PDB-4l6d: Crystal structure of 5-carboxyvanillate decarboxylase from Sphing...

ID or keywords:

Entry

Database: PDB / ID: 4l6d

Title

Crystal structure of 5-carboxyvanillate decarboxylase from Sphingomonas paucimobilis complexed with vanillic acid

Components

5-carboxyvanillate decarboxylase

Keywords

HYDROLASE / amidohydrolase fold /

vanillic acid

Function / homology

Function and homology information

secondary metabolic process / organic cyclic compound metabolic process /

: / carboxy-lyase activity /

hydrolase activity /

metal ion binding /

cytosol
Similarity search - Function

Biological species

Sphingomonas paucimobilis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.449 Å

Authors

Fedorov, A.A. / Fedorov, E.V. / Vladimirova, A. / Raushel, F.M. / Almo, S.C.

Citation

Journal: To be Published
Title: Crystal structure of 5-carboxyvanillate decarboxylase from Sphingomonas paucimobilis complexed with vanillic acid
Authors: Fedorov, A.A. / Fedorov, E.V. / Vladimirova, A. / Raushel, F.M. / Almo, S.C.

History

Deposition	Jun 12, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 13, 2013	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 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_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4l6d.cif.gz	1.1 MB	Display	PDBx/mmCIF format
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PDBx/mmJSON format	4l6d.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/l6/4l6d ftp://data.pdbj.org/pub/pdb/validation_reports/l6/4l6d	HTTPS FTP

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Related structure data

Related structure data	4icmS 4l86 PDB Unreleased entry S: Starting model for refinement
Similar structure data	4ni8-1 4ng3-1 1zbq-2 1gz6-1 5gnw-3 4ni8-3 4ng3-3 4icm-2 1gz6-2 4inf-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

4icmS

4l86
PDB Unreleased entry

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#215 - Nov 2017 Aspartate Transcarbamoylase similarity (2) #158 - Feb 2013 Proton-Gated Urea Channel similarity (2)

Deposited unit

A: 5-carboxyvanillate decarboxylase

B: 5-carboxyvanillate decarboxylase

C: 5-carboxyvanillate decarboxylase

D: 5-carboxyvanillate decarboxylase

E: 5-carboxyvanillate decarboxylase

F: 5-carboxyvanillate decarboxylase

G: 5-carboxyvanillate decarboxylase

H: 5-carboxyvanillate decarboxylase

hetero molecules

303 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: 5-carboxyvanillate decarboxylase

H: 5-carboxyvanillate decarboxylase

hetero molecules

defined by author&software
75.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: 5-carboxyvanillate decarboxylase

G: 5-carboxyvanillate decarboxylase

hetero molecules

defined by author&software
75.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: 5-carboxyvanillate decarboxylase

F: 5-carboxyvanillate decarboxylase

hetero molecules

defined by author&software
75.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: 5-carboxyvanillate decarboxylase

E: 5-carboxyvanillate decarboxylase

hetero molecules

defined by author&software
75.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	80.592, 96.917, 97.029
Angle α, β, γ (deg.)	109.71, 90.53, 111.89
Int Tables number	1
Space group name H-M	P1

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein	5-carboxyvanillate decarboxylase Mass: 37071.203 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sphingomonas paucimobilis (bacteria) / Gene: ligW / Production host: Escherichia coli (E. coli) / References: UniProt: Q8RJ47

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Non-polymers , 6 types, 3493 molecules

#2: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mn
#3: Chemical	ChemComp-VNL / 4-HYDROXY-3-METHOXYBENZOATE / vanillate / Vanillic acid Mass: 167.139 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C₈H₇O₄
#4: Chemical	ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES Mass: 238.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₈H₁₈N₂O₄S / Comment: pH buffer*YM
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#7: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 3454 / 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: 2.21 Å³/Da / Density % sol: 44.23 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20% PEG 10000, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 16, 2012
Radiation	Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.075 Å / Relative weight: 1
Reflection	Resolution: 1.449→37.219 Å / Num. all: 423754 / Num. obs: 423754 / % possible obs: 94.08 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software

Name	Version	Classification
CBASS		data collection
BALBES		phasing
PHENIX	(phenix.refine: 1.8_1069)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4ICM

4icm

Resolution: 1.449→37.219 Å / SU ML: 0.13 / σ(F): 1.97 / Phase error: 16.87 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1683	21271	5.02 %
R_work	0.1456	-	-
obs	0.1468	423754	94.08 %
all	-	423754	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.449→37.219 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	20872	0	342	3454	24668

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	21940
X-RAY DIFFRACTION	f_angle_d	1.163	29856
X-RAY DIFFRACTION	f_dihedral_angle_d	12.607	8123
X-RAY DIFFRACTION	f_chiral_restr	0.081	3241
X-RAY DIFFRACTION	f_plane_restr	0.008	3940

