PDB-5o3m: Crystal structure of apo Klebsiella pneumoniae 3,4-dihydroxybenzo...

ID or keywords:

Entry

Database: PDB / ID: 5o3m

Title

Crystal structure of apo Klebsiella pneumoniae 3,4-dihydroxybenzoic acid decarboxylase (AroY)

Components

Protocatechuate decarboxylase

Keywords

LYASE /

Decarboxylase /

prFMN /

UbiD

Function / homology

UbiD decarboxylyase family / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase Rift-related domain / carboxy-lyase activity /

pentane-1,5-diol / Putative carboxylyase-related protein /

Protocatechuate decarboxylase

Function and homology information

Biological species

Klebsiella pneumoniae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.23 Å

Authors

Marshall, S.A. / Leys, D.

Funding support

United Kingdom, 1items

Citation

Journal: Angew Chem Int Ed Engl / Year: 2017
Title: Regioselective para-Carboxylation of Catechols with a Prenylated Flavin Dependent Decarboxylase.
Authors: Stefan E Payer / Stephen A Marshall / Natalie Bärland / Xiang Sheng / Tamara Reiter / Andela Dordic / Georg Steinkellner / Christiane Wuensch / Susann Kaltwasser / Karl Fisher / Stephen E J ...
Abstract: The utilization of CO as a carbon source for organic synthesis meets the urgent demand for more sustainability in the production of chemicals. Herein, we report on the enzyme-catalyzed para- ...

History

Deposition	May 24, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 13, 2017	Provider: repository / Type: Initial release
Revision 1.1	Oct 11, 2017	Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.name
Revision 1.2	Oct 25, 2017	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5o3m.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb5o3m.ent.gz	964.9 KB	Display	PDB format
PDBx/mmJSON format	5o3m.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/o3/5o3m ftp://data.pdbj.org/pub/pdb/validation_reports/o3/5o3m	HTTPS FTP

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Related structure data

Related structure data	3718C 5ny5C 5o3nC C: citing same article (ref.)
Similar structure data	5o3n-1 5ny5-1 4c56-d 6h6v-d 20301 5m1d-1 5m1c-1 5vjq-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

Deposited unit

A: Protocatechuate decarboxylase

B: Protocatechuate decarboxylase

C: Protocatechuate decarboxylase

D: Protocatechuate decarboxylase

E: Protocatechuate decarboxylase

F: Protocatechuate decarboxylase

hetero molecules

338 kDa, 6 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)	81.880, 209.700, 116.020
Angle α, β, γ (deg.)	90.00, 107.63, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Protocatechuate decarboxylase / / 3 / 4-dihydroxybenzoic acid decarboxylase Mass: 56239.926 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: aroY / Production host: Escherichia coli (E. coli) / References: UniProt: B9A9M6, UniProt: A6T7M3*PLUS
#2: Chemical	ChemComp-9JE / pentane-1,5-diol / Pentane-1,5-diol Mass: 104.148 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₅H₁₂O₂
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1246 / 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: 2.81 Å³/Da / Density % sol: 56.28 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Morpheus II (Molecular Dimensions) H3 40 mM Polyamines (Spermine tetrahydrochloride, Spermidine trihydrochloride, 1,4-Diaminobutane dihydrochloride, DL-Ornithine monohydrochloride) 0.1 M ...Details: Morpheus II (Molecular Dimensions) H3 40 mM Polyamines (Spermine tetrahydrochloride, Spermidine trihydrochloride, 1,4-Diaminobutane dihydrochloride, DL-Ornithine monohydrochloride) 0.1 M Buffer system 4 (MOPSO/Bis-Tris) 50% precipitant mix 7 (20% w/v PEG 8000, 40% w/v 1,5-Pentanediol)

Crystal

Density Matthews: 2.81 Å³/Da / Density % sol: 56.28 %

Crystal grow

Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Morpheus II (Molecular Dimensions) H3 40 mM Polyamines (Spermine tetrahydrochloride, Spermidine trihydrochloride, 1,4-Diaminobutane dihydrochloride, DL-Ornithine monohydrochloride) 0.1 M ...

