PDB-4ymi: Crystal structure of probable nicotinate-nucleotide adenylyltrans...

ID or keywords:

Entry

Database: PDB / ID: 4ymi

Title

Crystal structure of probable nicotinate-nucleotide adenylyltransferase from Mycobacterium abcessus in complex with NADP

Components

Probable nicotinate-nucleotide adenylyltransferase

Keywords

TRANSFERASE / SSGCID / 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 / ATP binding
Similarity search - Function

Biological species

Mycobacterium abscessus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

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 abcessus in complex with NADP
Authors: Abendroth, J. / Dranow, D.M. / Korotkov, K.V. / Lorimer, D.D. / Edwards, T.E.

History

Deposition	Mar 6, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 9, 2016	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4ymi.cif.gz	174.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4ymi.ent.gz	136.4 KB	Display	PDB format
PDBx/mmJSON format	4ymi.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4ymi_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	4ymi_full_validation.pdf.gz	1.2 MB	Display
Data in XML	4ymi_validation.xml.gz	19.9 KB	Display
Data in CIF	4ymi_validation.cif.gz	28.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ym/4ymi ftp://data.pdbj.org/pub/pdb/validation_reports/ym/4ymi	HTTPS FTP

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Related structure data

Related structure data	3e27S S: Starting model for refinement
Similar structure data	5deo-1 1n4m-3 4s1o-5 3e27-1 2qyf-2 3brk-d 5das-2 2qsd-2 6d6z-d 5jmq-d 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: SSGCID-MyabA.00448.a

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#210 - Jun 2017 Adenine Riboswitch in Action similarity (1) #130 - Oct 2010 Riboswitches similarity (1) #156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (1)

Deposited unit

A: Probable nicotinate-nucleotide adenylyltransferase

B: Probable nicotinate-nucleotide adenylyltransferase

hetero molecules

52.8 kDa, 2 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)	63.290, 115.240, 56.760
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
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 Mass: 25501.695 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium abscessus (bacteria) / Strain: ATCC 19977 / DSM 44196 / Gene: nadD, MAB_1621 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: B1MMZ4, nicotinate-nucleotide adenylyltransferase
#2: Chemical	ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₂₈N₇O₁₇P₃
#3: Chemical	ChemComp-ADE / ADENINE Mass: 135.127 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₅H₅N₅
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 305 / 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: 2.03 Å³/Da / Density % sol: 39.5 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: MCSG1 screen, h1: 200mM Ammonium fluoride, 20% PEG 3350; MyavA.00448.a.A1.PS00938 at 20mg/ml with 3mM NAAP; cryo: 20% EG in 2 steps; tray 261031h1, puck nip6-3, degraded NAAP modeled as ADE

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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: Feb 25, 2015

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→50 Å / Num. all: 46345 / Num. obs: 46195 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4 % / B_iso Wilson estimate: 17.93 Å² / R_merge F obs: 0.999 / R_merge(I) obs: 0.051 / R_rim(I) all: 0.058 / Χ²: 0.992 / Net I/σ(I): 18.66 / Num. measured all: 185695

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Highest resolution (Å)	Redundancy (%)	R_merge F obs	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	R_rim(I) all	% possible all
1.7-1.74		3.6	0.868	0.539	2.63	12045	3354	3350	0.631	99.9
1.74-1.79			0.914	0.434	3.49	13253	3300	3292	0.499	99.8
1.79-1.84			0.946	0.347	4.36	13164	3219	3214	0.398	99.8
1.84-1.9			0.963	0.264	5.66	12592	3091	3084	0.303	99.8
1.9-1.96			0.975	0.209	7.39	12405	3038	3035	0.239	99.9
1.96-2.03			0.984	0.166	9.05	11984	2928	2926	0.19	99.9
2.03-2.11			0.989	0.138	10.84	11642	2844	2842	0.158	99.9
2.11-2.19			0.992	0.104	13.89	11063	2703	2695	0.119	99.7
2.19-2.29			0.995	0.086	16.13	10729	2625	2617	0.098	99.7
2.29-2.4			0.996	0.075	18.05	10311	2520	2517	0.086	99.9
2.4-2.53			0.997	0.063	20.77	9729	2383	2374	0.073	99.6
2.53-2.69			0.997	0.053	24.12	9277	2282	2276	0.061	99.7
2.69-2.87			0.998	0.043	28.38	8667	2131	2127	0.05	99.8
2.87-3.1			0.999	0.036	33.6	8095	1996	1992	0.041	99.8
3.1-3.4			0.999	0.031	38.99	7411	1851	1839	0.036	99.4
3.4-3.8			0.999	0.025	45.39	6578	1669	1664	0.029	99.7
3.8-4.39			0.999	0.022	51.61	5935	1500	1498	0.025	99.9
4.39-5.38			0.999	0.018	53.08	4987	1288	1283	0.021	99.6
5.38-7.6			0.999	0.02	50.36	3877	1014	1007	0.023	99.3
	7.6		0.999	0.017	54.3	1951	609	563	0.02	92.4

