PDB-5cxx: Structure of a CE1 ferulic acid esterase, AmCE1/Fae1A, from Anaer...

ID or keywords:

Entry

Database: PDB / ID: 5cxx

Title

Structure of a CE1 ferulic acid esterase, AmCE1/Fae1A, from Anaeromyces mucronatus in complex with Ferulic acid

Components

ferulic acid esterase, AmCE1/Fae1A

Keywords

HYDROLASE /

Ferulic acid /

esterase / anaerobic fungi / alpha/beta-hydrolase

Function / homology

Function and homology information

feruloyl esterase /

feruloyl esterase activity
Similarity search - Function

Biological species

Anaeromyces mucronatus (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.55 Å

Authors

Gruninger, R.J. / Abbott, D.W.

Citation

Journal: Biochem.J. / Year: 2016
Title: Contributions of a unique beta-clamp to substrate recognition illuminates the molecular basis of exolysis in ferulic acid esterases.
Authors: Gruninger, R.J. / Cote, C. / McAllister, T.A. / Abbott, D.W.

History

Deposition	Jul 29, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 27, 2016	Provider: repository / Type: Initial release
Revision 1.1	Nov 1, 2017	Group: Author supporting evidence / Database references / Derived calculations Category: citation / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5cxx.cif.gz	360.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5cxx.ent.gz	296.4 KB	Display	PDB format
PDBx/mmJSON format	5cxx.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

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

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Related structure data

Related structure data	5cxuSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4qdt-d 6d63-1 2owp-d 4u0p-d 4ikr-d 5cxu-d 6s0u-5 3no2-d 4tzs-2 2x63-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) 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

5cxuSC

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: ferulic acid esterase, AmCE1/Fae1A

B: ferulic acid esterase, AmCE1/Fae1A

C: ferulic acid esterase, AmCE1/Fae1A

hetero molecules

95.1 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: ferulic acid esterase, AmCE1/Fae1A

hetero molecules

defined by author&software
Evidence: gel filtration
31.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: ferulic acid esterase, AmCE1/Fae1A

hetero molecules

defined by author&software
Evidence: gel filtration
31.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: ferulic acid esterase, AmCE1/Fae1A

hetero molecules

defined by author&software
Evidence: gel filtration
31.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	99.790, 152.650, 154.120
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	23
Space group name H-M	I222

Components on special symmetry positions

ID	Model	Components
1	1	A-410- HOH
2	1	A-574- HOH
3	1	C-471- HOH

Details

biological unit was supported by gel filtration method

#1: Protein	ferulic acid esterase, AmCE1/Fae1A Mass: 31078.926 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Anaeromyces mucronatus (fungus) / Gene: fae1A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: F2YCB6, feruloyl esterase
#2: Chemical	ChemComp-FER / 3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID / FERULIC ACID / Ferulic acid Mass: 194.184 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Formula: C₁₀H₁₀O₄
#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 856 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 3.13 Å³/Da / Density % sol: 60.7 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 200 mM ammonium sulfate, 16% PEG 3350, 16% glycerol

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
Detector	Type: RAYONIX MX-300 / Detector: CCD / Date: May 30, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.55→48.69 Å / Num. obs: 169434 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.5 / Redundancy: 7.5 % / R_merge(I) obs: 0.07037 / R_sym value: 0.0756 / Net I/av σ(I): 16.2 / Net I/σ(I): 16.2
Reflection shell	Resolution: 1.55→1.605 Å / Redundancy: 7.4 % / R_merge(I) obs: 0.43 / Mean I/σ(I) obs: 1.93 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.8.4_1496	refinement
XDS		data reduction
XDS		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5CXU

5cxu

Resolution: 1.55→48.69 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.05 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1596	8471	5 %	Random
R_work	0.1414	-	-	-
obs	0.1423	169424	99.97 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.55→48.69 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6548	0	81	856	7485

