PDB-9tcx: Structure of an LPMO expressed in E.coli (LsAA9A) at 7.00x10^4 Gy

ID or keywords:

Entry

Database: PDB / ID: 9tcx

Title

Structure of an LPMO expressed in E.coli (LsAA9A) at 7.00x10^4 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: 1.624 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	9tcx.cif.gz	75.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9tcx.ent.gz		Display	PDB format
PDBx/mmJSON format	9tcx.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/9tcx ftp://data.pdbj.org/pub/pdb/validation_reports/tc/9tcx	HTTPS FTP

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Related structure data

Related structure data	9tcvC 9tcyC 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 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)	48.885, 48.885, 109.648
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	76
Space group name H-M	P4₁

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Protein , 1 types, 1 molecules AAA

#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

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Non-polymers , 6 types, 406 molecules

#2: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 5 / 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.: 3 / Source method: obtained synthetically / Formula: SO₄
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 393 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.59 Å³/Da / Density % sol: 52.57 %
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 EIGER2 S 16M / Detector: PIXEL / Date: Feb 3, 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: 1.62→48.96 Å / Num. obs: 21896 / % possible obs: 92.6 % / Redundancy: 12.9 % / CC_1/2: 0.994 / Net I/σ(I): 7.5
Reflection shell	Resolution: 1.62→1.79 Å / Num. unique obs: 1095 / CC_1/2: 0.744 / % possible all: 71.5

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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: 1.624→48.96 Å / Cor.coef. F_o:F_c: 0.958 / Cor.coef. F_o:F_c free: 0.924 / SU B: 2.254 / SU ML: 0.076 / Cross valid method: FREE R-VALUE / ESU R: 0.137 / ESU R Free: 0.136
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2171	1048	4.786 %
R_work	0.1631	20848	-
all	0.166	-	-
obs	-	21896	67.587 %

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: 10.95 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.142 Å²	0 Å²	0 Å²
2-	-	0.142 Å²	0 Å²
3-	-	-	-0.283 Å²

Refinement step

Cycle: LAST / Resolution: 1.624→48.96 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1787	0	40	393	2220

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.013	1954
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	1727
X-RAY DIFFRACTION	r_angle_refined_deg	1.532	1.636	2705
X-RAY DIFFRACTION	r_angle_other_deg	1.347	1.572	3988
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.086	5	256
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.691	23.763	93
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.288	15	259
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.951	15	7
X-RAY DIFFRACTION	r_chiral_restr	0.07	0.2	261
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	2334
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	444
X-RAY DIFFRACTION	r_nbd_refined	0.21	0.2	387
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.193	0.2	1727
X-RAY DIFFRACTION	r_nbtor_refined	0.163	0.2	923
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.079	0.2	780
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.166	0.2	265
X-RAY DIFFRACTION	r_metal_ion_refined	0.036	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.285	0.2	14
X-RAY DIFFRACTION	r_nbd_other	0.289	0.2	57
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.184	0.2	34
X-RAY DIFFRACTION	r_mcbond_it	0.668	1.016	990
X-RAY DIFFRACTION	r_mcbond_other	0.627	1.001	984
X-RAY DIFFRACTION	r_mcangle_it	1.002	1.5	1245
X-RAY DIFFRACTION	r_mcangle_other	1.001	1.503	1246
X-RAY DIFFRACTION	r_scbond_it	0.942	1.101	964
X-RAY DIFFRACTION	r_scbond_other	0.877	1.077	953
X-RAY DIFFRACTION	r_scangle_it	1.397	1.635	1457
X-RAY DIFFRACTION	r_scangle_other	1.346	1.601	1440
X-RAY DIFFRACTION	r_lrange_it	4.424	13.711	2307
X-RAY DIFFRACTION	r_lrange_other	4.205	13.151	2263

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.624-1.666	0.251	5	0.309	95	0.306	2389	0.758	0.845	4.1859	0.358
1.666-1.712	0.298	12	0.315	235	0.315	2331	0.858	0.879	10.5963	0.347
1.712-1.762	0.254	16	0.27	389	0.269	2261	0.89	0.887	17.9124	0.301
1.762-1.816	0.315	26	0.227	573	0.231	2212	0.894	0.892	27.0796	0.251
1.816-1.875	0.246	32	0.228	759	0.229	2131	0.9	0.888	37.1187	0.24
1.875-1.941	0.272	63	0.208	1112	0.211	2049	0.886	0.902	57.345	0.217
1.941-2.014	0.249	71	0.196	1550	0.198	1981	0.893	0.914	81.8274	0.201
2.014-2.096	0.236	63	0.189	1800	0.19	1935	0.907	0.927	96.2791	0.195
2.096-2.189	0.26	73	0.179	1742	0.182	1815	0.913	0.936	100	0.186
2.189-2.296	0.207	98	0.167	1657	0.169	1755	0.939	0.948	100	0.171
2.296-2.42	0.213	94	0.147	1585	0.151	1679	0.934	0.955	100	0.15
2.42-2.566	0.22	86	0.151	1505	0.154	1591	0.938	0.954	100	0.15
2.566-2.743	0.201	55	0.149	1422	0.151	1477	0.941	0.955	100	0.152
2.743-2.962	0.223	58	0.165	1328	0.167	1386	0.939	0.952	100	0.167
2.962-3.243	0.209	81	0.162	1206	0.165	1287	0.953	0.96	100	0.168
3.243-3.624	0.207	61	0.148	1079	0.151	1140	0.958	0.971	100	0.154
3.624-4.181	0.186	49	0.129	995	0.132	1044	0.962	0.976	100	0.137
4.181-5.111	0.116	40	0.111	815	0.111	855	0.981	0.98	100	0.126
5.111-7.189	0.241	43	0.17	635	0.174	678	0.954	0.96	100	0.191
7.189-48.95	0.289	22	0.193	366	0.2	388	0.915	0.941	100	0.226

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