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.92 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 5, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.92 Å / Relative weight: 1
Reflection	Resolution: 2.23→38.08 Å / Num. obs: 180400 / % possible obs: 99.8 % / Redundancy: 3.4 % / R_merge(I) obs: 0.1145 / Net I/σ(I): 8.2
Reflection shell	Resolution: 2.23→2.27 Å / Redundancy: 3.5 % / R_merge(I) obs: 0.8952 / Mean I/σ(I) obs: 1.27 / Num. unique all: 17981 / CC_1/2: 0.566 / % possible all: 99.91

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Processing

Software

Name	Version	Classification
PHENIX	(dev_2689)	refinement
xia2		data reduction
xia2		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.23→38.08 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.68

	R_factor	Num. reflection	% reflection
R_free	0.2086	8846	4.91 %
R_work	0.1625	-	-
obs	0.1647	180312	99.82 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.23→38.08 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	22261	0	70	1246	23577

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	22844
X-RAY DIFFRACTION	f_angle_d	0.836	31115
X-RAY DIFFRACTION	f_dihedral_angle_d	12.557	13854
X-RAY DIFFRACTION	f_chiral_restr	0.054	3521
X-RAY DIFFRACTION	f_plane_restr	0.006	4144

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 (%)
2.23-2.2553	0.3565	294	0.2837	5691	X-RAY DIFFRACTION	100
2.2553-2.2819	0.3072	298	0.2605	5704	X-RAY DIFFRACTION	100
2.2819-2.3097	0.3315	302	0.2588	5686	X-RAY DIFFRACTION	100
2.3097-2.3389	0.3072	295	0.2512	5709	X-RAY DIFFRACTION	100
2.3389-2.3697	0.2927	319	0.2467	5685	X-RAY DIFFRACTION	100
2.3697-2.4022	0.3003	295	0.2367	5730	X-RAY DIFFRACTION	100
2.4022-2.4365	0.2765	336	0.23	5609	X-RAY DIFFRACTION	100
2.4365-2.4728	0.3278	314	0.2258	5748	X-RAY DIFFRACTION	100
2.4728-2.5115	0.2782	268	0.2189	5700	X-RAY DIFFRACTION	100
2.5115-2.5526	0.2568	291	0.2053	5745	X-RAY DIFFRACTION	100
2.5526-2.5966	0.2578	280	0.1924	5695	X-RAY DIFFRACTION	100
2.5966-2.6439	0.2483	275	0.1871	5779	X-RAY DIFFRACTION	100
2.6439-2.6947	0.2459	310	0.1784	5643	X-RAY DIFFRACTION	100
2.6947-2.7497	0.2358	299	0.1789	5714	X-RAY DIFFRACTION	100
2.7497-2.8095	0.2233	291	0.1728	5739	X-RAY DIFFRACTION	100
2.8095-2.8748	0.2447	296	0.1742	5707	X-RAY DIFFRACTION	100
2.8748-2.9467	0.2301	299	0.1685	5678	X-RAY DIFFRACTION	100
2.9467-3.0263	0.2455	263	0.1718	5776	X-RAY DIFFRACTION	100
3.0263-3.1153	0.2156	309	0.1718	5689	X-RAY DIFFRACTION	100
3.1153-3.2158	0.2403	349	0.1657	5687	X-RAY DIFFRACTION	100
3.2158-3.3307	0.2244	289	0.1753	5740	X-RAY DIFFRACTION	100
3.3307-3.464	0.2238	298	0.1692	5690	X-RAY DIFFRACTION	100
3.464-3.6215	0.2037	288	0.1673	5747	X-RAY DIFFRACTION	100
3.6215-3.8123	0.1867	305	0.1592	5709	X-RAY DIFFRACTION	100
3.8123-4.0509	0.1845	299	0.1455	5721	X-RAY DIFFRACTION	100
4.0509-4.3633	0.1652	268	0.126	5768	X-RAY DIFFRACTION	100
4.3633-4.8017	0.1285	270	0.1104	5782	X-RAY DIFFRACTION	100
4.8017-5.4949	0.1591	292	0.1202	5747	X-RAY DIFFRACTION	100
