PDB-5ey0: Crystal structure of CodY from Staphylococcus aureus with GTP and Ile

ID or keywords:

Entry

Database: PDB / ID: 5ey0

Title

Crystal structure of CodY from Staphylococcus aureus with GTP and Ile

Components

GTP-sensing transcriptional pleiotropic repressor CodY

Keywords

TRANSCRIPTION / GTP-sensing / pleiotropic transcription regulator

Function / homology

Function and homology information

DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / GTP binding / DNA binding / cytoplasm
Similarity search - Function

Biological species

Staphylococcus aureus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Han, A. / Hwang, K.Y.

Citation

Journal: Nucleic Acids Res. / Year: 2016
Title: The structure of the pleiotropic transcription regulator CodY provides insight into its GTP-sensing mechanism
Authors: Han, A.R. / Kang, H.R. / Son, J. / Kwon, D.H. / Kim, S. / Lee, W.C. / Song, H.K. / Song, M.J. / Hwang, K.Y.

History

Deposition	Nov 24, 2015	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Sep 14, 2016	Provider: repository / Type: Initial release
Revision 1.1	Sep 21, 2016	Group: Database references
Revision 1.2	Nov 16, 2016	Group: Database references
Revision 1.3	Nov 8, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5ey0.cif.gz	224.7 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	5ey0_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	5ey0_full_validation.pdf.gz	1.1 MB	Display
Data in XML	5ey0_validation.xml.gz	25.7 KB	Display
Data in CIF	5ey0_validation.cif.gz	37.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ey/5ey0 ftp://data.pdbj.org/pub/pdb/validation_reports/ey/5ey0	HTTPS FTP

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Related structure data

Related structure data	5ey1C 5ey2C 2b0lS 2b18S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4lwo-2 4zmx-d 7chk-d 2gki-d 7kfl-d 2q0o-d 4q6u-d 5tze-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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#183 - Mar 2015 Phototropin similarity (1) #152 - Aug 2012 cAMP-dependent Protein Kinase similarity (1)

Deposited unit

B: GTP-sensing transcriptional pleiotropic repressor CodY

A: GTP-sensing transcriptional pleiotropic repressor CodY

hetero molecules

62.8 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)	45.894, 76.028, 158.023
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	GTP-sensing transcriptional pleiotropic repressor CodY Mass: 30736.295 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (strain Mu3 / ATCC 700698) (bacteria) Strain: Mu3 / ATCC 700698 / Gene: codY, SAHV_1245 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: A7X1N2, UniProt: Q2FZ27*PLUS
#2: Chemical	ChemComp-ILE / ISOLEUCINE Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Formula: C₆H₁₃NO₂
#3: Chemical	ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE Mass: 523.180 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Formula: C₁₀H₁₆N₅O₁₄P₃ / Comment: GTP, energy-carrying molecule*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 446 / 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: 2.4 Å³/Da / Density % sol: 48.78 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.9 / Details: ammonium acetate, sodium citrate dehydrate, PEG400

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 23, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.6→30 Å / Num. obs: 69602 / % possible obs: 94.3 % / Redundancy: 3.9 % / R_merge(I) obs: 0.072 / Net I/σ(I): 23.72
Reflection shell	Resolution: 1.6→1.63 Å / Redundancy: 2.8 % / R_merge(I) obs: 0.313 / Mean I/σ(I) obs: 2.8 / % possible all: 92.8

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
PHENIX	1.9_1692	model building
HKL-2000		data processing
HKL-2000		data reduction
HKL-2000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2B0L and 2B18

2b0l

2b18

Resolution: 1.6→29.941 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.48 / Phase error: 19.6 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2091	3416	4.91 %
R_work	0.1777	-	-
obs	0.1793	69602	94.05 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.6→29.941 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4024	0	32	446	4502

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	4096
X-RAY DIFFRACTION	f_angle_d	1.076	5517
X-RAY DIFFRACTION	f_dihedral_angle_d	18.753	1581
X-RAY DIFFRACTION	f_chiral_restr	0.046	660
X-RAY DIFFRACTION	f_plane_restr	0.004	689

