PDB-9tcv: Structure of an LPMO expressed in E.coli (LsAA9A) at 5.37x10^4 Gy

ID or keywords:

Entry

Database: PDB / ID: 9tcv

Title

Structure of an LPMO expressed in E.coli (LsAA9A) at 5.37x10^4 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	9tcv.cif.gz	71.7 KB	Display	PDBx/mmCIF format
PDB format	pdb9tcv.ent.gz		Display	PDB format
PDBx/mmJSON format	9tcv.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/9tcv ftp://data.pdbj.org/pub/pdb/validation_reports/tc/9tcv	HTTPS FTP

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Related structure data

Related structure data	9tcxC 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

25.8 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)	49.472, 49.472, 109.624
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 , 5 types, 319 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.: 1 / Source method: obtained synthetically / Formula: SO₄
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 311 / 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: 2.66 Å³/Da / Density % sol: 53.68 %
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: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 4, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8731 Å / Relative weight: 1
Reflection	Resolution: 1.85→109.62 Å / Num. obs: 22367 / % possible obs: 99.5 % / Redundancy: 13.6 % / CC_1/2: 0.995 / Net I/σ(I): 8.1
Reflection shell	Resolution: 1.85→1.89 Å / Num. unique obs: 1271 / CC_1/2: 0.748

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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→49.472 Å / Cor.coef. F_o:F_c: 0.963 / Cor.coef. F_o:F_c free: 0.955 / SU B: 4.05 / SU ML: 0.112 / Cross valid method: FREE R-VALUE / ESU R: 0.152 / ESU R Free: 0.137
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2277	1156	5.193 %
R_work	0.1936	21106	-
all	0.195	-	-
obs	-	22262	99.043 %

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: 25.497 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.22 Å²	-0 Å²	-0 Å²
2-	-	1.22 Å²	-0 Å²
3-	-	-	-2.441 Å²

Refinement step

Cycle: LAST / Resolution: 1.85→49.472 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1787	0	27	311	2125

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.013	1892
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	1681
X-RAY DIFFRACTION	r_angle_refined_deg	1.509	1.638	2611
X-RAY DIFFRACTION	r_angle_other_deg	1.329	1.57	3875
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.22	5	244
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.781	23.556	90
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.137	15	248
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.644	15	7
X-RAY DIFFRACTION	r_chiral_restr	0.065	0.2	254
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	2234
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	428
X-RAY DIFFRACTION	r_nbd_refined	0.208	0.2	359
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.19	0.2	1654
X-RAY DIFFRACTION	r_nbtor_refined	0.161	0.2	921
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	786
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.162	0.2	208
X-RAY DIFFRACTION	r_metal_ion_refined	0.012	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.236	0.2	11
X-RAY DIFFRACTION	r_nbd_other	0.208	0.2	29
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.157	0.2	16
X-RAY DIFFRACTION	r_mcbond_it	1.854	2.583	960
X-RAY DIFFRACTION	r_mcbond_other	1.717	2.568	954
X-RAY DIFFRACTION	r_mcangle_it	2.202	3.846	1197
X-RAY DIFFRACTION	r_mcangle_other	2.202	3.849	1198
X-RAY DIFFRACTION	r_scbond_it	2.208	2.719	932
X-RAY DIFFRACTION	r_scbond_other	2.193	2.712	929
X-RAY DIFFRACTION	r_scangle_it	3.075	4.04	1411
X-RAY DIFFRACTION	r_scangle_other	3.046	4.028	1406
X-RAY DIFFRACTION	r_lrange_it	5.176	32.344	2188
X-RAY DIFFRACTION	r_lrange_other	4.862	31.566	2111

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
1.85-1.898	1.638	80	1.892	1408	1.877	1683	0.496	0.462	88.4136	2.25
1.898-1.95	0.367	92	0.419	1504	0.415	1601	0.81	0.796	99.6877	0.425
1.95-2.007	0.292	88	0.256	1480	0.258	1570	0.876	0.877	99.8726	0.259
2.007-2.068	0.282	78	0.227	1454	0.23	1534	0.886	0.902	99.8696	0.227
2.068-2.136	0.252	75	0.208	1390	0.21	1465	0.889	0.916	100	0.206
2.136-2.211	0.293	72	0.195	1338	0.2	1410	0.892	0.92	100	0.192
2.211-2.294	0.333	71	0.196	1312	0.202	1383	0.857	0.919	100	0.195
2.294-2.388	0.232	70	0.186	1262	0.189	1333	0.925	0.929	99.925	0.184
2.388-2.493	0.253	57	0.178	1231	0.181	1289	0.924	0.935	99.9224	0.174
2.493-2.615	0.252	57	0.168	1164	0.172	1222	0.91	0.948	99.9182	0.165
2.615-2.756	0.201	72	0.162	1086	0.165	1159	0.949	0.956	99.9137	0.161
2.756-2.922	0.262	40	0.176	1053	0.179	1093	0.924	0.948	100	0.176
2.922-3.123	0.259	40	0.191	982	0.194	1023	0.933	0.952	99.9023	0.19
3.123-3.373	0.185	56	0.173	900	0.173	957	0.963	0.971	99.8955	0.174
3.373-3.693	0.188	49	0.169	846	0.17	896	0.96	0.969	99.8884	0.174
3.693-4.126	0.191	50	0.152	761	0.155	811	0.973	0.97	100	0.159
4.126-4.758	0.114	34	0.127	660	0.126	695	0.983	0.98	99.8561	0.137
4.758-5.814	0.155	31	0.154	573	0.154	604	0.97	0.977	100	0.166
5.814-8.167	0.242	29	0.187	448	0.19	477	0.944	0.964	100	0.198
8.167-49.472	0.127	15	0.179	254	0.176	270	0.97	0.962	99.6296	0.197

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