5.4949-6.9167	0.1709	299	0.1309	5729	X-RAY DIFFRACTION	100
6.9167-39.0231	0.1293	255	0.1221	5719	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	3.0154	-0.9054	-0.5771	2.0318	-0.0696	1.0023	-0.0894	0.205	-0.4008	0.0171	0.0811	-0.2485	0.0908	0.1262	-0.0053	0.2258	-0.0237	-0.0057	0.4179	-0.094	0.3688	25.3785	-16.8407	-7.1333
2	1.4628	-0.3346	-0.5693	0.946	-0.0634	1.5733	-0.0251	0.3343	-0.1129	-0.1215	0.0096	-0.0298	0.0221	-0.0061	0.0257	0.1765	-0.0175	-0.0168	0.2916	-0.0505	0.2145	-5.389	-11.8718	-2.7746
3	1.2852	-0.1059	0.3931	1.6821	0.9909	3.0116	0.0101	0.2799	0.285	-0.5304	-0.2639	0.3631	-1.2205	-0.8167	0.216	0.7517	0.3149	-0.1055	0.7486	0.0344	0.3787	-19.648	16.9499	-22.4201
4	1.3383	-0.1188	-0.3908	1.041	-0.023	1.5516	0.0444	0.1921	0.0535	-0.1101	-0.0092	-0.1192	-0.1585	0.0641	-0.0342	0.2401	-0.0184	-0.0114	0.2746	0.0093	0.226	-2.804	6.999	2.637
5	1.0283	-0.2679	-0.3669	1.4546	0.8155	1.6909	-0.076	0.0784	-0.4375	0.2446	-0.124	0.3567	0.466	-0.1682	0.1901	0.5539	-0.0292	0.1578	0.2581	-0.0755	0.621	-20.2058	-52.3653	8.1513
6	1.3975	-0.362	-0.0549	1.604	0.0661	1.2061	-0.1557	-0.1117	-0.3433	0.2848	0.0876	-0.0293	0.369	0.1529	0.0744	0.3164	0.0672	0.0375	0.2165	0.0096	0.3046	-5.3481	-28.0593	22.3317
7	2.4462	0.2789	-0.6045	1.239	-0.3303	1.6605	-0.0571	-0.0576	-0.0339	-0.0464	0.0573	0.0506	0.0583	-0.2838	0.0028	0.2163	0.0505	-0.0326	0.2754	-0.0122	0.2078	-51.9772	5.4895	45.3948
8	1.3986	0.1356	-0.2522	0.7955	0.2029	1.0262	-0.0424	-0.1738	0.0453	0.1279	0.0397	0.0206	-0.1016	0.0541	0.0086	0.2502	0.0405	-0.0197	0.2364	0.006	0.2141	-20.9254	5.3087	38.6539
9	1.3145	0.2238	-0.1574	1.1761	-0.4713	1.7462	0.0429	-0.0387	0.5319	0.0544	-0.0773	-0.1144	-0.4554	0.0632	0.0291	0.4142	-0.0096	0.022	0.218	-0.0242	0.468	-5.9784	39.3842	31.5003
10	1.6647	-0.0157	-0.4775	0.9439	0.2181	0.9167	0.068	0.1752	0.1861	-0.0218	0.0053	0.0999	-0.1886	-0.1272	-0.0843	0.2553	0.0357	-0.024	0.2271	0.0282	0.2314	-23.8557	15.2959	21.8241
11	1.8602	-0.0704	-0.509	1.1513	-0.2654	2.0724	-0.0485	-0.8045	-0.3012	0.9429	0.0492	0.0444	0.1115	0.3624	-0.0053	1.2072	0.2235	0.048	0.7354	0.1605	0.4564	-6.0404	-30.1641	60.7138
12	0.9284	0.0035	-0.1418	1.1786	0.1821	1.5073	-0.1786	-0.0971	-0.3157	0.3113	0.0381	0.1302	0.4496	-0.0389	0.1206	0.3663	0.0381	0.0998	0.2129	0.0182	0.3281	-21.0437	-23.6083	33.7978

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 4:334)
2	X-RAY DIFFRACTION	2	(chain A and resid 335:496)
3	X-RAY DIFFRACTION	3	(chain B and resid 4:333)
4	X-RAY DIFFRACTION	4	(chain B and resid 334:493)
5	X-RAY DIFFRACTION	5	(chain C and resid 4:334)
6	X-RAY DIFFRACTION	6	(chain C and resid 335:492)
7	X-RAY DIFFRACTION	7	(chain D and resid 4:334)
8	X-RAY DIFFRACTION	8	(chain D and resid 335:493)
9	X-RAY DIFFRACTION	9	(chain E and resid 4:333)
10	X-RAY DIFFRACTION	10	(chain E and resid 334:494)
11	X-RAY DIFFRACTION	11	(chain F and resid 5:326)
12	X-RAY DIFFRACTION	12	(chain F and resid 327:492)

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