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.02	6973
X-RAY DIFFRACTION	f_angle_d	1.753	9505
X-RAY DIFFRACTION	f_dihedral_angle_d	14.308	2632
X-RAY DIFFRACTION	f_chiral_restr	0.101	1018
X-RAY DIFFRACTION	f_plane_restr	0.01	1226

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 (%)
1.55-1.5676	0.3274	278	0.2981	5287	X-RAY DIFFRACTION	100
1.5676-1.5861	0.2872	280	0.2671	5319	X-RAY DIFFRACTION	100
1.5861-1.6054	0.2542	280	0.2411	5323	X-RAY DIFFRACTION	100
1.6054-1.6257	0.2558	279	0.2384	5287	X-RAY DIFFRACTION	100
1.6257-1.6471	0.2617	280	0.2165	5324	X-RAY DIFFRACTION	100
1.6471-1.6697	0.2115	283	0.2072	5376	X-RAY DIFFRACTION	100
1.6697-1.6935	0.2189	280	0.1968	5323	X-RAY DIFFRACTION	100
1.6935-1.7188	0.199	279	0.1759	5298	X-RAY DIFFRACTION	100
1.7188-1.7457	0.2101	280	0.1761	5341	X-RAY DIFFRACTION	100
1.7457-1.7743	0.1901	282	0.1688	5366	X-RAY DIFFRACTION	100
1.7743-1.8049	0.188	280	0.1618	5305	X-RAY DIFFRACTION	100
1.8049-1.8377	0.1868	282	0.1538	5360	X-RAY DIFFRACTION	100
1.8377-1.8731	0.1877	279	0.1463	5303	X-RAY DIFFRACTION	100
1.8731-1.9113	0.1671	281	0.1429	5340	X-RAY DIFFRACTION	100
1.9113-1.9529	0.1745	282	0.1391	5368	X-RAY DIFFRACTION	100
1.9529-1.9983	0.1797	281	0.1388	5333	X-RAY DIFFRACTION	100
1.9983-2.0483	0.1704	281	0.138	5338	X-RAY DIFFRACTION	100
2.0483-2.1036	0.1654	282	0.1338	5366	X-RAY DIFFRACTION	100
2.1036-2.1655	0.1622	282	0.1298	5358	X-RAY DIFFRACTION	100
2.1655-2.2354	0.1543	282	0.1313	5344	X-RAY DIFFRACTION	100
2.2354-2.3153	0.1573	282	0.1304	5364	X-RAY DIFFRACTION	100
2.3153-2.408	0.1631	282	0.1381	5361	X-RAY DIFFRACTION	100
2.408-2.5176	0.1465	283	0.1362	5370	X-RAY DIFFRACTION	100
2.5176-2.6504	0.1502	284	0.1394	5403	X-RAY DIFFRACTION	100
2.6504-2.8164	0.1588	283	0.1345	5363	X-RAY DIFFRACTION	100
2.8164-3.0338	0.1464	285	0.1341	5419	X-RAY DIFFRACTION	100
3.0338-3.3391	0.1456	285	0.1323	5425	X-RAY DIFFRACTION	100
3.3391-3.8221	0.1374	287	0.1238	5457	X-RAY DIFFRACTION	100
3.8221-4.8147	0.1204	288	0.1139	5472	X-RAY DIFFRACTION	100
4.8147-48.7139	0.1571	299	0.1499	5660	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	2.1864	0.2179	0.5996	0.8545	0.1259	1.0035	-0.0126	-0.187	0.0823	0.1254	-0.0866	-0.1132	-0.1078	0.2472	0.0013	0.2168	-0.0265	-0.0139	0.144	0.0225	0.1815	111.3275	29.8806	34.582
2	1.6221	0.2838	0.3409	1.029	-0.2172	1.2267	-0.0311	-0.1329	0.0928	0.1769	-0.0194	0.0418	-0.0789	0.0653	0.049	0.2183	-0.02	0.0165	0.1503	0.011	0.1548	102.746	27.8649	35.4446
3	1.5824	0.6707	0.1114	1.4763	0.3348	1.6573	-0.085	-0.0527	-0.0412	-0.0419	-0.0311	0.0494	0.0932	-0.061	0.1145	0.1995	-0.0076	0.032	0.1483	0.0327	0.1764	98.5891	21.0653	28.5721
4	1.1521	-0.2925	-0.3415	1.157	0.2472	1.5588	-0.0351	0.047	0.0667	0.0528	0.0063	0.1307	-0.032	-0.0757	0.0364	0.1977	-0.013	0.0241	0.1729	0.0226	0.1986	94.5878	26.9328	26.5061
