PDB-3u37: An Acetyl Xylan Esterase (Est2A) from the Rumen Bacterium Butyriv...

ID or keywords:

Entry

Database: PDB / ID: 3u37

Title

An Acetyl Xylan Esterase (Est2A) from the Rumen Bacterium Butyrivibrio proteoclasticus.

Components

Acetyl-xylan esterase Est2A

Keywords

HYDROLASE

Function / homology

Function and homology information

carboxylic ester hydrolase activity
Similarity search - Function

Biological species

Butyrivibrio proteoclasticus B316 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Till, M. / Arcus, V.

Citation

Journal: Proteins / Year: 2013
Title: Structure and function of an acetyl xylan esterase (Est2A) from the rumen bacterium Butyrivibrio proteoclasticus.
Authors: Till, M. / Goldstone, D.C. / Attwood, G.T. / Moon, C.D. / Kelly, W.J. / Arcus, V.L.

History

Deposition	Oct 5, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 13, 2013	Provider: repository / Type: Initial release
Revision 1.1	Apr 17, 2013	Group: Database references
Revision 1.2	Feb 28, 2024	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 / struct_ncs_dom_lim / 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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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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Download

PDBx/mmCIF format	3u37.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb3u37.ent.gz	962.9 KB	Display	PDB format
PDBx/mmJSON format	3u37.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3u37_validation.pdf.gz	538.5 KB	Display	wwPDB validaton report
Full document	3u37_full_validation.pdf.gz	589.7 KB	Display
Data in XML	3u37_validation.xml.gz	114.4 KB	Display
Data in CIF	3u37_validation.cif.gz	159 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/u3/3u37 ftp://data.pdbj.org/pub/pdb/validation_reports/u3/3u37	HTTPS FTP

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Related structure data

Related structure data	4devC C: citing same article (ref.)
Similar structure data	4dev-2 4dev-1 1z0b-1 5jmo-d 5vg3-d 1z0w-1 1z0c-1 6bba-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) 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

4devC

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#4 - Apr 2000 Collagen similarity (1) #116 - Aug 2009 Sulfotransferases similarity (1)

Deposited unit

A: Acetyl-xylan esterase Est2A

B: Acetyl-xylan esterase Est2A

C: Acetyl-xylan esterase Est2A

D: Acetyl-xylan esterase Est2A

E: Acetyl-xylan esterase Est2A

F: Acetyl-xylan esterase Est2A

G: Acetyl-xylan esterase Est2A

H: Acetyl-xylan esterase Est2A

hetero molecules

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

1

A: Acetyl-xylan esterase Est2A

B: Acetyl-xylan esterase Est2A

C: Acetyl-xylan esterase Est2A

D: Acetyl-xylan esterase Est2A

hetero molecules

defined by author
185 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

E: Acetyl-xylan esterase Est2A

F: Acetyl-xylan esterase Est2A

G: Acetyl-xylan esterase Est2A

H: Acetyl-xylan esterase Est2A

hetero molecules

defined by author
185 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

A: Acetyl-xylan esterase Est2A

C: Acetyl-xylan esterase Est2A

hetero molecules

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

4

B: Acetyl-xylan esterase Est2A

D: Acetyl-xylan esterase Est2A

hetero molecules

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

5

E: Acetyl-xylan esterase Est2A

G: Acetyl-xylan esterase Est2A

hetero molecules

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

6

F: Acetyl-xylan esterase Est2A

H: Acetyl-xylan esterase Est2A

hetero molecules

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

Unit cell

Length a, b, c (Å)	96.128, 90.282, 99.175
Angle α, β, γ (deg.)	99.80, 90.21, 92.56
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / Refine code: _

