PDB-4oy7: Structure of cellulose active LPMO CelS2 (ScLPMO10C) in complex w...

ID or keywords:

Entry

Database: PDB / ID: 4oy7

Title

Structure of cellulose active LPMO CelS2 (ScLPMO10C) in complex with Copper.

Components

Putative secreted cellulose binding protein

Keywords

OXIDOREDUCTASE / LPMO / AA10 / CBM33 / PMO / GH61 / cellulose degradation / copper monooxygenase

Function / homology

Function and homology information

xyloglucan metabolic process /

polysaccharide binding / hydrolase activity, hydrolyzing O-glycosyl compounds /

metal ion binding
Similarity search - Function

Biological species

Streptomyces coelicolor (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.5 Å

Authors

Forsberg, Z. / Mackenzie, A.K. / Sorlie, M. / Rohr, A.K. / Helland, R. / Arvai, A.S. / Vaaje-Kolstad, G. / Eijsink, V.G.H.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structural and functional characterization of a conserved pair of bacterial cellulose-oxidizing lytic polysaccharide monooxygenases.
Authors: Forsberg, Z. / Mackenzie, A.K. / Srlie, M. / Rhr, A.K. / Helland, R. / Arvai, A.S. / Vaaje-Kolstad, G. / Eijsink, V.G.

History

Deposition	Feb 11, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 28, 2014	Provider: repository / Type: Initial release
Revision 1.1	Jun 25, 2014	Group: Database references
Revision 1.2	Feb 4, 2015	Group: Derived calculations
Revision 1.3	Dec 27, 2023	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / pdbx_validate_close_contact / refine_hist / struct_conn / struct_keywords / struct_ncs_dom_lim / symmetry Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _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_conn.ptnr2_label_seq_id / _struct_keywords.text / _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 / _symmetry.Int_Tables_number

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oy/4oy7 ftp://data.pdbj.org/pub/pdb/validation_reports/oy/4oy7	HTTPS FTP

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Related structure data

Related structure data	4oy6C 4oy8C C: citing same article (ref.)
Similar structure data	4k19-2 6bp1-d 6t5u-2 3b3a-d 3pir-d 1p2s-d 5uk9-2 6p8x-3 6p8w-2 3tgp-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) 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

4oy6C

4oy8C

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	#141 - Sep 2011 O-GlcNAc Transferase similarity (1)

Deposited unit

A: Putative secreted cellulose binding protein

B: Putative secreted cellulose binding protein

C: Putative secreted cellulose binding protein

D: Putative secreted cellulose binding protein

E: Putative secreted cellulose binding protein

F: Putative secreted cellulose binding protein

G: Putative secreted cellulose binding protein

H: Putative secreted cellulose binding protein

hetero molecules

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

1

A: Putative secreted cellulose binding protein

hetero molecules

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

2

B: Putative secreted cellulose binding protein

hetero molecules

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

3

C: Putative secreted cellulose binding protein

hetero molecules

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

4

D: Putative secreted cellulose binding protein

hetero molecules

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

5

E: Putative secreted cellulose binding protein

hetero molecules

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

6

F: Putative secreted cellulose binding protein

hetero molecules

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

7

G: Putative secreted cellulose binding protein

hetero molecules

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

8

H: Putative secreted cellulose binding protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	83.858, 122.856, 156.000
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F
7	1	G
8	1	H

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 5 / Auth seq-ID: 35 - 228 / Label seq-ID: 1 - 194

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B
3	C	C
4	D	D
5	E	E
6	F	F
7	G	G
8	H	H

NCS oper:

ID	Code	Matrix	Vector
1	given	(1), (1), (1)
2	given	(-0.99999, -0.004215, 0.001457), (0.004212, -0.999989, -0.001931), (0.001465, -0.001925, 0.999997)	37.05206, 122.92495, 0.06527
3	given	(-0.654417, 0.756082, 0.008784), (0.75613, 0.654407, 0.004397), (-0.002424, 0.00952, -0.999952)	-12.8764, 3.25605, 93.13166
4	given	(0.649294, -0.760482, 0.009187), (-0.76053, -0.649294, 0.003397), (0.003382, -0.009193, -0.999952)	49.6431, 119.10192, 94.15599
5	given	(-0.066242, 0.997799, 0.002938), (-0.997461, -0.066142, -0.026408), (-0.026156, -0.00468, 0.999647)	-40.40804, 86.50828, 0.93836
6	given	(0.067441, -0.997718, 0.00336), (0.997385, 0.06733, -0.026267), (0.025981, 0.005122, 0.999649)	79.73208, 41.59645, -0.66123
7	given	(0.79503, 0.606567, 0.0017), (0.606132, -0.79456, 0.035763), (0.023044, -0.027403, -0.999359)	-36.25828, 95.81179, 95.0377
8	given	(-0.788612, -0.614891, 8.3E-5), (-0.614378, 0.78796, 0.040719), (-0.025103, 0.032061, -0.999171)	75.85928, 27.07233, 92.67082

