PDB-9tdf: Structure of an LPMO expressed in E.coli (LsAA9A) merged from mul...

ID or keywords:

Entry

Database: PDB / ID: 9tdf

Title

Structure of an LPMO expressed in E.coli (LsAA9A) merged from multiple crystals with an average dose of 88.5kGy at room temperature

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

Huang, Z. / Nan, J. / 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	9tdf.cif.gz	66.4 KB	Display	PDBx/mmCIF format
PDB format	pdb9tdf.ent.gz		Display	PDB format
PDBx/mmJSON format	9tdf.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/td/9tdf ftp://data.pdbj.org/pub/pdb/validation_reports/td/9tdf	HTTPS FTP

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Related structure data

Related structure data	9tcvC 9tcxC 9tcyC 9tczC 9td0C 9td1C 9td6C 9td8C 9td9C 9tdbC 9tdcC 9tddC 9tdeC 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

25.6 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)	49.660, 49.660, 109.610
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-CU / COPPER (II) ION Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.68 Å³/Da / Density % sol: 54.02 %
Crystal grow	Temperature: 278 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 25 mM sodium acetate pH 5.5, 20 mM sodium chloride

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Data collection

Diffraction	Mean temperature: 298 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: MAX IV / Beamline: MicroMAX / Wavelength: 0.9544 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 2, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9544 Å / Relative weight: 1
Reflection	Resolution: 1.85→49.66 Å / Num. obs: 21161 / % possible obs: 93.6 % / Redundancy: 2.8 % / CC_1/2: 0.963 / Net I/σ(I): 3.35
Reflection shell	Resolution: 1.85→1.98 Å / Redundancy: 2.87 % / Num. unique obs: 3818 / CC_1/2: 0.401 / % possible all: 91.9

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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→49.66 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.94 / SU B: 4.613 / SU ML: 0.124 / Cross valid method: FREE R-VALUE / ESU R: 0.139 / ESU R Free: 0.128
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2122	1102	5.208 %
R_work	0.1792	20059	-
all	0.181	-	-
obs	-	21161	93.529 %

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: 18.776 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.343 Å²	0 Å²	0 Å²
2-	-	0.343 Å²	-0 Å²
3-	-	-	-0.685 Å²

Refinement step

Cycle: LAST / Resolution: 1.85→49.66 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1787	0	10	150	1947

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.013	1886
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	1682
X-RAY DIFFRACTION	r_angle_refined_deg	1.467	1.638	2613
X-RAY DIFFRACTION	r_angle_other_deg	1.29	1.57	3885
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.722	5	248
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.253	23.556	90
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.554	15	250
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.82	15	7
X-RAY DIFFRACTION	r_chiral_restr	0.064	0.2	257
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	2222
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	428
X-RAY DIFFRACTION	r_nbd_refined	0.189	0.2	304
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.183	0.2	1530
X-RAY DIFFRACTION	r_nbtor_refined	0.159	0.2	920
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.077	0.2	820
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.137	0.2	113
X-RAY DIFFRACTION	r_metal_ion_refined	0.006	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.065	0.2	4
X-RAY DIFFRACTION	r_nbd_other	0.182	0.2	28
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.149	0.2	9
X-RAY DIFFRACTION	r_mcbond_it	1.216	1.897	956
X-RAY DIFFRACTION	r_mcbond_other	1.205	1.89	955
X-RAY DIFFRACTION	r_mcangle_it	1.943	2.835	1198
X-RAY DIFFRACTION	r_mcangle_other	1.948	2.843	1199
X-RAY DIFFRACTION	r_scbond_it	1.612	2.046	930
X-RAY DIFFRACTION	r_scbond_other	1.541	2.023	923
X-RAY DIFFRACTION	r_scangle_it	2.527	3.023	1409
X-RAY DIFFRACTION	r_scangle_other	2.514	3.008	1402
X-RAY DIFFRACTION	r_lrange_it	4.261	22.848	2039
X-RAY DIFFRACTION	r_lrange_other	4.127	22.65	2016

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	0.363	78	0.33	1450	0.332	1661	0.524	0.509	91.9928	0.336
1.898-1.95	0.276	88	0.298	1401	0.297	1624	0.716	0.696	91.6872	0.302
1.95-2.006	0.252	84	0.261	1375	0.26	1574	0.821	0.799	92.6938	0.262
2.006-2.068	0.296	75	0.246	1357	0.249	1552	0.806	0.846	92.268	0.243
2.068-2.136	0.292	70	0.232	1309	0.235	1469	0.827	0.857	93.8734	0.227
2.136-2.21	0.256	71	0.218	1285	0.22	1439	0.867	0.877	94.2321	0.215
2.21-2.294	0.266	68	0.212	1218	0.215	1374	0.875	0.898	93.5953	0.207
2.294-2.387	0.247	68	0.203	1199	0.206	1348	0.904	0.909	93.9911	0.198
2.387-2.493	0.208	51	0.192	1182	0.193	1299	0.916	0.911	94.9192	0.184
2.493-2.614	0.28	56	0.179	1109	0.184	1234	0.869	0.924	94.4084	0.174
2.614-2.755	0.193	68	0.175	1023	0.176	1161	0.941	0.936	93.9707	0.171
2.755-2.922	0.293	39	0.174	1016	0.178	1115	0.886	0.928	94.6188	0.173
2.922-3.123	0.242	37	0.168	933	0.171	1023	0.914	0.937	94.8192	0.169
3.123-3.372	0.163	55	0.138	867	0.139	975	0.963	0.968	94.5641	0.138
3.372-3.692	0.145	45	0.121	791	0.123	890	0.975	0.977	93.9326	0.123
3.692-4.125	0.125	45	0.113	725	0.113	826	0.981	0.979	93.2203	0.117
4.125-4.758	0.123	34	0.095	635	0.096	704	0.983	0.984	95.0284	0.1
4.758-5.814	0.105	29	0.112	556	0.111	607	0.982	0.981	96.3756	0.12
5.814-8.166	0.202	27	0.156	416	0.158	477	0.934	0.955	92.8721	0.167
8.166-49.66	0.432	14	0.329	212	0.335	271	0.872	0.89	83.3948	0.826

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