PDB-9td0: Structure of an LPMO expressed in E.coli (LsAA9A) at 5.27x10^4 Gy

ID or keywords:

Entry

Database: PDB / ID: 9td0

Title

Structure of an LPMO expressed in E.coli (LsAA9A) at 5.27x10^4 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: 2.07 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	9td0.cif.gz	70 KB	Display	PDBx/mmCIF format
PDB format	pdb9td0.ent.gz		Display	PDB format
PDBx/mmJSON format	9td0.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/9td0 ftp://data.pdbj.org/pub/pdb/validation_reports/td/9td0	HTTPS FTP

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Related structure data

Related structure data	9tcvC 9tcxC 9tcyC 9tczC 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

26.7 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)	48.290, 48.290, 109.560
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 / Sugars , 2 types, 3 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

#2: Polysaccharide

beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose

Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 504.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellotriose

Descriptor	Type	Program
DGlcpb1-4DGlcpb1-4DGlcpb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5]/1-1-1/a4-b1_b4-c1	WURCS	PDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}	LINUCS	PDB-CARE

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Non-polymers , 5 types, 161 molecules

#3: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Chemical	ChemComp-CU / COPPER (II) ION Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#6: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.53 Å³/Da / Density % sol: 51.36 %
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: 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: 2.07→48.34 Å / Num. obs: 15289 / % possible obs: 100 % / Redundancy: 10.8 % / CC_1/2: 0.994 / Net I/σ(I): 6.73
Reflection shell	Resolution: 2.07→2.12 Å / Num. unique obs: 1120 / CC_1/2: 0.571 / % possible all: 100

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Processing

Software

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

Refinement

Method to determine structure:

FOURIER SYNTHESIS / Resolution: 2.07→48.337 Å / Cor.coef. F_o:F_c: 0.959 / Cor.coef. F_o:F_c free: 0.941 / SU B: 6.737 / SU ML: 0.166 / Cross valid method: FREE R-VALUE / ESU R: 0.214 / ESU R Free: 0.177
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2214	775	5.069 %
R_work	0.1755	14514	-
all	0.178	-	-
obs	-	15289	99.987 %

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: 29.863 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.45 Å²	0 Å²	-0 Å²
2-	-	1.45 Å²	-0 Å²
3-	-	-	-2.9 Å²

Refinement step

Cycle: LAST / Resolution: 2.07→48.337 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1787	0	87	152	2026

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.013	1985
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	1756
X-RAY DIFFRACTION	r_angle_refined_deg	1.736	1.691	2753
X-RAY DIFFRACTION	r_angle_other_deg	1.314	1.62	4053
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.149	5	250
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.477	23.474	95
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.104	15	254
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.202	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.076	0.2	287
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	2278
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	442
X-RAY DIFFRACTION	r_nbd_refined	0.191	0.2	393
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.182	0.2	1711
X-RAY DIFFRACTION	r_nbtor_refined	0.164	0.2	947
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.079	0.2	859
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.159	0.2	147
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.095	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.189	0.2	15
X-RAY DIFFRACTION	r_nbd_other	0.204	0.2	65
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.311	0.2	9
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.213	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	2.041	3.03	969
X-RAY DIFFRACTION	r_mcbond_other	2.028	3.023	966
X-RAY DIFFRACTION	r_mcangle_it	2.692	4.532	1216
X-RAY DIFFRACTION	r_mcangle_other	2.691	4.535	1217
X-RAY DIFFRACTION	r_scbond_it	2.677	3.344	1016
X-RAY DIFFRACTION	r_scbond_other	2.657	3.34	1013
X-RAY DIFFRACTION	r_scangle_it	3.708	4.973	1533
X-RAY DIFFRACTION	r_scangle_other	3.686	4.965	1528
X-RAY DIFFRACTION	r_lrange_it	4.953	37.754	2210
X-RAY DIFFRACTION	r_lrange_other	4.889	37.634	2189

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 (%)
2.07-2.124	0.337	60	0.302	1058	X-RAY DIFFRACTION	100
2.124-2.182	0.28	49	0.257	1050	X-RAY DIFFRACTION	100
2.182-2.245	0.287	56	0.247	1013	X-RAY DIFFRACTION	100
2.245-2.314	0.323	57	0.23	983	X-RAY DIFFRACTION	100
2.314-2.389	0.251	55	0.217	950	X-RAY DIFFRACTION	100
2.389-2.473	0.315	37	0.2	930	X-RAY DIFFRACTION	100
2.473-2.566	0.29	42	0.191	897	X-RAY DIFFRACTION	100
2.566-2.671	0.269	67	0.181	840	X-RAY DIFFRACTION	100
2.671-2.789	0.277	25	0.18	828	X-RAY DIFFRACTION	100
2.789-2.925	0.306	29	0.182	802	X-RAY DIFFRACTION	100
2.925-3.082	0.247	38	0.176	762	X-RAY DIFFRACTION	100
3.082-3.268	0.205	46	0.157	701	X-RAY DIFFRACTION	100
3.268-3.493	0.175	31	0.151	680	X-RAY DIFFRACTION	99.8596
3.493-3.771	0.202	41	0.139	607	X-RAY DIFFRACTION	100
3.771-4.129	0.17	33	0.131	571	X-RAY DIFFRACTION	100
4.129-4.612	0.113	26	0.109	515	X-RAY DIFFRACTION	100
4.612-5.318	0.17	34	0.12	460	X-RAY DIFFRACTION	100
5.318-6.494	0.184	21	0.148	380	X-RAY DIFFRACTION	100
6.494-9.104	0.211	18	0.177	309	X-RAY DIFFRACTION	100
9.104-48.337	0.273	10	0.321	178	X-RAY DIFFRACTION	99.4709

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Protein / Sugars , 2 types, 3 molecules AAA

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Non-polymers , 5 types, 161 molecules

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