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 (%)
1.449-1.4653	0.2705	723	0.2378	12560	X-RAY DIFFRACTION	88
1.4653-1.4825	0.2445	701	0.2274	12900	X-RAY DIFFRACTION	91
1.4825-1.5006	0.2536	691	0.2171	13007	X-RAY DIFFRACTION	91
1.5006-1.5196	0.24	661	0.217	13178	X-RAY DIFFRACTION	91
1.5196-1.5396	0.2236	720	0.2041	13004	X-RAY DIFFRACTION	92
1.5396-1.5607	0.2232	641	0.1863	13064	X-RAY DIFFRACTION	91
1.5607-1.583	0.2068	725	0.1769	13016	X-RAY DIFFRACTION	91
1.583-1.6066	0.2066	660	0.1689	13075	X-RAY DIFFRACTION	92
1.6066-1.6317	0.1938	682	0.1665	13000	X-RAY DIFFRACTION	92
1.6317-1.6584	0.1965	646	0.1613	13161	X-RAY DIFFRACTION	92
1.6584-1.687	0.1901	690	0.1553	13217	X-RAY DIFFRACTION	92
1.687-1.7177	0.1967	740	0.1599	13170	X-RAY DIFFRACTION	93
1.7177-1.7507	0.1968	711	0.1625	13200	X-RAY DIFFRACTION	93
1.7507-1.7865	0.193	699	0.1554	13184	X-RAY DIFFRACTION	93
1.7865-1.8253	0.1767	714	0.1455	13296	X-RAY DIFFRACTION	93
1.8253-1.8678	0.1707	669	0.1425	13420	X-RAY DIFFRACTION	94
1.8678-1.9145	0.1831	709	0.1461	13340	X-RAY DIFFRACTION	94
1.9145-1.9663	0.1765	743	0.1428	13452	X-RAY DIFFRACTION	94
1.9663-2.0241	0.18	692	0.1398	13539	X-RAY DIFFRACTION	95
2.0241-2.0894	0.1613	646	0.1321	13663	X-RAY DIFFRACTION	96
2.0894-2.1641	0.1464	702	0.1267	13690	X-RAY DIFFRACTION	96
2.1641-2.2507	0.1599	719	0.1366	13782	X-RAY DIFFRACTION	96
2.2507-2.3532	0.1607	735	0.1367	13791	X-RAY DIFFRACTION	97
2.3532-2.4772	0.1617	786	0.1413	13883	X-RAY DIFFRACTION	97
2.4772-2.6324	0.1644	758	0.1428	13827	X-RAY DIFFRACTION	97
2.6324-2.8356	0.1607	731	0.1437	13929	X-RAY DIFFRACTION	98
2.8356-3.1208	0.1663	753	0.1436	13974	X-RAY DIFFRACTION	98
3.1208-3.572	0.1574	733	0.1398	14004	X-RAY DIFFRACTION	98
3.572-4.4992	0.1313	743	0.1228	14068	X-RAY DIFFRACTION	99
4.4992-37.2312	0.1451	748	0.1345	14089	X-RAY DIFFRACTION	99

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	0.3762	0.0697	0.0352	0.4508	0.0009	0.4239	0.0001	0.0197	-0.039	-0.045	0.0079	0.0225	0.0497	-0.0145	-0.0033	0.0475	-0.0116	-0.0044	0.0496	0.0035	0.0468	-47.1966	57.4513	46.7784
2	0.3852	-0.0348	-0.0094	0.3813	-0.0031	0.377	-0.004	-0.0303	-0.0312	0.0283	0.0115	0.0394	0.0441	-0.0437	-0.0035	0.0497	-0.0093	0.0034	0.057	0.0065	0.0433	-49.1926	53.3639	91.9387
3	0.4729	-0.083	0.13	0.5348	-0.0271	0.5217	-0.0317	-0.09	0.0184	0.0582	0.0197	0.0998	-0.0422	-0.1166	0.0119	0.0516	0.0148	0.0172	0.0966	-0.0082	0.0837	-63.8724	96.0822	94.7065
4	0.3739	-0.0717	0.0469	0.4514	0.0217	0.355	-0.0152	0.0207	0.034	-0.0273	0.0013	0.0433	-0.0365	-0.0413	0.0094	0.0361	-0.0003	-0.0023	0.054	0.0046	0.0589	-62.0728	99.9772	50.0368
5	0.4281	-0.0779	0.1496	0.3974	-0.1411	0.8993	-0.0622	0.0254	0.0931	0.0162	-0.0178	-0.0411	-0.1871	0.1005	0.0279	0.0747	-0.0376	-0.018	0.0494	0.0175	0.0867	-33.0044	114.1104	57.5531
6	0.4009	-0.1071	0.109	0.5452	0.0309	0.5194	-0.0454	-0.0545	0.0536	0.0871	0.0347	-0.0598	-0.0439	0.0226	0.0068	0.0633	0.0044	-0.0171	0.0604	-0.0142	0.0688	-31.8974	101.1654	101.0951
7	0.4111	-0.0586	0.0203	0.3836	-0.0238	0.3907	0.0011	-0.0215	-0.0043	0.0218	0.0019	-0.0626	0.0209	0.053	-0.001	0.0433	0.0028	-0.0038	0.0555	-0.0028	0.0567	-16.9659	60.0588	88.6257
8	0.4084	0.0695	0.0383	0.5451	-0.0075	0.3018	-0.0161	0.0573	-0.0262	-0.0632	0.0211	-0.0839	0.0112	0.0544	0.0051	0.0389	-0.0092	0.0192	0.0771	-0.0055	0.0635	-18.276	73.4364	45.0768

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain A
2	X-RAY DIFFRACTION	2	chain B
3	X-RAY DIFFRACTION	3	chain C
4	X-RAY DIFFRACTION	4	chain D
5	X-RAY DIFFRACTION	5	chain E
6	X-RAY DIFFRACTION	6	chain F
7	X-RAY DIFFRACTION	7	chain G
8	X-RAY DIFFRACTION	8	chain H

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