5	1.8418	-0.4518	0.0722	1.5185	0.0208	1.485	-0.0301	0.3569	0.0944	-0.084	-0.039	0.0277	0.0457	0.0062	0.0597	0.1582	-0.0324	0.0201	0.2013	0.0414	0.1394	101.7285	26.5396	12.4265
6	1.9655	0.123	-0.3115	0.7691	0.0731	1.8096	0.0329	0.1324	0.1886	0.0295	-0.0126	-0.1097	-0.1184	0.1652	-0.0304	0.1688	-0.0315	0.0052	0.2015	0.0538	0.1679	112.0844	30.0103	21.9735
7	2.2622	0.7325	0.0533	4.1829	1.8882	2.9604	-0.0235	-0.2928	-0.1193	0.2364	-0.0265	0.1336	0.2708	-0.4989	0.0305	0.2825	0.0075	0.0616	0.3165	0.0411	0.2039	71.7205	33.9259	25.0482
8	0.9553	-0.2823	-0.0416	1.2892	0.4772	2.3746	0.0396	0.0943	-0.2024	0.0625	-0.0706	0.0974	0.2517	-0.3191	0.0041	0.1867	-0.0114	0.0382	0.2279	-0.0451	0.2194	73.8854	29.7415	7.6758
9	0.9653	0.1853	0.1802	2.0982	1.0195	1.8613	0.063	0.188	-0.0769	-0.2419	-0.0385	-0.0008	-0.1803	-0.2877	-0.0192	0.1855	0.0561	0.034	0.2402	-0.03	0.1723	74.8989	40.2599	3.1781
10	4.3152	-0.3988	-0.5249	2.9573	-0.3423	2.668	0.1704	0.6571	0.608	-0.306	-0.0689	0.002	-0.5449	-0.3167	-0.072	0.3719	0.0957	0.062	0.2183	-0.0103	0.1954	78.1983	55.1983	4.582
11	2.9924	-1.2931	0.4488	2.2094	-0.2315	1.3908	0.0518	-0.0555	0.2417	-0.1026	0.0025	-0.0917	-0.4083	-0.2751	-0.0384	0.2743	0.0939	0.0587	0.2046	-0.0305	0.1977	77.9563	53.8803	15.0551
12	1.0853	-0.0818	-0.4081	2.1167	0.483	1.8342	-0.0562	-0.0065	0.0214	0.1086	0.0036	0.123	-0.085	-0.3811	0.0423	0.1791	0.0537	0.0468	0.2223	-0.0166	0.1597	74.9036	42.573	19.7144
13	0.8049	-0.1344	0.1629	1.5091	0.1095	0.5727	-0.0061	-0.1402	0.3568	0.0385	0.2309	-0.8245	-0.119	0.3687	-0.185	0.2277	-0.0131	0.0492	0.3363	-0.123	0.4724	84.3712	79.5849	39.5893
14	0.8788	-0.2182	-0.3483	1.9716	0.9072	1.2153	0.04	-0.1305	0.1527	-0.0226	0.1382	-0.4701	0.0009	0.3108	-0.1231	0.189	0.0617	0.0264	0.2861	-0.0706	0.3027	80.8338	69.4021	35.8996
15	2.9072	-2.0594	2.5056	3.0972	-3.2185	6.2384	0.0947	0.0628	-0.0905	-0.2029	-0.0527	0.0069	0.3883	0.0801	-0.0624	0.2221	0.059	0.0383	0.1765	-0.0484	0.201	68.2262	62.205	31.0188
16	2.1365	0.6373	0.2235	1.6352	2.5081	4.2388	0.0507	-0.2205	-0.1796	0.4071	0.1499	-0.5638	0.5627	0.3412	-0.1693	0.2751	0.1383	-0.0502	0.3162	-0.0346	0.3021	82.8339	59.2327	43.8755
17	1.6057	-0.4233	-0.1238	1.3997	-0.3924	0.5546	0.0407	-0.1203	0.0262	0.0655	0.0095	-0.1249	0.0646	0.1135	-0.0407	0.204	0.0445	0.0047	0.2072	-0.0482	0.2064	67.8973	70.1541	40.8758
18	2.0133	-0.1002	0.0828	1.9203	-0.6308	3.1783	0.103	-0.0136	-0.0259	0.013	-0.0055	0.1946	0.2385	-0.2049	-0.1128	0.2102	0.0345	0.0204	0.1735	-0.035	0.2168	57.182	70.8344	37.3965
19	1.6387	0.4242	-0.1359	2.3226	-0.19	2.6041	0.1097	-0.075	0.1439	-0.0392	-0.0659	0.069	-0.1154	-0.0855	-0.0948	0.1928	0.0366	0.043	0.1709	-0.0443	0.2083	61.1064	80.4229	39.6082
20	1.6789	-0.6452	0.0839	2.8549	0.5229	0.7745	0.0425	-0.0751	0.2277	-0.0128	0.1458	-0.3493	-0.1406	0.1906	-0.1782	0.1738	0.002	0.0541	0.2216	-0.074	0.2822	73.2904	82.639	40.6511