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

R rigid body: 0.6

	Highest resolution	Lowest resolution
Rotation	42.61 Å	2.48 Å

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: dev_1977)	refinement
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing
ARP		model building
Coot		model building
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: pdb entry 3e27 chain B

3e27

Resolution: 1.7→28.81 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.46 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1945	4846	10.53 %	Random selection
R_work	0.1658	-	-	-
obs	0.1689	46021	99.06 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.7→28.81 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2872	0	116	305	3293

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	3113
X-RAY DIFFRACTION	f_angle_d	1.04	4282
X-RAY DIFFRACTION	f_dihedral_angle_d	11.991	1068
X-RAY DIFFRACTION	f_chiral_restr	0.052	486
X-RAY DIFFRACTION	f_plane_restr	0.005	538

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 (%)
1.7-1.7193	0.2833	130	0.2311	1112	X-RAY DIFFRACTION	81
1.7193-1.7395	0.2658	158	0.2383	1335	X-RAY DIFFRACTION	100
1.7395-1.7608	0.2801	162	0.2267	1375	X-RAY DIFFRACTION	100
1.7608-1.783	0.2374	160	0.2118	1363	X-RAY DIFFRACTION	100
1.783-1.8065	0.2221	163	0.1987	1380	X-RAY DIFFRACTION	100
1.8065-1.8312	0.2445	160	0.2044	1360	X-RAY DIFFRACTION	100
1.8312-1.8574	0.2129	160	0.1898	1353	X-RAY DIFFRACTION	100
1.8574-1.8851	0.2315	161	0.1816	1371	X-RAY DIFFRACTION	100
1.8851-1.9146	0.2168	159	0.1854	1353	X-RAY DIFFRACTION	100
1.9146-1.946	0.2359	161	0.1849	1360	X-RAY DIFFRACTION	100
1.946-1.9795	0.2461	163	0.1751	1389	X-RAY DIFFRACTION	100
1.9795-2.0155	0.2041	159	0.1751	1352	X-RAY DIFFRACTION	100
2.0155-2.0542	0.2218	160	0.1758	1358	X-RAY DIFFRACTION	100
2.0542-2.0962	0.2215	164	0.1699	1391	X-RAY DIFFRACTION	100
2.0962-2.1417	0.2077	161	0.1585	1362	X-RAY DIFFRACTION	100
2.1417-2.1915	0.1983	162	0.1598	1384	X-RAY DIFFRACTION	100
2.1915-2.2463	0.1844	160	0.1619	1360	X-RAY DIFFRACTION	100
2.2463-2.307	0.1931	168	0.1518	1374	X-RAY DIFFRACTION	100
2.307-2.3749	0.187	164	0.1561	1372	X-RAY DIFFRACTION	100
2.3749-2.4515	0.1988	157	0.161	1385	X-RAY DIFFRACTION	100
2.4515-2.5391	0.2025	169	0.1673	1366	X-RAY DIFFRACTION	100
2.5391-2.6407	0.2046	161	0.1614	1389	X-RAY DIFFRACTION	100
2.6407-2.7608	0.2092	146	0.163	1412	X-RAY DIFFRACTION	100
2.7608-2.9062	0.1836	160	0.1655	1392	X-RAY DIFFRACTION	100
2.9062-3.0881	0.1819	172	0.1629	1373	X-RAY DIFFRACTION	100
3.0881-3.3262	0.2069	178	0.1633	1401	X-RAY DIFFRACTION	99
3.3262-3.6603	0.1708	156	0.1562	1408	X-RAY DIFFRACTION	100
3.6603-4.1886	0.1688	172	0.142	1421	X-RAY DIFFRACTION	100
4.1886-5.2719	0.1504	163	0.1403	1452	X-RAY DIFFRACTION	100
5.2719-28.8141	0.1809	177	0.1838	1472	X-RAY DIFFRACTION	97

