PDB-6o15: Crystal structure of a putative oxidoreductase YjhC from Escheric...

ID or keywords:

Entry

Database: PDB / ID: 6o15

Title

Crystal structure of a putative oxidoreductase YjhC from Escherichia coli in complex with NAD(H)

Components

Uncharacterized oxidoreductase YjhC

Keywords

OXIDOREDUCTASE / Gfo/Idh/MocA / Rossmann Fold

Function / homology

Function and homology information

Lyases; Carbon-oxygen lyases; Hydro-lyases / N-acetylneuraminate catabolic process / hydro-lyase activity / nucleotide binding / DNA damage response / protein homodimerization activity
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.35 Å

Authors

Horne, C.R. / Kind, L. / Davies, J.S. / Dobson, R.C.

Funding support

New Zealand, 1items

Citation

Journal: Proteins / Year: 2020
Title: On the structure and function of Escherichia coli YjhC: An oxidoreductase involved in bacterial sialic acid metabolism.
Authors: Horne, C.R. / Kind, L. / Davies, J.S. / Dobson, R.C.J.

History

Deposition	Feb 17, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 27, 2019	Provider: repository / Type: Initial release
Revision 1.1	Apr 15, 2020	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2	Oct 11, 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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PDBx/mmCIF format	6o15.cif.gz	429.8 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	6o15_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	6o15_full_validation.pdf.gz	1 MB	Display
Data in XML	6o15_validation.xml.gz	37.6 KB	Display
Data in CIF	6o15_validation.cif.gz	58.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/o1/6o15 ftp://data.pdbj.org/pub/pdb/validation_reports/o1/6o15	HTTPS FTP

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Related structure data

Related structure data	5a02S S: Starting model for refinement
Similar structure data	5a04-3 6z3b-d 3db2-2 2q4e-d 5a03-2 5a06-2 3db2-1 3gfg-2 1vmi-1 4koa-1 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: Uncharacterized oxidoreductase YjhC

B: Uncharacterized oxidoreductase YjhC

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: SAXS

Unit cell

Length a, b, c (Å)	51.514, 84.673, 188.118
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Uncharacterized oxidoreductase YjhC Mass: 41441.500 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: yjhC, b4280, JW5769 / Plasmid: pET30a / Details (production host): His-Tag / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P39353, Oxidoreductases
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C₂₁H₂₇N₇O₁₄P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 933 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.49 Å³/Da / Density % sol: 50.39 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 1.5 M Ammonium sulfate, 0.1 M Sodium acetate / Temp details: Cooled Crystallization Incubator

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Australian Synchrotron

/ Beamline: MX2 / Wavelength: 0.9573 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 6, 2018

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9573 Å / Relative weight: 1

Reflection

Resolution: 1.35→45.182 Å / Num. obs: 181008 / % possible obs: 99.9 % / Redundancy: 12.8 % / B_iso Wilson estimate: 16.57 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.084 / R_pim(I) all: 0.024 / R_rim(I) all: 0.088 / Net I/av σ(I): 1 / Net I/σ(I): 14.2

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. measured all	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Net I/σ(I) obs	% possible all
1.35-1.37	7.8	2.106	68650	8815	0.552	0.795	2.255	1	99.3
7.39-45.18	11.6	0.039	14639	1262	0.999	0.012	0.04	39.1	99.5

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Processing

Software

Name	Version	Classification
PHENIX		refinement
Aimless	CCP4 Program Suite v7.0.068	data scaling
PHASER	CCP4 Program Suite v7.0.068	phasing
PDB_EXTRACT	data extraction version: 3.15	data extraction
Coot	coot-0.8.9.2	model building
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5A02

5a02

Resolution: 1.35→45.18 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.2

	R_factor	Num. reflection	% reflection
R_free	0.1687	9103	5.04 %
R_work	0.1498	-	-
obs	0.1508	180786	99.86 %