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 (%)
1.5996-1.6225	0.2764	109	0.2859	2515	X-RAY DIFFRACTION	86
1.6225-1.6467	0.2918	127	0.2636	2728	X-RAY DIFFRACTION	93
1.6467-1.6724	0.2519	135	0.2553	2698	X-RAY DIFFRACTION	94
1.6724-1.6998	0.2913	138	0.2534	2738	X-RAY DIFFRACTION	94
1.6998-1.7291	0.2608	139	0.2476	2689	X-RAY DIFFRACTION	93
1.7291-1.7606	0.2738	168	0.226	2728	X-RAY DIFFRACTION	95
1.7606-1.7944	0.2626	152	0.2317	2715	X-RAY DIFFRACTION	95
1.7944-1.831	0.2709	141	0.221	2759	X-RAY DIFFRACTION	94
1.831-1.8709	0.2208	145	0.2033	2715	X-RAY DIFFRACTION	95
1.8709-1.9144	0.2422	149	0.2007	2770	X-RAY DIFFRACTION	95
1.9144-1.9622	0.2093	133	0.1907	2736	X-RAY DIFFRACTION	94
1.9622-2.0153	0.2352	141	0.1835	2779	X-RAY DIFFRACTION	95
2.0153-2.0746	0.2072	144	0.179	2737	X-RAY DIFFRACTION	95
2.0746-2.1415	0.2047	146	0.1752	2734	X-RAY DIFFRACTION	94
2.1415-2.218	0.1911	152	0.1687	2754	X-RAY DIFFRACTION	94
2.218-2.3068	0.1986	126	0.1632	2760	X-RAY DIFFRACTION	93
2.3068-2.4117	0.2008	139	0.1705	2734	X-RAY DIFFRACTION	93
2.4117-2.5388	0.2135	147	0.1754	2734	X-RAY DIFFRACTION	93
2.5388-2.6978	0.2029	145	0.1682	2737	X-RAY DIFFRACTION	93
2.6978-2.9059	0.1905	145	0.1679	2734	X-RAY DIFFRACTION	94
2.9059-3.1981	0.2312	139	0.1711	2798	X-RAY DIFFRACTION	94
3.1981-3.6601	0.186	149	0.1525	2866	X-RAY DIFFRACTION	95
3.6601-4.6087	0.1639	157	0.1424	2920	X-RAY DIFFRACTION	97
4.6087-29.946	0.2041	150	0.1694	3108	X-RAY DIFFRACTION	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	1.7807	0.4989	0.1552	1.3187	0.1732	0.8439	0.0046	-0.0028	0.1053	-0.0022	0.0297	-0.0551	-0.1205	0.0944	-0.0393	0.1146	-0.0031	-0.0096	0.0989	-0.0192	0.1062	25.7879	11.4167	-8.0118
2	2.3883	-1.5261	2.4872	2.2629	-2.04	3.7838	-0.0259	0.1369	0.1043	-0.2308	0.0024	0.088	-0.1781	-0.0326	-0.0026	0.2031	0.0022	-0.0424	0.1774	0.0115	0.1525	11.392	11.3602	-24.9604
3	1.3562	-0.351	-0.2268	1.1197	-0.196	1.4689	0.1776	-0.7945	0.1728	0.7987	0.0988	-0.2349	-0.0672	0.0766	-0.0633	0.6397	0.0002	-0.0841	0.5476	-0.0066	0.2039	-4.5051	36.4332	-35.7013
4	5.0342	-4.0333	2.5952	2	-6.3374	9.0535	0.057	-0.039	0.0615	-0.1526	-0.0738	0.0801	0.0396	0.1054	0.038	0.1672	-0.062	-0.0603	0.1731	-0.0329	0.1831	35.3675	16.8269	-8.9102
5	1.3794	0.5511	0.025	1.0819	0.0889	0.7923	-0.0335	0.0664	-0.1643	-0.0395	0.0147	0.0264	0.0974	-0.0189	0.0176	0.118	-0.0019	-0.0037	0.1037	-0.0048	0.1085	1.4907	-12.6619	-14.1485
6	2.4342	-1.91	2.5222	3.2477	-3.3405	5.1183	-0.0218	0.2799	0.2568	-0.1198	-0.0413	0.0283	-0.2025	-0.0865	0.0389	0.1683	0.0138	-0.0152	0.1873	0.0368	0.1565	0.3965	6.4356	-23.6861
7	2.6173	-0.378	1.378	2.0791	-1.0349	1.1101	0.1314	-0.7814	-0.642	-0.1085	0.0075	-0.0734	0.3777	-0.4994	-0.0236	0.4491	0.0299	-0.038	0.6336	0.2172	0.7199	-20.3963	14.7734	-50.6154
8	6.5765	3.8167	-1.3783	8.3782	-4.6145	7.8557	-0.0253	-0.233	-0.3009	0.0441	-0.045	0.1205	-0.1429	0.0202	0.073	0.1239	-0.0665	-0.0171	0.1905	-0.0091	0.1843	-8.336	-17.8871	-13.4543

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 1 through 136 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 137 through 178 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 179 through 255 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 301 through 301 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 1 through 136 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 137 through 178 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 179 through 255 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 301 through 301 )

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