PDB-5vir: Crystal structure of probable nicotinate-nucleotide adenylyltrans...

ID or keywords:

Entry

Database: PDB / ID: 5vir

Title

Crystal structure of probable nicotinate-nucleotide adenylyltransferase from Mycobacterium abscessus in complex with NADP and compound FOL0091

Components

Probable nicotinate-nucleotide adenylyltransferase

Keywords

TRANSFERASE / SSGCID /

nicotinate-nucleotide adenylyltransferase /

Mycobacterium avium /

Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

nicotinate-nucleotide adenylyltransferase /

nicotinate-nucleotide adenylyltransferase activity / NAD biosynthetic process /

Biological species

Mycobacterium abscessus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal structure of probable nicotinate-nucleotide adenylyltransferase from Mycobacterium abcesus in complex with NADP and compound FOL0091
Authors: Abendroth, J. / Davies, D.R. / Korotkov, K.V. / Lorimer, D.D. / Edwards, T.E.

History

Deposition	Apr 17, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 26, 2017	Provider: repository / Type: Initial release
Revision 1.1	May 31, 2017	Group: Refinement description
Revision 1.2	Oct 4, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5vir.cif.gz	173.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5vir.ent.gz	135.1 KB	Display	PDB format
PDBx/mmJSON format	5vir.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/vi/5vir ftp://data.pdbj.org/pub/pdb/validation_reports/vi/5vir	HTTPS FTP

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Related structure data

Related structure data	4ymiS S: Starting model for refinement
Similar structure data	5fuc-2 3sea-3 3v03-2 4cih-d 533 5vae-1 4db3-2 4f5s-1 1ufr-d 5xn7-2 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
Other databases	TargetTrack: MyabA.00448.a

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Probable nicotinate-nucleotide adenylyltransferase

B: Probable nicotinate-nucleotide adenylyltransferase

hetero molecules

52.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Probable nicotinate-nucleotide adenylyltransferase

B: Probable nicotinate-nucleotide adenylyltransferase

hetero molecules

A: Probable nicotinate-nucleotide adenylyltransferase

B: Probable nicotinate-nucleotide adenylyltransferase

hetero molecules

defined by author&software
Evidence: gel filtration
106 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	63.380, 116.110, 55.520
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	Probable nicotinate-nucleotide adenylyltransferase / Deamido-NAD(+) diphosphorylase / Deamido-NAD(+) pyrophosphorylase / Nicotinate mononucleotide ...Deamido-NAD(+) diphosphorylase / Deamido-NAD(+) pyrophosphorylase / Nicotinate mononucleotide adenylyltransferase / NaMN adenylyltransferase Mass: 25501.695 Da / Num. of mol.: 2 / Fragment: MyavA.00448.a.A1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium abscessus (bacteria) Strain: ATCC 19977 / DSM 44196 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543 Gene: nadD, MAB_1621 / Plasmid: MyavA.00448.a.A1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: B1MMZ4, nicotinate-nucleotide adenylyltransferase
#2: Chemical	ChemComp-9CG / 1H,3H-naphtho[1,8-cd]pyran-1-one Mass: 184.191 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₂H₈O₂
#3: Chemical	ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₂₈N₇O₁₇P₃
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 285 / 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: 2.01 Å³/Da / Density % sol: 38.7 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.43 Details: MCSG F9 optimization screen D3: 50mM BisTris/HCl pH 6.43, 22.7% pentaerythriol ethoxylate 15/4, 50mM Ammonium sulfate, MyabA.00445.a.A1.PS00938 at 20mg/ml: soaked for 3 days in 2.5ul 50mM ...Details: MCSG F9 optimization screen D3: 50mM BisTris/HCl pH 6.43, 22.7% pentaerythriol ethoxylate 15/4, 50mM Ammonium sulfate, MyabA.00445.a.A1.PS00938 at 20mg/ml: soaked for 3 days in 2.5ul 50mM BisTris/HCl pH 6.43, 30% pentaerythriol ethoxylate 15/4, 50mM Ammonium sulfate saturated with FOL 0091 from 2.5ul evaporated 50mM methanol stock: cryo: direct: tray 287611 D3: puck OBR5-2.

Crystal

Density Matthews: 2.01 Å³/Da / Density % sol: 38.7 %

Crystal grow

Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.43
Details: MCSG F9 optimization screen D3: 50mM BisTris/HCl pH 6.43, 22.7% pentaerythriol ethoxylate 15/4, 50mM Ammonium sulfate, MyabA.00445.a.A1.PS00938 at 20mg/ml: soaked for 3 days in 2.5ul 50mM ...