Dom-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	TRP	TRP	A	A	3 - 374	35 - 406
2	1	TRP	TRP	B	B	3 - 374	35 - 406
1	2	TRP	TRP	A	A	3 - 374	35 - 406
2	2	TRP	TRP	C	C	3 - 374	35 - 406
1	3	TRP	TRP	A	A	3 - 374	35 - 406
2	3	TRP	TRP	D	D	3 - 374	35 - 406
1	4	PHE	PHE	A	A	3 - 375	35 - 407
2	4	PHE	PHE	E	E	3 - 375	35 - 407
1	5	PHE	PHE	A	A	3 - 375	35 - 407
2	5	PHE	PHE	F	F	3 - 375	35 - 407
1	6	TRP	TRP	A	A	3 - 374	35 - 406
2	6	TRP	TRP	G	G	3 - 374	35 - 406
1	7	TRP	TRP	A	A	3 - 374	35 - 406
2	7	TRP	TRP	H	H	3 - 374	35 - 406
1	8	GLU	GLU	B	B	3 - 376	35 - 408
2	8	GLU	GLU	C	C	3 - 376	35 - 408
1	9	GLU	GLU	B	B	3 - 376	35 - 408
2	9	GLU	GLU	D	D	3 - 376	35 - 408
1	10	TRP	TRP	B	B	3 - 374	35 - 406
2	10	TRP	TRP	E	E	3 - 374	35 - 406
1	11	TRP	TRP	B	B	3 - 374	35 - 406
2	11	TRP	TRP	F	F	3 - 374	35 - 406
1	12	GLU	GLU	B	B	3 - 376	35 - 408
2	12	GLU	GLU	G	G	3 - 376	35 - 408
1	13	PHE	PHE	B	B	3 - 375	35 - 407
2	13	PHE	PHE	H	H	3 - 375	35 - 407
1	14	GLU	GLU	C	C	3 - 376	35 - 408
2	14	GLU	GLU	D	D	3 - 376	35 - 408
1	15	TRP	TRP	C	C	3 - 374	35 - 406
2	15	TRP	TRP	E	E	3 - 374	35 - 406
1	16	TRP	TRP	C	C	3 - 374	35 - 406
2	16	TRP	TRP	F	F	3 - 374	35 - 406
1	17	GLU	GLU	C	C	3 - 376	35 - 408
2	17	GLU	GLU	G	G	3 - 376	35 - 408
1	18	PHE	PHE	C	C	3 - 375	35 - 407
2	18	PHE	PHE	H	H	3 - 375	35 - 407
1	19	TRP	TRP	D	D	3 - 374	35 - 406
2	19	TRP	TRP	E	E	3 - 374	35 - 406
1	20	TRP	TRP	D	D	3 - 374	35 - 406
2	20	TRP	TRP	F	F	3 - 374	35 - 406
1	21	GLU	GLU	D	D	3 - 376	35 - 408
2	21	GLU	GLU	G	G	3 - 376	35 - 408
1	22	PHE	PHE	D	D	3 - 375	35 - 407
2	22	PHE	PHE	H	H	3 - 375	35 - 407
1	23	PHE	PHE	E	E	3 - 375	35 - 407
2	23	PHE	PHE	F	F	3 - 375	35 - 407
1	24	TRP	TRP	E	E	3 - 374	35 - 406
2	24	TRP	TRP	G	G	3 - 374	35 - 406
1	25	TRP	TRP	E	E	3 - 374	35 - 406
2	25	TRP	TRP	H	H	3 - 374	35 - 406
1	26	TRP	TRP	F	F	3 - 374	35 - 406
2	26	TRP	TRP	G	G	3 - 374	35 - 406
1	27	TRP	TRP	F	F	3 - 374	35 - 406
2	27	TRP	TRP	H	H	3 - 374	35 - 406
1	28	PHE	PHE	G	G	3 - 375	35 - 407
2	28	PHE	PHE	H	H	3 - 375	35 - 407

NCS ensembles :

#1: Protein	Acetyl-xylan esterase Est2A Mass: 46258.855 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Butyrivibrio proteoclasticus B316 (bacteria) Strain: ATCC 51982 / DSM 14932 / B316 / Gene: est2A, bpr_I2939 / Plasmid: pDest17 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: E0RVY7
#2: Chemical	ChemComp-ACY / ACETIC ACID Mass: 60.052 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₂H₄O₂
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1140 / 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: 2.49 Å³/Da / Density % sol: 50.65 %
Crystal grow	Temperature: 291 K / pH: 4.6 Details: 8% (w/v) PEG 4000, 0.1 M Sodium acetate pH 4.6. , VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9756
Detector	Type: ADSC QUANTUM 315r / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9756 Å / Relative weight: 1
Reflection	Resolution: 2.1→24.856 Å / Num. obs: 171075

