PDB-8b48: Structure of Lentithecium fluviatile carbohydrate esterase from t...

ID or keywords:

Entry

Database: PDB / ID: 8b48

Title

Structure of Lentithecium fluviatile carbohydrate esterase from the CE15 family (LfCE15C)

Components

Carbohydrate esterase family 15 protein

Keywords

HYDROLASE / Lignocellulose degradation

Function / homology

Alpha/Beta hydrolase fold / FORMIC ACID / Carbohydrate esterase family 15 protein

Function and homology information

Biological species

Lentithecium fluviatile (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.65 Å

Authors

Scholzen, K. / Mazurkewich, S. / Poulsen, J.C.N. / Larsbrink, J. / Lo Leggio, L.

Funding support

Denmark, 2items

Citation

Journal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Structural and functional investigation of a fungal member of carbohydrate esterase family 15 with potential specificity for rare xylans.
Authors: Mazurkewich, S. / Scholzen, K.C. / Brusch, R.H. / Poulsen, J.C.N. / Theibich, Y. / Huttner, S. / Olsson, L. / Larsbrink, J. / Lo Leggio, L.

History

Deposition	Sep 20, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 7, 2023	Provider: repository / Type: Initial release
Revision 1.1	Feb 7, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8b48.cif.gz	314.8 KB	Display	PDBx/mmCIF format
PDB format	pdb8b48.ent.gz	245.2 KB	Display	PDB format
PDBx/mmJSON format	8b48.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8b48_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	8b48_full_validation.pdf.gz	1.7 MB	Display
Data in XML	8b48_validation.xml.gz	56.1 KB	Display
Data in CIF	8b48_validation.cif.gz	78.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b4/8b48 ftp://data.pdbj.org/pub/pdb/validation_reports/b4/8b48	HTTPS FTP

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Related structure data

Related structure data	3picS S: Starting model for refinement
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Carbohydrate esterase family 15 protein

B: Carbohydrate esterase family 15 protein

C: Carbohydrate esterase family 15 protein

D: Carbohydrate esterase family 15 protein

hetero molecules

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

1

A: Carbohydrate esterase family 15 protein

hetero molecules

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

2

B: Carbohydrate esterase family 15 protein

hetero molecules

defined by author
44.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Carbohydrate esterase family 15 protein

hetero molecules

defined by author
44.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Carbohydrate esterase family 15 protein

hetero molecules

defined by author
44.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	70.740, 79.570, 86.010
Angle α, β, γ (deg.)	113.322, 98.531, 94.440
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	2	A
4	2	C
5	3	A
6	3	D
7	4	B
8	4	C
9	5	B
10	5	D
11	6	C
12	6	D

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	SER	SER	LEU	LEU	A	A	20 - 389	4 - 373
2	2	1	SER	SER	LEU	LEU	B	B	20 - 389	4 - 373
3	3	2	SER	SER	LEU	LEU	A	A	20 - 389	4 - 373
4	4	2	SER	SER	LEU	LEU	C	C	20 - 389	4 - 373
5	5	3	CYS	CYS	GLY	GLY	A	A	21 - 388	5 - 372
6	6	3	CYS	CYS	GLY	GLY	D	D	21 - 388	5 - 372
7	7	4	SER	SER	LEU	LEU	B	B	20 - 389	4 - 373
8	8	4	SER	SER	LEU	LEU	C	C	20 - 389	4 - 373
9	9	5	CYS	CYS	GLY	GLY	B	B	21 - 388	5 - 372
10	10	5	CYS	CYS	GLY	GLY	D	D	21 - 388	5 - 372
11	11	6	CYS	CYS	GLY	GLY	C	C	21 - 388	5 - 372
12	12	6	CYS	CYS	GLY	GLY	D	D	21 - 388	5 - 372

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Carbohydrate esterase family 15 protein Mass: 43225.551 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lentithecium fluviatile (fungus) / Gene: K458DRAFT_349146 / Production host: Komagataella pastoris (fungus) / Strain (production host): SMD1168H / References: UniProt: A0A6G1IIU9

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Sugars , 3 types, 4 molecules

#2: Polysaccharide

alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...

Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1	WURCS	PDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}	LINUCS	PDB-CARE

#3: Polysaccharide

alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...

Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1	WURCS	PDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}	LINUCS	PDB-CARE

#4: Polysaccharide

alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...

Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DManpa1-3DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1	WURCS	PDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}	LINUCS	PDB-CARE

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Non-polymers , 2 types, 305 molecules

#5: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH₂O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 303 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.51 Å³/Da / Density % sol: 51.08 %
Crystal grow	Temperature: 277.15 K / Method: vapor diffusion, sitting drop Details: Protein stock: 13.7 mg/mL in 20 mM Tris pH 8.0 Reservoir: 0.2 M Ammonium formate pH 6.6, 20 %w/v PEG 3350 Drop: 3:1 protein to reservoir ratio

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.980779 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 1, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.980779 Å / Relative weight: 1
Reflection	Resolution: 2.65→47.254 Å / Num. obs: 47781 / % possible obs: 97.4 % / Redundancy: 3.8 % / CC_1/2: 0.982 / Net I/σ(I): 4.3
Reflection shell	Resolution: 2.65→2.72 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 1 / Num. unique obs: 3530 / CC_1/2: 0.513 / % possible all: 97.2

