PDB-5hup: Crystal Structure of NadC from Streptococcus pyogenes

ID or keywords:

Entry

Database: PDB / ID: 5hup

Title

Crystal Structure of NadC from Streptococcus pyogenes

Components

Nicotinate-nucleotide pyrophosphorylase (Carboxylating)

Keywords

TRANSFERASE / Quinolinate phosphoribosyltransferase

Function / homology

Function and homology information

nicotinate-nucleotide diphosphorylase (carboxylating) / nicotinate-nucleotide diphosphorylase (carboxylating) activity / NAD+ biosynthetic process
Similarity search - Function

Biological species

Streptococcus pyogenes serotype M4 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 3.42 Å

Authors

Booth, W.T. / Chruszcz, M.

Citation

Journal: FEBS J. / Year: 2017
Title: Streptococcus pyogenes quinolinate-salvage pathway-structural and functional studies of quinolinate phosphoribosyl transferase and NH3 -dependent NAD(+) synthetase.
Authors: Booth, W.T. / Morris, T.L. / Mysona, D.P. / Shah, M.J. / Taylor, L.K. / Karlin, T.W. / Clary, K. / Majorek, K.A. / Offermann, L.R. / Chruszcz, M.

History

Deposition	Jan 27, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 25, 2017	Provider: repository / Type: Initial release
Revision 1.1	Jul 12, 2017	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Aug 23, 2017	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3	Sep 27, 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 / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5hup.cif.gz	643.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5hup.ent.gz	535.7 KB	Display	PDB format
PDBx/mmJSON format	5hup.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5hup_validation.pdf.gz	493.1 KB	Display	wwPDB validaton report
Full document	5hup_full_validation.pdf.gz	505.2 KB	Display
Data in XML	5hup_validation.xml.gz	57 KB	Display
Data in CIF	5hup_validation.cif.gz	77.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hu/5hup ftp://data.pdbj.org/pub/pdb/validation_reports/hu/5hup	HTTPS FTP

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Related structure data

Related structure data	5huhC 5hujC 5hulC 5huoSC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5huo-1 5hul-2 5huo-2 4kwv-d 5hul-1 5ayz-1 5ayz-2 5ayx-d 4i9a-1 4kww-d 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: Nicotinate-nucleotide pyrophosphorylase (Carboxylating)

B: Nicotinate-nucleotide pyrophosphorylase (Carboxylating)

C: Nicotinate-nucleotide pyrophosphorylase (Carboxylating)

E: Nicotinate-nucleotide pyrophosphorylase (Carboxylating)

F: Nicotinate-nucleotide pyrophosphorylase (Carboxylating)

H: Nicotinate-nucleotide pyrophosphorylase (Carboxylating)

hetero molecules

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

1

A: Nicotinate-nucleotide pyrophosphorylase (Carboxylating)

C: Nicotinate-nucleotide pyrophosphorylase (Carboxylating)

E: Nicotinate-nucleotide pyrophosphorylase (Carboxylating)

hetero molecules

A: Nicotinate-nucleotide pyrophosphorylase (Carboxylating)

C: Nicotinate-nucleotide pyrophosphorylase (Carboxylating)

E: Nicotinate-nucleotide pyrophosphorylase (Carboxylating)

hetero molecules

defined by author&software
209 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Nicotinate-nucleotide pyrophosphorylase (Carboxylating)

F: Nicotinate-nucleotide pyrophosphorylase (Carboxylating)

H: Nicotinate-nucleotide pyrophosphorylase (Carboxylating)

hetero molecules

B: Nicotinate-nucleotide pyrophosphorylase (Carboxylating)

F: Nicotinate-nucleotide pyrophosphorylase (Carboxylating)

