PDB-9hj5: Engineered Fructosyl Peptide Oxidase - D7 mutant

ID or keywords:

Entry

Database: PDB / ID: 9hj5

Title

Engineered Fructosyl Peptide Oxidase - D7 mutant

Components

Engineered Fructosyl Peptide Oxidase - D7 mutant

Keywords

OXIDOREDUCTASE / Amadoriase / FAD / Engineered enzyme / deglycating enzyme

Function / homology

FLAVIN-ADENINE DINUCLEOTIDE

Function and homology information

Biological species

Parastagonospora nodorum SN15 (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.093 Å

Authors

Parisini, E. / Bhattacharya, S. / Rozanov, L.

Funding support

European Union, 1items

Citation

Journal: To Be Published
Title: Engineered Fructosyl Peptide Oxidase - D7 mutant
Authors: Bhattacharya, S. / Rozanov, L. / Parisini, E.

History

Deposition	Nov 28, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 10, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9hj5.cif.gz	344.6 KB	Display	PDBx/mmCIF format
PDB format	pdb9hj5.ent.gz	273.7 KB	Display	PDB format
PDBx/mmJSON format	9hj5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9hj5_validation.pdf.gz	928 KB	Display	wwPDB validaton report
Full document	9hj5_full_validation.pdf.gz	946.1 KB	Display
Data in XML	9hj5_validation.xml.gz	42.6 KB	Display
Data in CIF	9hj5_validation.cif.gz	55.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hj/9hj5 ftp://data.pdbj.org/pub/pdb/validation_reports/hj/9hj5	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Engineered Fructosyl Peptide Oxidase - D7 mutant

B: Engineered Fructosyl Peptide Oxidase - D7 mutant

hetero molecules

96.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	54.083, 54.120, 82.657
Angle α, β, γ (deg.)	80.071, 85.533, 89.837
Int Tables number	1
Space group name H-M	P1

#1: Protein	Engineered Fructosyl Peptide Oxidase - D7 mutant Mass: 47242.941 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Parastagonospora nodorum SN15 (fungus) / Production host: Escherichia coli (E. coli)
#2: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.51 Å³/Da / Density % sol: 43.49 %
Crystal grow	Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 12% PEG 8K, 5% Ethanol, 0.1M Tris-HCl pH 8.0

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 19, 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: 2.093→53.974 Å / Num. obs: 52616 / % possible obs: 96.89 % / Redundancy: 3.2 % / CC_1/2: 0.982 / Net I/σ(I): 5.2
Reflection shell	Resolution: 2.093→2.129 Å / Num. unique obs: 2633 / CC_1/2: 0.357

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0352	refinement
autoPROC		data reduction
autoPROC		data scaling
REFMAC		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.093→53.974 Å / Cor.coef. F_o:F_c: 0.957 / Cor.coef. F_o:F_c free: 0.924 / WR_factor R_free: 0.271 / WR_factor R_work: 0.202 / SU B: 7.061 / SU ML: 0.179 / Average fsc free: 0.9495 / Average fsc work: 0.969 / Cross valid method: FREE R-VALUE / ESU R: 0.235 / ESU R Free: 0.207
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2571	2614	4.968 %
R_work	0.1928	50002	-
all	0.196	-	-
obs	-	52616	96.913 %

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: 41.645 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.093 Å²	-0.435 Å²	0.058 Å²
2-	-	-0.465 Å²	0.233 Å²
3-	-	-	0.601 Å²

Refinement step

Cycle: LAST / Resolution: 2.093→53.974 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6514	0	136	280	6930

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	6932
X-RAY DIFFRACTION	r_bond_other_d	0.005	0.016	6313
X-RAY DIFFRACTION	r_angle_refined_deg	1.519	1.648	9419
X-RAY DIFFRACTION	r_angle_other_deg	0.533	1.569	14744
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.82	5	855
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	9.841	5	40
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.231	10	1146
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.084	10	297
X-RAY DIFFRACTION	r_chiral_restr	0.077	0.2	1002
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	7838
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	1400
X-RAY DIFFRACTION	r_nbd_refined	0.23	0.2	1498
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.205	0.2	6564
X-RAY DIFFRACTION	r_nbtor_refined	0.186	0.2	3362
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.083	0.2	3654
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.198	0.2	366
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.034	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.271	0.2	13
X-RAY DIFFRACTION	r_nbd_other	0.153	0.2	54
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.235	0.2	3
X-RAY DIFFRACTION	r_mcbond_it	3.77	4.212	3376
X-RAY DIFFRACTION	r_mcbond_other	3.766	4.212	3376
X-RAY DIFFRACTION	r_mcangle_it	5.383	6.305	4232
X-RAY DIFFRACTION	r_mcangle_other	5.383	6.307	4233
X-RAY DIFFRACTION	r_scbond_it	3.985	4.592	3556
X-RAY DIFFRACTION	r_scbond_other	3.985	4.592	3557
X-RAY DIFFRACTION	r_scangle_it	5.918	6.722	5182
X-RAY DIFFRACTION	r_scangle_other	5.917	6.722	5183
X-RAY DIFFRACTION	r_lrange_it	8.236	52.175	8151
X-RAY DIFFRACTION	r_lrange_other	8.178	52.124	8105

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
2.093-2.147	0.333	209	0.301	3619	0.303	4012	0.918	0.935	95.4138	0.303
2.147-2.206	0.318	189	0.277	3556	0.279	3893	0.928	0.946	96.1983	0.279
2.206-2.27	0.332	178	0.263	3524	0.266	3837	0.925	0.953	96.4816	0.261
2.27-2.339	0.317	166	0.259	3382	0.261	3684	0.934	0.955	96.3084	0.254
2.339-2.416	0.338	143	0.238	3258	0.242	3540	0.924	0.963	96.0734	0.235
2.416-2.501	0.285	183	0.221	3153	0.225	3478	0.948	0.97	95.9172	0.214
2.501-2.595	0.27	142	0.217	3020	0.219	3374	0.956	0.971	93.7167	0.209
2.595-2.7	0.314	165	0.196	2881	0.202	3227	0.95	0.977	94.3911	0.189
2.7-2.82	0.23	160	0.176	2868	0.179	3084	0.966	0.982	98.1842	0.172
2.82-2.957	0.247	137	0.181	2738	0.184	2927	0.965	0.98	98.2234	0.178
2.957-3.117	0.258	148	0.182	2597	0.187	2787	0.957	0.98	98.493	0.181
3.117-3.305	0.256	132	0.18	2495	0.184	2667	0.963	0.981	98.5002	0.182
3.305-3.533	0.245	106	0.195	2350	0.197	2486	0.963	0.978	98.7932	0.201
3.533-3.814	0.264	119	0.177	2200	0.181	2339	0.957	0.982	99.1449	0.188
3.814-4.176	0.216	134	0.176	1977	0.178	2139	0.974	0.982	98.691	0.191
4.176-4.666	0.226	102	0.157	1750	0.161	1903	0.972	0.985	97.32	0.178
4.666-5.381	0.235	87	0.159	1583	0.163	1734	0.973	0.986	96.3091	0.187
5.381-6.574	0.202	27	0.177	1384	0.178	1420	0.978	0.984	99.3662	0.207
6.574-9.228	0.24	74	0.169	1059	0.173	1136	0.967	0.984	99.7359	0.21
9.228-53.974	0.238	13	0.179	607	0.18	623	0.993	0.977	99.5185	0.23

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