Solvent computation

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

Displacement parameters

B_iso max: 136.02 Å² / B_iso mean: 27.4841 Å² / B_iso min: 10.06 Å²

Refinement step

Cycle: final / Resolution: 1.35→45.18 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5515	0	155	933	6603
B_iso mean	-	-	26.11	38.49	-
Num. residues	-	-	-	-	710

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	5824
X-RAY DIFFRACTION	f_angle_d	1.061	7894
X-RAY DIFFRACTION	f_chiral_restr	0.076	872
X-RAY DIFFRACTION	f_plane_restr	0.007	1003
X-RAY DIFFRACTION	f_dihedral_angle_d	20.542	2127

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.35-1.3653	0.3321	320	5555	X-RAY DIFFRACTION	99
1.3653-1.3814	0.3181	310	5676	X-RAY DIFFRACTION	100
1.3814-1.3983	0.2646	285	5616	X-RAY DIFFRACTION	99
1.3983-1.416	0.2553	302	5680	X-RAY DIFFRACTION	100
1.416-1.4346	0.2451	285	5704	X-RAY DIFFRACTION	100
1.4346-1.4542	0.2163	297	5609	X-RAY DIFFRACTION	100
1.4542-1.475	0.2462	317	5692	X-RAY DIFFRACTION	100
1.475-1.497	0.23	302	5637	X-RAY DIFFRACTION	100
1.497-1.5204	0.2222	308	5673	X-RAY DIFFRACTION	100
1.5204-1.5454	0.2118	307	5662	X-RAY DIFFRACTION	100
1.5454-1.572	0.1929	309	5711	X-RAY DIFFRACTION	100
1.572-1.6006	0.1844	315	5667	X-RAY DIFFRACTION	100
1.6006-1.6314	0.186	276	5669	X-RAY DIFFRACTION	100
1.6314-1.6647	0.1854	298	5745	X-RAY DIFFRACTION	100
1.6647-1.7009	0.1765	310	5647	X-RAY DIFFRACTION	100
1.7009-1.7405	0.1805	303	5681	X-RAY DIFFRACTION	100
1.7405-1.784	0.1621	285	5758	X-RAY DIFFRACTION	100
1.784-1.8322	0.1614	319	5691	X-RAY DIFFRACTION	100
1.8322-1.8861	0.1736	296	5695	X-RAY DIFFRACTION	100
1.8861-1.947	0.1746	319	5693	X-RAY DIFFRACTION	100
1.947-2.0166	0.1532	327	5728	X-RAY DIFFRACTION	100
2.0166-2.0973	0.1492	331	5692	X-RAY DIFFRACTION	100
2.0973-2.1928	0.1494	270	5784	X-RAY DIFFRACTION	100
2.1928-2.3084	0.1546	292	5758	X-RAY DIFFRACTION	100
2.3084-2.453	0.1608	294	5790	X-RAY DIFFRACTION	100
2.453-2.6424	0.1517	294	5783	X-RAY DIFFRACTION	100
2.6424-2.9083	0.1621	291	5836	X-RAY DIFFRACTION	100
2.9083-3.329	0.1632	286	5846	X-RAY DIFFRACTION	100
3.329-4.1937	0.1448	337	5876	X-RAY DIFFRACTION	100
4.1937-45.18	0.1641	318	6129	X-RAY DIFFRACTION	100