H: Nicotinate-nucleotide pyrophosphorylase (Carboxylating)

hetero molecules

defined by author&software
209 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	108.149, 188.816, 222.181
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	SER	SER	ASP	ASP	A	A	5 - 289	30 - 314
2	1	SER	SER	ASP	ASP	B	B	5 - 289	30 - 314
1	2	LEU	LEU	LEU	LEU	A	A	8 - 288	33 - 313
2	2	LEU	LEU	LEU	LEU	C	C	8 - 288	33 - 313
1	3	SER	SER	TYR	TYR	A	A	5 - 287	30 - 312
2	3	SER	SER	TYR	TYR	E	D	5 - 287	30 - 312
1	4	THR	THR	LEU	LEU	A	A	6 - 288	31 - 313
2	4	THR	THR	LEU	LEU	F	E	6 - 288	31 - 313
1	5	SER	SER	ASP	ASP	A	A	5 - 289	30 - 314
2	5	SER	SER	ASP	ASP	H	F	5 - 289	30 - 314
1	6	LEU	LEU	LEU	LEU	B	B	8 - 288	33 - 313
2	6	LEU	LEU	LEU	LEU	C	C	8 - 288	33 - 313
1	7	SER	SER	TYR	TYR	B	B	5 - 287	30 - 312
2	7	SER	SER	TYR	TYR	E	D	5 - 287	30 - 312
1	8	THR	THR	LEU	LEU	B	B	6 - 288	31 - 313
2	8	THR	THR	LEU	LEU	F	E	6 - 288	31 - 313
1	9	SER	SER	ASP	ASP	B	B	5 - 289	30 - 314
2	9	SER	SER	ASP	ASP	H	F	5 - 289	30 - 314
1	10	LEU	LEU	TYR	TYR	C	C	8 - 287	33 - 312
2	10	LEU	LEU	TYR	TYR	E	D	8 - 287	33 - 312
1	11	LEU	LEU	ASP	ASP	C	C	8 - 289	33 - 314
2	11	LEU	LEU	ASP	ASP	F	E	8 - 289	33 - 314
1	12	LEU	LEU	LEU	LEU	C	C	8 - 288	33 - 313
2	12	LEU	LEU	LEU	LEU	H	F	8 - 288	33 - 313
1	13	THR	THR	TYR	TYR	E	D	6 - 287	31 - 312
2	13	THR	THR	TYR	TYR	F	E	6 - 287	31 - 312
1	14	SER	SER	TYR	TYR	E	D	5 - 287	30 - 312
2	14	SER	SER	TYR	TYR	H	F	5 - 287	30 - 312
1	15	THR	THR	LEU	LEU	F	E	6 - 288	31 - 313
2	15	THR	THR	LEU	LEU	H	F	6 - 288	31 - 313

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

#1: Protein	Nicotinate-nucleotide pyrophosphorylase (Carboxylating) Mass: 34496.980 Da / Num. of mol.: 6 / Fragment: UNP residues 10-299 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes serotype M4 (strain MGAS10750) (bacteria) Strain: MGAS10750 / Gene: nadC, MGAS10750_Spy1186 / Plasmid: pjExpress411 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q1J647, nicotinate-nucleotide diphosphorylase (carboxylating)
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: SO₄

#1: Protein

Nicotinate-nucleotide pyrophosphorylase (Carboxylating)

Mass: 34496.980 Da / Num. of mol.: 6 / Fragment: UNP residues 10-299
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Streptococcus pyogenes serotype M4 (strain MGAS10750) (bacteria)
Strain: MGAS10750 / Gene: nadC, MGAS10750_Spy1186 / Plasmid: pjExpress411 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q1J647, nicotinate-nucleotide diphosphorylase (carboxylating)

#2: Chemical

ChemComp-SO4 / SULFATE ION

Mass: 96.063 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: SO₄

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.74 Å³/Da / Density % sol: 55.11 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / pH: 6.5 Details: 0.48 M Ammonium Sulfate, 25% PEG 6000, 0.1 M BIS-TRIS

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97919 Å
Detector	Type: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 25, 2015
Radiation	Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97919 Å / Relative weight: 1
Reflection	Resolution: 3.4→20 Å / Num. obs: 25907 / % possible obs: 81.6 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / R_merge(I) obs: 0.107 / R_sym value: 0.107 / Net I/σ(I): 15.4
Reflection shell	Resolution: 3.4→3.46 Å / Redundancy: 3.6 % / R_merge(I) obs: 0.606 / Mean I/σ(I) obs: 3.3 / % possible all: 95.2

