1.6628	0.5952	1.6949	0.0453	-0.4043	-0.4352	0.3237	0.047	-0.0452	0.3182	-0.0671	-0.0927	0.1497	0.0035	-0.0434	0.0645	0.0494	0.135	-3.9708	-19.4933	43.8667
7	0.6303	0.0784	-0.3177	0.9411	1.3503	2.9662	0.0085	0.1156	0.1529	-0.185	0.127	-0.1319	-0.6014	-0.0661	-0.1568	0.1886	-0.0125	0.0904	0.0276	0.0663	0.1375	-1.1272	15.7446	20.9207
8	7.7633	-0.821	4.3907	8.6648	-2.1013	2.8803	-1.0533	0.9665	-0.0794	0.5242	1.7283	0.9912	-0.6196	-0.2966	-0.0358	0.7681	-0.1555	0.0765	0.3862	0.1715	0.3811	-5.7773	24.4661	5.1199
9	0.4409	0.1577	0.1535	1.0987	-0.2026	2.1776	0.2208	0.434	0.242	-0.3424	0.083	-0.1827	-0.6451	-0.0798	0.029	0.1904	0.0275	0.1242	0.0075	0.1355	0.1256	-0.6907	13.1855	14.3806
10	1.2472	-0.2985	-0.5101	2.2024	-1.1691	2.1888	-0.012	-0.0217	0.2584	0.2704	-0.0258	-0.2178	-0.3306	0.1191	0.0326	0.1052	-0.023	0.0184	0.0318	0.0108	0.1054	-1.7798	14.0866	38.2065
11	1.1311	0.7978	-0.6216	3.3138	-4.4202	6.3577	0.3316	-0.1863	-0.1002	0.5464	0.2117	-0.3459	-1.0405	0.619	-0.3776	0.576	-0.0867	-0.1705	0.3289	0.09	0.4981	9.1349	14.4095	49.1083
12	1.325	-0.4543	0.1871	2.5154	-0.0315	1.3676	-0.0455	-0.0923	0.2538	0.3552	0.0996	-0.1067	-0.249	-0.0345	-0.0542	0.1054	-0.0053	0.0137	0.031	-0.0244	0.0796	-4.8973	11.3893	43.6825
13	1.6953	-0.7165	-1.7277	1.4479	1.3055	2.2162	0.2669	0.6962	-0.1361	-0.0259	-0.5489	0.4227	0.045	-0.8251	0.2946	0.0211	0.0344	-0.0806	0.4309	-0.0735	0.1379	-24.0221	-8.9738	14.3129
14	6.8524	-2.9265	4.1337	6.0444	-5.5835	5.7082	0.2865	0.6815	0.5938	-0.5853	-1.34	-0.056	0.7873	-0.3854	0.862	0.3311	-0.1207	-0.0516	1.0152	-0.3687	0.2668	-23.2234	-21.3487	-0.0051
15	1.1317	0.5663	-1.3016	1.2327	1.0222	2.0648	0.1453	0.5638	-0.0329	-0.2171	-0.1199	0.1653	-0.0051	-0.6437	0.0064	0.062	0.0311	-0.0694	0.3638	-0.0012	0.1044	-16.7711	-10.1432	10.0345
16	1.5291	-0.387	2.4582	2.6485	1.3632	5.703	0.1695	0.9961	0.032	-0.3507	-0.802	1.0452	-0.3709	-2.0126	0.3491	0.1709	0.1913	-0.2106	1.2134	-0.1775	0.4179	-31.7737	-5.8813	5.059
17	0.3731	0.6021	-0.1743	3.9073	-0.6577	4.3374	0.0991	0.1689	-0.0605	0.1307	-0.0742	0.7785	-0.137	-0.5647	-0.0178	-0.0007	0.004	0.0081	0.2707	-0.0316	0.2009	-29.3543	-4.7431	29.8346
18	4.7328	3.8176	2.3229	6.3599	-1.2288	4.0684	-0.0482	-1.2389	1.6934	-3.2568	2.1622	-0.1985	-0.7178	0.085	-1.8254	0.9924	-0.6066	0.2564	1.12	-0.2447	0.9656	-39.0583	2.8063	41.1717
19	1.1056	0.363	-0.0651	1.8606	0.0906	1.5543	0.1632	0.0756	0.1559	0.0516	-0.1709	0.4923	-0.0163	-0.4997	0.0017	0.0083	-0.0088	0.0388	0.2095	-0.0246	0.1752	-29.3728	-3.3553	36.3148

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESI 2:43)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESI 44:64)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESI 65:136)
4	X-RAY DIFFRACTION	4	(CHAIN B AND RESI 2:51)
5	X-RAY DIFFRACTION	5	(CHAIN B AND RESI 52:60)
6	X-RAY DIFFRACTION	6	(CHAIN B AND RESI 61:136)
7	X-RAY DIFFRACTION	7	(CHAIN C AND RESI 2:51)
8	X-RAY DIFFRACTION	8	(CHAIN C AND RESI 52:64)
9	X-RAY DIFFRACTION	9	(CHAIN C AND RESI 65:136)
10	X-RAY DIFFRACTION	10	(CHAIN D AND RESI 2:52)
11	X-RAY DIFFRACTION	11	(CHAIN D AND RESI 53:68)
12	X-RAY DIFFRACTION	12	(CHAIN D AND RESI 69:136)
13	X-RAY DIFFRACTION	13	(CHAIN E AND RESI 2:51)
14	X-RAY DIFFRACTION	14	(CHAIN E AND RESI 52:64)
15	X-RAY DIFFRACTION	15	(CHAIN E AND RESI 65:122)
16	X-RAY DIFFRACTION	16	(CHAIN E AND RESI 123:136)
17	X-RAY DIFFRACTION	17	(CHAIN F AND RESI 2:51)
18	X-RAY DIFFRACTION	18	(CHAIN F AND RESI 52:62)
19	X-RAY DIFFRACTION	19	(CHAIN F AND RESI 63:136)

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