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 4:33 )	A	4 - 33
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 34:88 )	A	34 - 88
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 89:115 )	A	89 - 115
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 116:168 )	A	116 - 168
5	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 169:243 )	A	169 - 243
6	X-RAY DIFFRACTION	6	( CHAIN A AND RESID 244:274 )	A	244 - 274
7	X-RAY DIFFRACTION	7	( CHAIN B AND RESID 1:25 )	B	1 - 25
8	X-RAY DIFFRACTION	8	( CHAIN B AND RESID 26:88 )	B	26 - 88
9	X-RAY DIFFRACTION	9	( CHAIN B AND RESID 89:187 )	B	89 - 187
10	X-RAY DIFFRACTION	10	( CHAIN B AND RESID 188:212 )	B	188 - 212
11	X-RAY DIFFRACTION	11	( CHAIN B AND RESID 213:243 )	B	213 - 243
12	X-RAY DIFFRACTION	12	( CHAIN B AND RESID 244:274 )	B	244 - 274
13	X-RAY DIFFRACTION	13	( CHAIN C AND RESID 3:33 )	C	3 - 33
14	X-RAY DIFFRACTION	14	( CHAIN C AND RESID 34:115 )	C	34 - 115
15	X-RAY DIFFRACTION	15	( CHAIN C AND RESID 116:131 )	C	116 - 131
16	X-RAY DIFFRACTION	16	( CHAIN C AND RESID 132:146 )	C	132 - 146
17	X-RAY DIFFRACTION	17	( CHAIN C AND RESID 147:187 )	C	147 - 187
18	X-RAY DIFFRACTION	18	( CHAIN C AND RESID 188:212 )	C	188 - 212
19	X-RAY DIFFRACTION	19	( CHAIN C AND RESID 213:243 )	C	213 - 243
20	X-RAY DIFFRACTION	20	( CHAIN C AND RESID 244:274 )	C	244 - 274

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Yorodumi