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
SHARP		phasing
REFMAC	5	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.1→24.856 Å / Cor.coef. F_o:F_c: 0.939 / Cor.coef. F_o:F_c free: 0.913 / SU B: 13.082 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.287 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.242	8623	5 %	RANDOM
R_work	0.206	-	-	-
obs	0.208	162452	89.3 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 30.939 Å²

	B_aniso -1	B_aniso -2
1-	0 Å²	0 Å²
2-	-	0 Å²
3-	-	-

Refinement step

Cycle: LAST / Resolution: 2.1→24.856 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	23675	0	46	1140	24861

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.02	24262
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.17	1.945	32842
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.817	5	2982
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.571	24.992	1198
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.859	15	4111
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.243	15	112
X-RAY DIFFRACTION	r_chiral_restr	0.078	0.2	3492
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	18732
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

LS refinement shell

Resolution: 2.1→2.15 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.313	535	-
R_work	0.287	10508	-
obs	-	-	78.58 %

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	0.4668	-0.1118	-0.1453	0.2995	0.0309	0.2934	-0.0561	-0.0053	-0.0453	-0.0114	0.0731	-0.0343	0.0753	-0.1012	-0.0171	0.12	-0.0284	0.0355	0.0608	-0.0023	0.11	-16.7891	-21.4631	10.4237
2	0.5233	0.1725	-0.08	0.2889	-0.0773	0.2526	-0.05	0.0708	-0.0603	0.009	0.0271	0.0176	0.0446	0.0858	0.0228	0.1046	0.0216	0.0439	0.0743	-0.0279	0.0939	16.4431	-16.7559	-17.1758
3	0.5425	0.4143	-0.0921	0.6185	-0.3776	0.8366	-0.0575	-0.1326	0.1698	-0.0239	0.0342	0.0833	-0.1465	-0.1155	0.0234	0.1563	0.0493	0.0107	0.0939	-0.0649	0.1214	-11.4747	14.8006	21.5348
4	0.3807	-0.2452	-0.1422	0.2648	0.1515	0.8982	-0.0501	0.0937	0.1579	0.0688	-0.016	-0.0599	-0.1202	0.1009	0.0661	0.1534	-0.0454	-0.0164	0.0622	0.047	0.1533	11.1198	21.1992	-15.2719
5	0.5823	-0.1644	0.2072	0.3857	-0.0363	0.1943	-0.0755	-0.0253	0.0685	0.0173	0.0411	0.0048	-0.0447	0.0621	0.0344	0.0857	-0.0145	-0.0042	0.1085	-0.007	0.0658	64.2314	-3.4582	63.8353
6	0.4065	0.1188	0.1661	0.3104	0.0577	0.2954	-0.0571	0.0187	0.0501	0.001	0.0604	-0.0045	-0.0476	-0.0566	-0.0033	0.0874	0.0131	0.0022	0.08	0.0167	0.096	31.1601	1.0106	36.1011
7	0.4291	0.1717	0.233	0.2701	0.1876	0.8688	-0.0094	-0.0896	-0.1848	-0.0447	0.0516	-0.0494	0.0791	0.0426	-0.0422	0.0987	0.0212	0.0291	0.0751	0.0444	0.1376	59.0031	-41.4776	61.991
8	0.3685	-0.2281	0.0622	0.4063	-0.332	0.5773	-0.046	0.0787	-0.1127	-0.0369	0.0695	0.0496	0.119	-0.0913	-0.0235	0.1281	-0.0574	0.0209	0.077	-0.0356	0.1114	36.635	-35.2646	25.1557

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 375
2	X-RAY DIFFRACTION	2	B	3 - 376
3	X-RAY DIFFRACTION	3	C	3 - 376
4	X-RAY DIFFRACTION	4	D	3 - 376
5	X-RAY DIFFRACTION	5	E	3 - 375
6	X-RAY DIFFRACTION	6	F	3 - 375
7	X-RAY DIFFRACTION	7	G	3 - 376
8	X-RAY DIFFRACTION	8	H	2 - 376

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