#1: Protein	Putative secreted cellulose binding protein / ScLPMO10C Mass: 20996.857 Da / Num. of mol.: 8 / Fragment: UNP residues 35-230 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: A3(2) / Gene: SCO1188 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9RJY2
#2: Chemical	ChemComp-CU / COPPER (II) ION / Copper Mass: 63.546 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cu
#3: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1922 / 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: 2.39 Å³/Da / Density % sol: 48.58 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 9 % w/v PEG 10K, 0.1 M sodium citrate, 0.1 M calcium acetate, 5 % v/v glycerol

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.98 Å
Detector	Type: RAYONIX MX-225 / Detector: CCD / Date: Nov 27, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 1.5→47.9 Å / Num. obs: 254063 / % possible obs: 99.1 % / Redundancy: 3.9 % / R_merge(I) obs: 0.103 / R_sym value: 0.103 / Net I/σ(I): 5.9
Reflection shell	Resolution: 1.5→1.58 Å / Redundancy: 2.7 % / R_merge(I) obs: 0.54 / Mean I/σ(I) obs: 1.7 / % possible all: 94.2

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Processing

Software

Name: REFMAC / Version: 5.7.0032 / Classification: refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.5→47.9 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.95 / SU B: 2.928 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22238	12750	5 %	RANDOM
R_work	0.19374	-	-	-
obs	0.19517	241168	99.05 %	-

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: 10.646 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.17 Å²	0 Å²	0 Å²
2-	-	-0.15 Å²	-0 Å²
3-	-	-	0.32 Å²

Refinement step

Cycle: 1 / Resolution: 1.5→47.9 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11833	0	12	1922	13767

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.019	12374
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	10629
X-RAY DIFFRACTION	r_angle_refined_deg	1.385	1.931	16989
X-RAY DIFFRACTION	r_angle_other_deg	0.792	3.003	24491
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.316	5	1597
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.15	23.975	571
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.331	15	1608
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.818	15	64
X-RAY DIFFRACTION	r_chiral_restr	0.083	0.2	1732
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	14743
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3009
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	0.3	0.527	6343
X-RAY DIFFRACTION	r_mcbond_other	0.299	0.527	6342
X-RAY DIFFRACTION	r_mcangle_it	0.515	0.789	7946
X-RAY DIFFRACTION	r_mcangle_other	0.516	0.79	7947
X-RAY DIFFRACTION	r_scbond_it	0.434	0.55	6031
X-RAY DIFFRACTION	r_scbond_other	0.434	0.55	6032
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	0.666	0.814	9041
X-RAY DIFFRACTION	r_long_range_B_refined	4.504	5.752	16056
X-RAY DIFFRACTION	r_long_range_B_other	4.198	4.789	14916
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	1102	MEDIUM POSITIONAL	0.14	0.5
2	B	1102	MEDIUM POSITIONAL	0.13	0.5
3	C	1102	MEDIUM POSITIONAL	0.17	0.5
4	D	1102	MEDIUM POSITIONAL	0.14	0.5
5	E	1102	MEDIUM POSITIONAL	0.14	0.5
6	F	1102	MEDIUM POSITIONAL	0.17	0.5
7	G	1102	MEDIUM POSITIONAL	0.19	0.5
8	H	1102	MEDIUM POSITIONAL	0.19	0.5
1	A	1618	LOOSE POSITIONAL	0.36	5
2	B	1618	LOOSE POSITIONAL	0.3	5
3	C	1618	LOOSE POSITIONAL	0.35	5
4	D	1618	LOOSE POSITIONAL	0.39	5
5	E	1618	LOOSE POSITIONAL	0.32	5
6	F	1618	LOOSE POSITIONAL	0.28	5
7	G	1618	LOOSE POSITIONAL	0.39	5
8	H	1618	LOOSE POSITIONAL	0.37	5
1	A	1102	MEDIUM THERMAL	0.6	2
2	B	1102	MEDIUM THERMAL	0.57	2
3	C	1102	MEDIUM THERMAL	0.68	2
4	D	1102	MEDIUM THERMAL	0.78	2
5	E	1102	MEDIUM THERMAL	0.64	2
6	F	1102	MEDIUM THERMAL	0.73	2
7	G	1102	MEDIUM THERMAL	1.32	2
8	H	1102	MEDIUM THERMAL	0.82	2
1	A	1618	LOOSE THERMAL	0.68	10
2	B	1618	LOOSE THERMAL	0.67	10
3	C	1618	LOOSE THERMAL	0.75	10
4	D	1618	LOOSE THERMAL	0.91	10
5	E	1618	LOOSE THERMAL	0.75	10
6	F	1618	LOOSE THERMAL	0.75	10
7	G	1618	LOOSE THERMAL	1.18	10
8	H	1618	LOOSE THERMAL	0.87	10