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0135	refinement
HKL-2000		data scaling
HKL-2000		data reduction
REFMAC	5.8.0135	phasing

Refinement

Method to determine structure:

FOURIER SYNTHESIS
Starting model: 5HUO

5huo

Resolution: 3.42→20 Å / Cor.coef. F_o:F_c: 0.884 / Cor.coef. F_o:F_c free: 0.817 / SU B: 81.17 / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.817 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.29354	1221	5 %	RANDOM
R_work	0.23279	-	-	-
obs	0.23569	23334	78.86 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 86.544 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	5.39 Å²	0 Å²	0 Å²
2-	-	-1.95 Å²	0 Å²
3-	-	-	-3.43 Å²

Refinement step

Cycle: 1 / Resolution: 3.42→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12666	0	85	0	12751

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.019	12923
X-RAY DIFFRACTION	r_bond_other_d	0.01	0.02	12190
X-RAY DIFFRACTION	r_angle_refined_deg	1.558	1.958	17540
X-RAY DIFFRACTION	r_angle_other_deg	1.814	3	27787
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.978	5	1696
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.741	23.659	533
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.831	15	2042
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.953	15	83
X-RAY DIFFRACTION	r_chiral_restr	0.08	0.2	2116
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	14823
X-RAY DIFFRACTION	r_gen_planes_other	0.008	0.02	2976
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	2.844	5.452	6805
X-RAY DIFFRACTION	r_mcbond_other	2.844	5.452	6804
X-RAY DIFFRACTION	r_mcangle_it	4.796	8.178	8494
X-RAY DIFFRACTION	r_mcangle_other	4.796	8.178	8495
X-RAY DIFFRACTION	r_scbond_it	3.261	5.75	6118
X-RAY DIFFRACTION	r_scbond_other	3.201	5.668	6048
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	5.479	8.388	8944
X-RAY DIFFRACTION	r_long_range_B_refined	10.773	51.381	51284
X-RAY DIFFRACTION	r_long_range_B_other	10.773	51.381	51285
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	32078	0.08
1	2	B	32078	0.08
2	1	A	27306	0.1
2	2	C	27306	0.1
3	1	A	30860	0.09
3	2	E	30860	0.09
4	1	A	33036	0.06
4	2	F	33036	0.06
5	1	A	31812	0.09
5	2	H	31812	0.09
6	1	B	27212	0.1
6	2	C	27212	0.1
7	1	B	31092	0.09
7	2	E	31092	0.09
8	1	B	32498	0.07
8	2	F	32498	0.07
9	1	B	31862	0.09
9	2	H	31862	0.09
10	1	C	26060	0.12
10	2	E	26060	0.12
11	1	C	27442	0.1
11	2	F	27442	0.1
12	1	C	27518	0.09
12	2	H	27518	0.09
13	1	E	31140	0.09
13	2	F	31140	0.09
14	1	E	30376	0.11
14	2	H	30376	0.11
15	1	F	31918	0.08
15	2	H	31918	0.08

LS refinement shell

Resolution: 3.42→3.506 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.37	116	-
R_work	0.298	1767	-
obs	-	-	85.51 %