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	0.7974	0.0611	0.0384	0.551	-0.1911	1.2772	0.0104	0.2856	0.0107	-0.1622	-0.0659	-0.0255	-0.0606	0.1796	-0.0005	0.2129	-0.0089	-0.0041	0.2497	0.0331	0.1413	-5.3859	16.7905	-32.9304
2	0.35	0.0956	-0.0439	0.3629	-0.2916	0.5068	-0.0306	0.0883	0.0029	-0.126	0.0181	0.0292	0.0324	-0.001	0	0.1436	0.0027	-0.0145	0.1459	-0.0087	0.1463	-9.4674	9.5506	-12.9738
3	0.7136	0.0558	0.0912	0.611	-0.1225	0.5865	-0.0129	0.0887	0.003	-0.0551	0.0126	-0.0102	0.0383	-0.0376	-0	0.1236	-0.004	-0.0041	0.1168	-0.0139	0.1427	-8.4288	4.6976	-5.9045
4	0.39	0.1002	0.1191	0.3494	-0.0767	0.1226	0.0361	0.1137	-0.0332	-0.0418	-0.0102	0.1658	0.1537	-0.3969	-0	0.1763	-0.0064	-0.0269	0.2178	-0.0079	0.2133	-25.953	10.06	-10.9573
5	0.2901	0.1088	0.2876	0.3447	-0.1788	0.7165	-0.0742	0.0599	0.0628	-0.0292	0.0264	-0.0332	-0.1301	0.0069	-0	0.1471	0.0013	0.0002	0.1433	0.0036	0.1631	-2.8445	16.1198	-15.2258
6	0.5787	-0.3417	-0.2998	0.3893	-0.0773	0.864	-0.0571	-0.3328	-0.0271	0.1578	0.038	0.0188	0.1345	0.0441	-0.0032	0.2647	0.007	0.0197	0.2533	0.0364	0.1495	-9.679	-16.3595	35.6484
7	0.1944	-0.036	-0.1158	0.0867	-0.0373	0.2365	-0.0603	-0.13	-0.0697	0.1064	0.0249	-0.0934	0.2285	0.158	-0	0.2737	0.0542	-0.0008	0.2095	0.0387	0.1999	1.5209	-18.9654	24.2984
8	0.0633	-0.1499	0.0506	0.1348	-0.0142	0.0797	-0.0349	-0.0624	-0.0914	0.025	-0.0404	0.07	0.2573	-0.0184	0	0.2138	-0.024	0.0133	0.1568	0.0045	0.1886	-13.7076	-19.9958	11.5876
9	0.5501	0.0361	0.3064	0.2138	-0.2573	0.3673	-0.0411	-0.1097	0.0123	0.1173	0.0049	0.0009	-0.0493	-0.0764	-0	0.1599	0.0006	0.0116	0.1376	-0.014	0.1612	-8.0668	-2.0506	13.7006
10	0.5964	-0.0406	-0.0116	0.192	-0.1184	0.8291	-0.0142	-0.0446	-0.0155	0.049	0.0119	-0.0147	0.0096	-0.0479	-0	0.1185	0.0039	0.0003	0.1095	-0.0155	0.1512	-8.7193	-4.4124	5.7034
11	0.4725	-0.2754	-0.0646	0.4436	-0.1426	0.1513	0.0646	-0.0606	0.0472	0.1083	-0.0385	0.1195	-0.0985	-0.4669	-0.001	0.1597	-0.0063	0.0255	0.2867	-0.0194	0.2081	-26.8388	-8.3791	10.9248
12	0.2829	-0.1199	-0.3024	0.2606	-0.3024	1.3053	-0.0563	-0.0706	-0.0324	0.0045	0.0127	-0.0223	0.2593	0.043	-0.0013	0.1843	0.003	0.0061	0.1139	-0.0041	0.1584	-4.0752	-16.0838	15.0166

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 1 through 110 )	A	1 - 110
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 111 through 175 )	A	111 - 175
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 176 through 262 )	A	176 - 262
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 263 through 304 )	A	263 - 304
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 305 through 369 )	A	305 - 369
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 1 through 82 )	B	1 - 82
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 83 through 110 )	B	83 - 110
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 111 through 135 )	B	111 - 135
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 136 through 175 )	B	136 - 175
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 176 through 262 )	B	176 - 262
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 263 through 304 )	B	263 - 304
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 305 through 369 )	B	305 - 369

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