LS refinement shell

Resolution: 1.5→1.54 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.357	868	-
R_work	0.321	16080	-
obs	-	-	90.26 %

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	0.4647	-0.0535	0.0389	0.9843	0.0994	1.3238	-0.0107	0.0205	-0.0274	-0.071	-0.0344	-0.0741	-0.1075	0.0595	0.0451	0.0146	-0.0025	-0.0021	0.0054	0.0061	0.0344	32.0326	41.4435	66.443
2	0.4781	-0.0284	-0.0419	0.7241	-0.0025	1.3729	-0.014	0.0196	0.0136	-0.0369	-0.0207	0.0776	0.0762	-0.0722	0.0347	0.0126	-0.0019	-0.0017	0.0055	-0.0049	0.03	4.7824	81.383	66.5263
3	0.7139	0.0222	-0.018	0.7822	-0.0081	1.1433	0.0162	-0.0795	0.0214	0.0263	-0.0126	0.0957	-0.0812	-0.0322	-0.0036	0.0201	-0.0051	0.0038	0.0217	-0.0046	0.0255	-0.4362	58.7102	27.2353
4	0.6876	0.0154	-0.0152	0.8804	0.1125	1.4561	0.0018	-0.0687	-0.0195	0.0503	0.0112	-0.1035	0.1146	0.0368	-0.013	0.0252	-0.0018	-0.0111	0.0119	0.0013	0.0305	47.5265	64.0611	27.267
5	0.5769	0.0769	0.0595	0.4975	0.1715	0.9033	-0.0115	0.0367	0.0411	-0.0269	-0.0107	-0.0365	-0.0224	0.0085	0.0222	0.0025	-0.0004	-0.0025	0.0031	0.0056	0.022	38.3878	74.9269	66.9219
6	0.6245	0.1006	0.039	0.6022	-0.2516	0.9355	-0.0123	0.0433	-0.0338	-0.0368	-0.0077	0.0343	0.0285	0.0175	0.02	0.0064	-0.0006	0.0007	0.004	-0.0057	0.0229	-1.5752	47.956	66.9676
7	0.5268	-0.2977	-0.0742	0.9096	-0.2442	1.1309	-0.0243	-0.0319	0.0967	0.0648	-0.0036	-0.0632	-0.0549	0.0369	0.0279	0.0148	0.0076	-0.0052	0.0207	-0.0002	0.0467	20.6856	85.3969	26.7314
8	0.6919	-0.2217	0.2067	1.0968	0.2201	1.2567	-0.0204	-0.0638	-0.0837	0.1178	-0.0038	0.0254	0.0184	-0.0647	0.0243	0.0205	0.0044	-0.0027	0.0259	-0.0004	0.0294	26.3688	37.4888	26.737
9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	-0	0.2591	-0.1541	-0.0923	0.2384	0.0776	0.2664	38.8293	50.2754	75.672
10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	-0	0.1219	-0.0798	0.0329	0.2542	-0.0363	0.1452	-1.984	72.5455	75.822
11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	-0	0.1551	-0.025	-0.0407	0.1026	-0.0192	0.1179	1.765	69.7623	18.0823
12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	-0	0.2807	-0.0231	0.0443	0.0887	-0.0091	0.1001	45.1133	53.1015	18.0853
13	0	0	0	0	0	0	0	0	0	0	0	0	0	0	-0	0.1791	0.023	-0.0294	0.0614	-0.0208	0.078	28.9932	81.2159	75.89
14	0	0	0	0	0	0	0	0	0	0	0	0	0	0	-0	0.0967	0.0219	0.0105	0.104	-0.0006	0.0293	7.803	41.668	75.909
15	0	0	0	0	0	0	0	0	0	0	0	0	0	0	-0	0.0208	0.0066	-0.0019	0.0766	0.0467	0.0404	31.6102	82.3779	17.9863
16	0	0	0	0	0	0	0	0	0	0	0	0	0	0	-0	0.0433	-0.0097	-0.0134	0.0766	-0.0371	0.0392	15.4481	40.4819	17.9803

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	35 - 230
2	X-RAY DIFFRACTION	2	B	35 - 230
3	X-RAY DIFFRACTION	3	C	35 - 230
4	X-RAY DIFFRACTION	4	D	35 - 230
5	X-RAY DIFFRACTION	5	E	35 - 229
6	X-RAY DIFFRACTION	6	F	35 - 229
7	X-RAY DIFFRACTION	7	G	35 - 230
8	X-RAY DIFFRACTION	8	H	35 - 229
9	X-RAY DIFFRACTION	9	A	301
10	X-RAY DIFFRACTION	10	B	301
11	X-RAY DIFFRACTION	11	C	301
12	X-RAY DIFFRACTION	12	D	301
13	X-RAY DIFFRACTION	13	E	301
14	X-RAY DIFFRACTION	14	F	301
15	X-RAY DIFFRACTION	15	G	301
16	X-RAY DIFFRACTION	16	H	301

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