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	2.9901	-0.1312	-0.0452	2.3548	-0.3759	3.136	0.0045	0.0847	0.1611	-0.1411	-0.0417	-0.1679	-0.1143	0.168	-0.0006	0.1081	-0.0116	0.0171	0.0847	0.0197	0.1314	11.477	14.4033	9.167
2	3.7922	0.954	-0.668	2.3801	-1.2739	1.5256	-0.0428	0.1862	0.0385	-0.1985	-0.1588	-0.5849	-0.0272	0.2974	0.1292	0.1567	0.0203	0.0374	0.1869	0.0559	0.2329	20.1197	14.2733	4.5298
3	3.3507	0.5129	-1.3157	1.9519	-0.4134	1.5965	0.1889	0.057	0.4431	-0.1265	-0.0677	-0.338	-0.2052	0.1374	-0.125	0.262	-0.0087	0.0414	0.2371	0.0921	0.2879	17.1085	27.5962	2.1059
4	3.0122	0.2454	-0.7215	2.1378	-0.0316	2.8571	0.0708	0.101	0.4494	-0.0202	0.0283	0.0945	-0.366	-0.1087	-0.1427	0.1573	-0.0116	-0.0049	0.0612	0.0106	0.2126	4.1825	23.3478	12.9515
5	5.1783	0.8464	1.5428	2.0472	-1.1752	3.2827	0.0548	-0.5005	-0.0969	0.3846	-0.1086	-0.0031	-0.0849	-0.1064	-0.0542	0.1441	-0.0212	-0.01	0.1602	0.0198	0.1349	0.4655	10.298	23.3709
6	1.8001	-1.1573	1.9438	1.8282	-2.7327	5.029	-0.1233	-0.2897	0.2362	0.4213	-0.0875	-0.0257	-0.3828	-0.0193	0.1967	0.2313	0.0082	-0.0389	0.191	-0.0074	0.1264	10.6565	8.2793	27.2802
7	0.0013	-0.0013	0.0044	0.0033	-0.0001	0.0035	-0.0097	-0.0341	0.1088	0.0306	-0.0489	-0.0865	-0.0119	0.0829	0.0001	0.2181	-0.0271	0.016	0.1488	0.0184	0.3101	12.793	23.7811	12.754
8	2.328	-0.2296	-0.1925	1.9683	0.5108	2.1057	0.0366	-0.2451	0.1262	0.1631	-0.0348	0.4109	-0.1	-0.2782	-0.0232	0.1352	0.0015	0.0333	0.1584	-0.0206	0.2052	-20.8072	10.6228	23.5938
9	1.2516	-1.7395	-0.0515	3.8916	0.7621	0.4856	-0.1567	0.0623	0.135	0.6342	-0.1864	-0.1172	0.5301	-0.2334	0.3113	0.6205	-0.0657	0.1291	0.3037	-0.0997	0.5442	-20.0479	28.7066	26.5913
10	2.3119	-0.1105	-0.906	1.6779	-0.3633	2.8814	0.0661	0.1311	0.1393	-0.1086	-0.0235	0.1805	-0.1343	-0.0019	-0.0194	0.1256	-0.0008	-0.0248	0.0997	0.0097	0.1701	-8.8215	15.3385	10.3337
11	5.9926	0.4034	-1.1361	4.2993	1.3981	3.3414	-0.0678	0.4008	0.1026	-0.7455	-0.0816	0.2395	-0.1073	-0.1795	0.1144	0.2521	0.01	-0.0542	0.1745	-0.0091	0.1114	-13.0541	3.5416	2.8765
12	0.0007	0.0003	0.0006	0.0012	-0.0035	0.004	0.0377	-0.0038	0.0125	-0.0375	0.0345	0.0023	0.0182	-0.0607	0.0001	0.1827	0.0194	-0.0025	0.1935	-0.0186	0.267	-20.7092	16.9463	16.6184

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 6 through 69 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 70 through 103 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 104 through 130 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 131 through 179 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 180 through 190 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 191 through 203 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 301 through 301 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 5 through 137 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 138 through 157 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 158 through 190 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 191 through 203 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 300 through 300 )

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