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3PIC

3pic

Resolution: 2.65→47.254 Å / Cor.coef. F_o:F_c: 0.932 / Cor.coef. F_o:F_c free: 0.874 / SU B: 29.729 / SU ML: 0.509 / Cross valid method: FREE R-VALUE / ESU R Free: 0.415
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2977	2294	4.801 %
R_work	0.2379	45487	-
all	0.241	-	-
obs	-	47781	97.626 %

Solvent computation

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

Displacement parameters

B_iso mean: 59.101 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	4.938 Å²	-2.676 Å²	5.124 Å²
2-	-	-2.868 Å²	-2.909 Å²
3-	-	-	-0.623 Å²

Refinement step

Cycle: LAST / Resolution: 2.65→47.254 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11382	0	250	303	11935

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.013	12005
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	11023
X-RAY DIFFRACTION	r_angle_refined_deg	1.448	1.674	16324
X-RAY DIFFRACTION	r_angle_other_deg	1.183	1.604	25502
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.225	5	1485
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.509	22.208	566
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.73	15	1844
X-RAY DIFFRACTION	r_dihedral_angle_other_3_deg	13.788	15	2
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.085	15	64
X-RAY DIFFRACTION	r_chiral_restr	0.057	0.2	1626
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	15318
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	2738
X-RAY DIFFRACTION	r_nbd_refined	0.199	0.2	2371
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.187	0.2	10583
X-RAY DIFFRACTION	r_nbtor_refined	0.164	0.2	5701
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.085	0.2	5665
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.169	0.2	338
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.091	0.2	5
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.203	0.2	28
X-RAY DIFFRACTION	r_nbd_other	0.28	0.2	93
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.193	0.2	10
X-RAY DIFFRACTION	r_mcbond_it	4.419	6.155	5922
X-RAY DIFFRACTION	r_mcbond_other	4.418	6.155	5923
X-RAY DIFFRACTION	r_mcangle_it	6.859	9.224	7398
X-RAY DIFFRACTION	r_mcangle_other	6.858	9.226	7399
X-RAY DIFFRACTION	r_scbond_it	4.583	6.565	6083
X-RAY DIFFRACTION	r_scbond_other	4.583	6.565	6079
X-RAY DIFFRACTION	r_scangle_it	7.042	9.702	8921
X-RAY DIFFRACTION	r_scangle_other	7.041	9.702	8922
X-RAY DIFFRACTION	r_lrange_it	11.823	117.419	50523
X-RAY DIFFRACTION	r_lrange_other	11.821	117.476	50444
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.07	0.05	12100
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.06	0.05	12150
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.055	0.05	12143
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.064	0.05	12166
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.066	0.05	12104
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.046	0.05	12136

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.07015	0.0501
1	2	B	X-RAY DIFFRACTION	Local ncs	0.07015	0.0501
2	3	A	X-RAY DIFFRACTION	Local ncs	0.06031	0.0501
2	4	C	X-RAY DIFFRACTION	Local ncs	0.06031	0.0501
3	5	A	X-RAY DIFFRACTION	Local ncs	0.05543	0.0501
3	6	D	X-RAY DIFFRACTION	Local ncs	0.05543	0.0501
4	7	B	X-RAY DIFFRACTION	Local ncs	0.06425	0.0501
4	8	C	X-RAY DIFFRACTION	Local ncs	0.06425	0.0501
5	9	B	X-RAY DIFFRACTION	Local ncs	0.06601	0.0501
5	10	D	X-RAY DIFFRACTION	Local ncs	0.06601	0.0501
6	11	C	X-RAY DIFFRACTION	Local ncs	0.04614	0.0501
6	12	D	X-RAY DIFFRACTION	Local ncs	0.04614	0.0501

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 (%)
2.65-2.719	0.484	182	0.455	3350	X-RAY DIFFRACTION	97.3271
2.719-2.793	0.459	190	0.41	3256	X-RAY DIFFRACTION	98.1487
2.793-2.874	0.384	140	0.4	3227	X-RAY DIFFRACTION	97.6791
2.874-2.962	0.383	144	0.366	3135	X-RAY DIFFRACTION	98.1737
2.962-3.059	0.423	155	0.332	3022	X-RAY DIFFRACTION	97.8442
3.059-3.167	0.376	151	0.303	2876	X-RAY DIFFRACTION	97.8978
3.167-3.286	0.369	155	0.286	2779	X-RAY DIFFRACTION	97.8652
3.286-3.42	0.349	134	0.276	2710	X-RAY DIFFRACTION	97.6648
3.42-3.572	0.347	135	0.26	2570	X-RAY DIFFRACTION	97.1275
3.572-3.746	0.346	130	0.252	2457	X-RAY DIFFRACTION	96.8914
3.746-3.948	0.246	109	0.219	2369	X-RAY DIFFRACTION	97.1765
3.948-4.186	0.236	99	0.19	2169	X-RAY DIFFRACTION	96.5928
4.186-4.475	0.27	109	0.173	2072	X-RAY DIFFRACTION	97.0196
4.475-4.832	0.203	104	0.172	1931	X-RAY DIFFRACTION	97.7426
4.832-5.291	0.211	79	0.152	1807	X-RAY DIFFRACTION	97.619
5.291-5.912	0.205	72	0.168	1634	X-RAY DIFFRACTION	98.442
5.912-6.82	0.208	64	0.16	1443	X-RAY DIFFRACTION	98.0481
6.82-8.336	0.203	77	0.145	1211	X-RAY DIFFRACTION	98.6217
8.336-11.722	0.167	45	0.157	956	X-RAY DIFFRACTION	98.8154
11.722-47.254	0.448	20	0.27	513	X-RAY DIFFRACTION	94.8399

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