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-G / Wavelength: 0.97856 Å

Detector

Type: RAYONIX MX-300 / Detector: CCD / Date: Mar 16, 2017

Radiation

Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97856 Å / Relative weight: 1

Reflection

Resolution: 1.7→42.81 Å / Num. obs: 45713 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 6.107 % / B_iso Wilson estimate: 19.96 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.058 / R_rim(I) all: 0.063 / Χ²: 1.011 / Net I/σ(I): 17.72

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.7-1.74	6.119	0.543	3.12	3358	0.911	0.593	99.9
1.74-1.79	6.131	0.421	3.9	3267	0.944	0.46	99.9
1.79-1.84	6.155	0.336	4.95	3164	0.963	0.367	99.9
1.84-1.9	6.143	0.269	6.16	3063	0.976	0.293	99.9
1.9-1.96	6.157	0.208	7.91	2999	0.984	0.227	99.7
1.96-2.03	6.153	0.164	9.73	2880	0.99	0.179	99.8
2.03-2.11	6.148	0.141	11.6	2815	0.992	0.153	99.7
2.11-2.19	6.152	0.104	14.8	2657	0.995	0.114	99.4
2.19-2.29	6.134	0.087	17.12	2580	0.996	0.095	99.7
2.29-2.4	6.138	0.079	18.72	2503	0.997	0.086	99.8
2.4-2.53	6.121	0.068	21.28	2355	0.997	0.075	99.7
2.53-2.69	6.174	0.061	24.17	2220	0.998	0.066	99.5
2.69-2.87	6.158	0.053	27.84	2116	0.998	0.058	99.2
2.87-3.1	6.107	0.047	31.95	1954	0.998	0.051	99.5
3.1-3.4	6.122	0.041	35.15	1818	0.998	0.045	99.2
3.4-3.8	6.059	0.035	39.22	1662	0.999	0.038	99.6
3.8-4.39	6.035	0.033	42.67	1465	0.999	0.036	99.5
4.39-5.38	5.889	0.032	43.25	1276	0.999	0.035	99.5
5.38-7.6	5.754	0.033	41.86	998	0.999	0.036	99.3
7.6-50	5.13	0.032	42.3	563	0.998	0.035	93.8

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Processing

Software

Name	Version	Classification
XDS		data reduction
PHENIX		refinement
PDB_EXTRACT	3.22	data extraction
Coot		model building
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4YMI

4ymi

Resolution: 1.7→42.81 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.45

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1993	2027	4.44 %	RANDOM, 0
R_work	0.1676	-	-	-
obs	0.169	45697	99.58 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 93.8 Å² / B_iso mean: 32.1965 Å² / B_iso min: 7.8 Å²

Refinement step

Cycle: final / Resolution: 1.7→42.81 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2873	0	124	286	3283
B_iso mean	-	-	26.84	39.25	-
Num. residues	-	-	-	-	377

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	3127
X-RAY DIFFRACTION	f_angle_d	0.81	4309
X-RAY DIFFRACTION	f_chiral_restr	0.053	488
X-RAY DIFFRACTION	f_plane_restr	0.006	587
X-RAY DIFFRACTION	f_dihedral_angle_d	12.7	1859

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.7-1.7425	0.2937	123	0.2526	3107	3230	100
1.7425-1.7896	0.2568	129	0.2259	3107	3236	100
1.7896-1.8423	0.2351	163	0.2096	3051	3214	100
1.8423-1.9018	0.1959	157	0.1966	3067	3224	100
1.9018-1.9697	0.2285	143	0.1857	3081	3224	100
1.9697-2.0486	0.2157	150	0.1819	3107	3257	100
2.0486-2.1418	0.2272	142	0.1755	3072	3214	100
2.1418-2.2547	0.1803	141	0.1623	3096	3237	100
2.2547-2.396	0.1837	146	0.161	3110	3256	100
2.396-2.581	0.2233	148	0.1662	3107	3255	100
2.581-2.8407	0.2066	142	0.1718	3131	3273	99
2.8407-3.2516	0.186	148	0.1638	3150	3298	99
3.2516-4.0961	0.1785	144	0.15	3180	3324	100
4.0961-42.8236	0.1878	151	0.1531	3304	3455	98