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	0.712	0.168	0.3492	4.3984	-0.5749	1.0984	-0.0483	0.0688	0.0044	-0.4275	0.1038	-0.4065	0.2632	0.2497	-0.0555	0.1272	0.0555	0.0259	0.3049	-0.0688	0.0762	-45.502	-8.646	-12.773
2	1.2036	0.8491	-0.1565	4.5482	1.4537	1.7648	0.0687	-0.1752	0.2919	0.1483	-0.0364	0.1236	-0.0528	-0.0263	-0.0323	0.0896	-0.0974	0.0251	0.2599	-0.0401	0.0814	-51.714	18.519	-6.753
3	2.9607	4.6453	-1.2481	9.2419	-3.9995	2.7017	-0.061	-0.0779	0.0132	-0.0841	-0.022	-0.0222	0.0328	0.0232	0.0829	0.1564	0.1126	0.1075	0.2783	0.0134	0.3149	-43.223	-42.697	-47.19
4	0.2432	0.4381	-0.4764	3.2517	-1.9432	3.0701	0.021	-0.1562	-0.0728	-0.0156	-0.106	-0.4673	0.1113	0.3911	0.085	0.013	-0.0071	-0.0118	0.2391	0.0228	0.2871	-27.232	-32.702	-64.085
5	4.5525	1.0611	0.513	1.0557	-0.1697	2.917	0.0808	-0.1917	-0.3516	-0.2528	-0.2562	-0.2889	0.148	0.5799	0.1754	0.1362	-0.0461	0.0804	0.5097	0.0354	0.4609	-14.812	9.022	-19.902
6	0.2382	0.2433	-0.4652	0.6185	-0.1596	1.2594	0.0986	-0.4524	-0.2946	-0.0361	-0.4483	-0.3766	-0.3681	1.0851	0.3497	0.1529	-0.3762	-0.0895	1.4865	0.3572	0.7698	7.564	13.602	-3.844
7	3.6423	-0.507	1.1131	1.8067	-1.0892	1.3985	0.178	-0.5305	-0.2039	0.4807	-0.3748	-0.4344	-0.5679	0.7478	0.1968	0.4135	-0.5426	-0.1716	1.0447	0.0702	0.4216	-12.204	22.293	5.599
8	2.4553	1.2036	1.984	0.9598	0.3259	4.1497	0.2738	-0.1174	-0.0197	0.1524	-0.0813	-0.2558	-0.2282	0.3144	-0.1925	0.1808	-0.205	0.1429	0.3561	-0.0747	0.4421	-28.333	27.387	-18.224
9	8.1779	-1.2052	-1.2101	0.6516	0.5335	2.9009	-0.057	0.1576	-0.5523	-0.2128	0.0106	0.2383	-0.0316	0.0016	0.0463	0.1426	-0.0049	-0.0188	0.0582	-0.0396	0.2824	-66.623	-18.431	-62.525
10	5.1752	-0.1376	0.4679	0.9111	-0.0224	0.3688	0.0509	0.1131	0.089	-0.0439	-0.0151	-0.1075	-0.2399	-0.0381	-0.0358	0.1976	-0.0075	0.05	0.2009	-0.0224	0.0447	-45.907	-3.625	-65.414
11	0.7888	-0.8919	-0.1163	3.3978	-0.8218	1.8007	0.0519	0.0632	0.0157	-0.3651	0.0227	0.0446	0.1052	0.1114	-0.0745	0.0548	0.0153	-0.0111	0.0887	0.0415	0.2092	-45.45	-36.964	-77.518
12	0.808	-0.2208	-0.2098	1.7007	-1.5177	2.3021	-0.0572	0.0014	-0.0173	-0.0169	0.0099	0.0836	0.1772	0.2942	0.0473	0.0831	0.0563	0.0252	0.1506	-0.0231	0.2335	-41.132	-60.626	-60.006

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	5 - 137
2	X-RAY DIFFRACTION	2	A	138 - 289
3	X-RAY DIFFRACTION	3	B	5 - 39
4	X-RAY DIFFRACTION	4	B	40 - 289
5	X-RAY DIFFRACTION	5	C	8 - 160
6	X-RAY DIFFRACTION	6	C	161 - 289
7	X-RAY DIFFRACTION	7	E	5 - 137
8	X-RAY DIFFRACTION	8	E	138 - 288
9	X-RAY DIFFRACTION	9	F	6 - 41
10	X-RAY DIFFRACTION	10	F	42 - 289
11	X-RAY DIFFRACTION	11	H	5 - 133
12	X-RAY DIFFRACTION	12	H	134 - 289

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-Structure viewers

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-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

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-Assembly

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-Experimental details

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-Data collection

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+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

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Movie

-
Structure viewers

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Viewer log

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This page

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This web site

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Options

+
Open data

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Basic information

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Structure visualization

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Downloads & links

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Download

-
Validation report

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Related structure data

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Links

-
Assembly

-
Components

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

+
About Yorodumi

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News

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

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Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

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Jul 12, 2017. Major update of PDB

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Yorodumi