PDB-9tcy: Structure of an LPMO expressed in E.coli (LsAA9A) at 4.89x10^4 Gy

ID or keywords:

Entry

Database: PDB / ID: 9tcy

Title

Structure of an LPMO expressed in E.coli (LsAA9A) at 4.89x10^4 Gy

Components

Auxiliary activity 9

Keywords

OXIDOREDUCTASE / lytic polysaccharide monooxygenase / copper-binding enzyme / AA9 family

Function / homology

Function and homology information

lytic cellulose monooxygenase (C4-dehydrogenating) / cellulose catabolic process / monooxygenase activity / extracellular region / metal ion binding
Similarity search - Function

Biological species

Panus similis (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 1.85 Å

Authors

Wei, Q. / Huang, Z. / Lo Leggio, L.

Funding support

Denmark, 2items

Citation

Journal: Acta Crystallogr D Struct Biol / Year: 2026
Title: Experimental estimation of copper-site geometry reproducibility in biologically relevant redox and saccharide-bound states of a model lytic polysaccharide monooxygenase.
Authors: Huang, Z. / Wei, Q. / Nan, J. / Norholm, M.H.H. / Liu, Z. / Hernandez-Rollan, C. / Johansen, K.S. / Lo Leggio, L.

History

Deposition	Nov 22, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 5, 2026	Provider: repository / Type: Initial release
Revision 1.1	Aug 12, 2026	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9tcy.cif.gz	71.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9tcy.ent.gz		Display	PDB format
PDBx/mmJSON format	9tcy.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/tc/9tcy ftp://data.pdbj.org/pub/pdb/validation_reports/tc/9tcy	HTTPS FTP

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Related structure data

Related structure data	9tcvC 9tcxC 9tczC 9td0C 9td1C 9td6C 9td8C 9td9C 9tdbC 9tdcC 9tddC 9tdeC 9tdfC 9tdhC 9tdiC 9tdjC 9tdkC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

AAA: Auxiliary activity 9

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: homology

Unit cell

Length a, b, c (Å)	48.540, 48.540, 109.510
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	76
Space group name H-M	P4₁

#1: Protein	Auxiliary activity 9 / LsAA9A lytic polysaccharide monooxygenase Mass: 25259.832 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Panus similis (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0S2GKZ1
#2: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₂H₃O₂
#3: Chemical	ChemComp-CU / COPPER (II) ION Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 319 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.55 Å³/Da / Density % sol: 51.83 %
Crystal grow	Temperature: 278 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 20 mM sodium acetate pH 5.5, 150 mM sodium chloride

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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: 0.9763 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 2, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 1.84→44.42 Å / Num. obs: 21593 / % possible obs: 100 % / Redundancy: 12.3 % / CC_1/2: 0.994 / Net I/σ(I): 6.29
Reflection shell	Resolution: 1.85→1.9 Å / Num. unique obs: 1585 / CC_1/2: 0.627 / % possible all: 99.7

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Processing

Software

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

Refinement

Method to determine structure:

FOURIER SYNTHESIS / Resolution: 1.85→44.416 Å / Cor.coef. F_o:F_c: 0.963 / Cor.coef. F_o:F_c free: 0.947 / SU B: 4.526 / SU ML: 0.127 / Cross valid method: FREE R-VALUE / ESU R: 0.156 / ESU R Free: 0.147
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2383	1120	5.187 %
R_work	0.1924	20473	-
all	0.195	-	-
obs	-	21593	99.944 %

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: 24.514 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.984 Å²	0 Å²	0 Å²
2-	-	0.984 Å²	-0 Å²
3-	-	-	-1.967 Å²

Refinement step

Cycle: LAST / Resolution: 1.85→44.416 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1787	0	49	319	2155

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.013	1909
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	1683
X-RAY DIFFRACTION	r_angle_refined_deg	1.524	1.637	2635
X-RAY DIFFRACTION	r_angle_other_deg	1.333	1.569	3875
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.382	5	244
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.522	23.696	92
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	9.878	15	246
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.361	15	7
X-RAY DIFFRACTION	r_chiral_restr	0.066	0.2	254
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	2247
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	431
X-RAY DIFFRACTION	r_nbd_refined	0.193	0.2	401
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.191	0.2	1701
X-RAY DIFFRACTION	r_nbtor_refined	0.162	0.2	937
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.079	0.2	801
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.151	0.2	225
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.006	0.2	1
X-RAY DIFFRACTION	r_metal_ion_refined	0.028	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.294	0.2	9
X-RAY DIFFRACTION	r_nbd_other	0.263	0.2	38
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.143	0.2	16
X-RAY DIFFRACTION	r_mcbond_it	1.591	2.476	959
X-RAY DIFFRACTION	r_mcbond_other	1.506	2.457	951
X-RAY DIFFRACTION	r_mcangle_it	1.965	3.685	1192
X-RAY DIFFRACTION	r_mcangle_other	1.966	3.69	1193
X-RAY DIFFRACTION	r_scbond_it	2.031	2.645	950
X-RAY DIFFRACTION	r_scbond_other	2.03	2.647	951
X-RAY DIFFRACTION	r_scangle_it	2.762	3.924	1439
X-RAY DIFFRACTION	r_scangle_other	2.761	3.925	1440
X-RAY DIFFRACTION	r_lrange_it	4.629	31.127	2253
X-RAY DIFFRACTION	r_lrange_other	4.633	31.142	2254

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 (%)
1.85-1.898	0.373	96	0.33	1489	X-RAY DIFFRACTION	99.7483
1.898-1.95	0.309	78	0.295	1473	X-RAY DIFFRACTION	100
1.95-2.006	0.269	88	0.268	1417	X-RAY DIFFRACTION	99.9336
2.006-2.068	0.277	79	0.234	1376	X-RAY DIFFRACTION	100
2.068-2.136	0.261	70	0.233	1357	X-RAY DIFFRACTION	100
2.136-2.211	0.326	70	0.217	1318	X-RAY DIFFRACTION	100
2.211-2.294	0.322	62	0.212	1273	X-RAY DIFFRACTION	100
2.294-2.387	0.248	69	0.214	1184	X-RAY DIFFRACTION	100
2.387-2.493	0.318	53	0.204	1164	X-RAY DIFFRACTION	99.9179
2.493-2.615	0.281	63	0.193	1118	X-RAY DIFFRACTION	100
2.615-2.756	0.264	57	0.199	1055	X-RAY DIFFRACTION	100
2.756-2.922	0.402	32	0.214	1024	X-RAY DIFFRACTION	100
2.922-3.123	0.29	47	0.207	954	X-RAY DIFFRACTION	100
3.123-3.372	0.218	54	0.184	864	X-RAY DIFFRACTION	100
3.372-3.692	0.194	47	0.158	807	X-RAY DIFFRACTION	100
3.692-4.125	0.177	46	0.134	730	X-RAY DIFFRACTION	100
4.125-4.758	0.122	35	0.108	651	X-RAY DIFFRACTION	100
4.758-5.813	0.187	33	0.149	545	X-RAY DIFFRACTION	100
5.813-8.164	0.231	26	0.188	432	X-RAY DIFFRACTION	100
8.164-44.416	0.17	15	0.228	242	X-RAY DIFFRACTION	99.2278

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