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	3.9637	-0.5268	0.3563	2.6107	-0.8157	3.8363	-0.0348	0.0206	0.321	-0.0532	-0.0434	-0.2174	-0.2481	0.2543	0.0541	0.1536	-0.0293	0.0137	0.131	0.0196	0.2089	12.1044	15.1532	9.9947
2	7.8294	5.0944	0.8799	7.4268	1.1631	1.4336	-0.1416	0.0087	0.0328	-0.106	0.0068	-0.5686	-0.1683	0.3395	0.0917	0.1635	-0.011	0.0132	0.2232	0.0631	0.2105	18.1837	12.4912	7.8563
3	3.8651	-0.3692	-0.585	3.9377	-0.3959	2.214	0.0923	0.2335	0.3708	-0.2251	-0.1154	-0.6712	-0.249	0.3716	-0.0007	0.28	-0.0228	0.0326	0.3344	0.1227	0.3669	19.0751	24.2996	1.1423
4	3.9252	-1.5705	-2.1228	3.902	0.268	4.9851	0.2133	0.4903	1.0859	-0.0801	-0.0612	0.4484	-0.5763	-0.1319	-0.3236	0.3395	-0.0199	-0.0627	0.2143	0.0728	0.4894	5.4892	26.8487	3.4891
5	5.6288	1.2611	2.2443	4.6056	-1.8386	4.2959	0.106	-0.5632	0.1809	0.4323	-0.1439	-0.0729	-0.2671	-0.2653	0.0295	0.1375	-0.0019	0.0129	0.1693	-0.0354	0.1619	1.8358	15.6545	21.8973
6	1.9531	0.5252	1.3961	8.4022	-1.6932	7.153	-0.0432	-0.4309	0.0604	0.898	0.0252	-0.2406	-0.2484	-0.0299	0.0695	0.2242	0.0158	-0.0361	0.1987	-0.0013	0.1565	10.0488	7.7005	25.9373
7	3.8555	0.0723	-0.9274	2.7342	0.2883	2.1076	0.0303	-0.3471	0.0931	0.2981	-0.0202	0.1685	-0.116	0.1417	0.0089	0.1771	0.0002	0.018	0.1668	-0.0295	0.2273	-13.1021	11.7052	23.9087
8	3.5876	0.0025	0.0437	2.6794	0.8908	3.4547	0.0149	0.137	0.1395	-0.1018	-0.0179	0.3182	-0.113	-0.2513	-0.0234	0.1136	0.0091	0.0151	0.1279	0.0027	0.2002	-19.9114	7.7693	16.1512
9	8.2836	-3.8082	1.5895	4.4888	-0.8388	1.605	-0.0504	-0.3064	-0.6986	-0.0673	0.1472	0.7161	0.104	-0.4313	-0.0845	0.1767	-0.0248	0.0076	0.2236	0.0018	0.2709	-21.4311	4.514	21.2368
10	4.8035	-0.82	-0.1472	4.0206	0.1208	3.9408	0.1143	-0.4682	0.1601	0.2043	-0.0121	0.5567	-0.0875	-0.4422	-0.1132	0.1895	0.0081	0.0661	0.2708	-0.0622	0.3421	-25.8361	15.1646	28.1524
11	4.451	-4.4256	-3.1061	6.0042	2.9542	3.2941	0.3231	0.0955	0.3785	0.3965	-0.4666	-0.2778	-0.0852	-0.2118	0.0924	0.5207	-0.0869	0.0784	0.3561	-0.1109	0.6668	-20.5161	28.7952	26.797
12	2.7369	-0.1054	-1.3787	1.8753	0.435	3.8815	0.0814	0.1552	0.216	-0.1617	-0.0442	0.1471	-0.2625	-0.0094	-0.0331	0.1336	0.0038	-0.0325	0.1227	0.0241	0.2287	-8.8664	15.5569	9.9697
13	4.613	-2.0158	-2.3527	7.6376	-0.1069	6.0657	-0.0173	0.0444	-0.0397	-0.6778	-0.0571	-0.0068	-0.0179	-0.2051	0.0811	0.2069	-0.0008	-0.0491	0.1736	-0.0007	0.1431	-12.1886	3.2912	3.5052

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 6 through 69 )	A	6 - 69
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 70 through 89 )	A	70 - 89
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 90 through 130 )	A	90 - 130
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 131 through 162 )	A	131 - 162
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 163 through 190 )	A	163 - 190
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 191 through 202 )	A	191 - 202
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 6 through 33 )	B	6 - 33
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 34 through 69 )	B	34 - 69
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 70 through 89 )	B	70 - 89
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 90 through 137 )	B	90 - 137
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 138 through 157 )	B	138 - 157
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 158 through 190 )	B	158 - 190
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 191 through 202 )	B	191 - 202

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