PDB-7x7i: Ancestral L-Lys oxidase (AncLLysO-2) ligand free form

ID or keywords:

Entry

Database: PDB / ID: 7x7i

Title

Ancestral L-Lys oxidase (AncLLysO-2) ligand free form

Components

FAD dependent enzyme

Keywords

OXIDOREDUCTASE / Ancestral Sequence Reconstruction / ligand free form

Function / homology

FLAVIN-ADENINE DINUCLEOTIDE

Function and homology information

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.55 Å

Authors

Motoyama, T. / Ishida, C. / Hasebe, F. / Ito, S. / Nakano, S.

Funding support

Japan, 3items

Organization	Grant number	Country
Japan Science and Technology	JPMJPR20AB	Japan
Japan Society for the Promotion of Science (JSPS)	21K05395	Japan
Japan Society for the Promotion of Science (JSPS)	19J23697	Japan

Citation

Journal: Acs Omega / Year: 2022
Title: Reaction Mechanism of Ancestral l-Lys alpha-Oxidase from Caulobacter Species Studied by Biochemical, Structural, and Computational Analysis
Authors: Motoyama, T. / Yamamoto, Y. / Ishida, C. / Hasebe, F. / Kawamura, Y. / Shigeta, Y. / Ito, S. / Nakano, S.

History

Deposition	Mar 9, 2022	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jan 18, 2023	Provider: repository / Type: Initial release
Revision 1.1	Oct 30, 2024	Group: Data collection / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7x7i.cif.gz	276.9 KB	Display	PDBx/mmCIF format
PDB format	pdb7x7i.ent.gz	210.4 KB	Display	PDB format
PDBx/mmJSON format	7x7i.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7x7i_validation.pdf.gz	902.3 KB	Display	wwPDB validaton report
Full document	7x7i_full_validation.pdf.gz	909.7 KB	Display
Data in XML	7x7i_validation.xml.gz	54.9 KB	Display
Data in CIF	7x7i_validation.cif.gz	85.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x7/7x7i ftp://data.pdbj.org/pub/pdb/validation_reports/x7/7x7i	HTTPS FTP

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Related structure data

Related structure data	7x7jC 7x7kC C: citing same article (ref.)
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: FAD dependent enzyme

B: FAD dependent enzyme

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	79.246, 76.533, 92.708
Angle α, β, γ (deg.)	90.000, 104.389, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	FAD dependent enzyme Mass: 65161.125 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / 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: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1365 / 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: 2.09 Å³/Da / Density % sol: 41.14 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350, 0.1 M NDSB-256

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 1, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.55→44.9 Å / Num. obs: 155511 / % possible obs: 99.8 % / Redundancy: 6.6 % / CC_1/2: 0.998 / Net I/σ(I): 12.6
Reflection shell	Resolution: 1.55→1.63 Å / Num. unique obs: 22407 / CC_1/2: 0.952

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0257	refinement
XDS		data reduction
SCALA		data scaling
AutoSol		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.55→44.9 Å / Cor.coef. F_o:F_c: 0.97 / Cor.coef. F_o:F_c free: 0.959 / SU B: 1.591 / SU ML: 0.057 / Cross valid method: FREE R-VALUE / ESU R: 0.081 / ESU R Free: 0.08
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.191	7653	4.93 %
R_work	0.163	147590	-
all	0.164	-	-
obs	-	155157	99.1 %

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: 20.92 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.001 Å²	0 Å²	-0.004 Å²
2-	-	0.001 Å²	0 Å²
3-	-	-	0.002 Å²

Refinement step

Cycle: LAST / Resolution: 1.55→44.9 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9024	0	106	1365	10495

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.012	9406
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	8074
X-RAY DIFFRACTION	r_angle_refined_deg	1.775	1.646	12902
X-RAY DIFFRACTION	r_angle_other_deg	1.561	1.565	18726
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.834	5	1164
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.802	23.266	496
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.824	15	1282
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.976	15	42
X-RAY DIFFRACTION	r_chiral_restr	0.091	0.2	1218
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	10840
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2048
X-RAY DIFFRACTION	r_nbd_refined	0.22	0.2	1940
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.191	0.2	7998
X-RAY DIFFRACTION	r_nbtor_refined	0.182	0.2	4748
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.083	0.2	3898
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.17	0.2	1066
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.033	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.247	0.2	26
X-RAY DIFFRACTION	r_nbd_other	0.256	0.2	86
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.189	0.2	34
X-RAY DIFFRACTION	r_mcbond_it	1.856	1.825	4662
X-RAY DIFFRACTION	r_mcbond_other	1.846	1.825	4661
X-RAY DIFFRACTION	r_mcangle_it	2.684	2.739	5824
X-RAY DIFFRACTION	r_mcangle_other	2.684	2.739	5825
X-RAY DIFFRACTION	r_scbond_it	2.388	1.975	4744
X-RAY DIFFRACTION	r_scbond_other	2.389	1.975	4741
X-RAY DIFFRACTION	r_scangle_it	3.519	2.897	7078
X-RAY DIFFRACTION	r_scangle_other	3.519	2.897	7079
X-RAY DIFFRACTION	r_lrange_it	5.386	23.318	11488
X-RAY DIFFRACTION	r_lrange_other	5.085	22.268	11040

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 (%)
1.55-1.589	0.29	542	0.244	10616	X-RAY DIFFRACTION	97.1951
1.589-1.633	0.269	547	0.228	10597	X-RAY DIFFRACTION	99.5978
1.633-1.68	0.226	555	0.204	10268	X-RAY DIFFRACTION	99.6318
1.68-1.732	0.227	521	0.204	9991	X-RAY DIFFRACTION	99.7249
1.732-1.789	0.242	498	0.192	9763	X-RAY DIFFRACTION	99.7764
1.789-1.851	0.208	462	0.179	9395	X-RAY DIFFRACTION	99.7874
1.851-1.921	0.216	461	0.178	9116	X-RAY DIFFRACTION	99.8644
1.921-2	0.217	445	0.17	8771	X-RAY DIFFRACTION	99.9458
2-2.088	0.217	386	0.173	8436	X-RAY DIFFRACTION	99.9207
2.088-2.19	0.197	421	0.161	8056	X-RAY DIFFRACTION	99.9764
2.19-2.309	0.188	391	0.151	7632	X-RAY DIFFRACTION	99.9875
2.309-2.449	0.168	397	0.145	7230	X-RAY DIFFRACTION	99.9738
2.449-2.618	0.181	365	0.145	6809	X-RAY DIFFRACTION	100
2.618-2.827	0.174	370	0.145	6293	X-RAY DIFFRACTION	100
2.827-3.097	0.172	310	0.154	5847	X-RAY DIFFRACTION	100
3.097-3.462	0.174	294	0.153	5285	X-RAY DIFFRACTION	99.9821
3.462-3.996	0.153	239	0.14	4677	X-RAY DIFFRACTION	99.9797
3.996-4.892	0.144	206	0.135	3964	X-RAY DIFFRACTION	100
4.892-6.908	0.225	161	0.183	3103	X-RAY DIFFRACTION	99.9694
6.908-44.9	0.216	82	0.172	1741	X-RAY DIFFRACTION	98.7541

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