PDB-8jhe: Hyper-thermostable ancestral L-amino acid oxidase 2 (HTAncLAAO2)

ID or keywords:

Entry

Database: PDB / ID: 8jhe

Title

Hyper-thermostable ancestral L-amino acid oxidase 2 (HTAncLAAO2)

Components

Hyper thermostable ancestral L-amino acid oxidase

Keywords

OXIDOREDUCTASE / L-amino acid oxidases / FAD-dependent / Ancestral sequence reconstruction

Function / homology

FLAVIN-ADENINE DINUCLEOTIDE

Function and homology information

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.201 Å

Authors

Kawamura, Y. / Ishida, C. / Miyata, R. / Miyata, A. / Hayashi, S. / Fujinami, D. / Ito, S. / Nakano, S.

Funding support

Japan, 3items

Organization	Grant number	Country
Japan Society for the Promotion of Science (JSPS)	18K14391	Japan
Japan Society for the Promotion of Science (JSPS)	21K05395	Japan
Japan Science and Technology	JPMJPR20AB	Japan

Citation

Journal: Commun Chem / Year: 2023
Title: Structural and functional analysis of hyper-thermostable ancestral L-amino acid oxidase that can convert Trp derivatives to D-forms by chemoenzymatic reaction.
Authors: Kawamura, Y. / Ishida, C. / Miyata, R. / Miyata, A. / Hayashi, S. / Fujinami, D. / Ito, S. / Nakano, S.

History

Deposition	May 23, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Oct 4, 2023	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8jhe.cif.gz	460 KB	Display	PDBx/mmCIF format
PDB format	pdb8jhe.ent.gz	360.3 KB	Display	PDB format
PDBx/mmJSON format	8jhe.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8jhe_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	8jhe_full_validation.pdf.gz	1.4 MB	Display
Data in XML	8jhe_validation.xml.gz	85.6 KB	Display
Data in CIF	8jhe_validation.cif.gz	128.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jh/8jhe ftp://data.pdbj.org/pub/pdb/validation_reports/jh/8jhe	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: Hyper thermostable ancestral L-amino acid oxidase

B: Hyper thermostable ancestral L-amino acid oxidase

C: Hyper thermostable ancestral L-amino acid oxidase

D: Hyper thermostable ancestral L-amino acid oxidase

hetero molecules

254 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Hyper thermostable ancestral L-amino acid oxidase

C: Hyper thermostable ancestral L-amino acid oxidase

hetero molecules

A: Hyper thermostable ancestral L-amino acid oxidase

C: Hyper thermostable ancestral L-amino acid oxidase

hetero molecules

A: Hyper thermostable ancestral L-amino acid oxidase

C: Hyper thermostable ancestral L-amino acid oxidase

hetero molecules

A: Hyper thermostable ancestral L-amino acid oxidase

C: Hyper thermostable ancestral L-amino acid oxidase

hetero molecules

defined by author&software
Evidence: electron microscopy
508 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Hyper thermostable ancestral L-amino acid oxidase

D: Hyper thermostable ancestral L-amino acid oxidase

hetero molecules

B: Hyper thermostable ancestral L-amino acid oxidase

D: Hyper thermostable ancestral L-amino acid oxidase

hetero molecules

B: Hyper thermostable ancestral L-amino acid oxidase

D: Hyper thermostable ancestral L-amino acid oxidase

hetero molecules

B: Hyper thermostable ancestral L-amino acid oxidase

D: Hyper thermostable ancestral L-amino acid oxidase

hetero molecules

defined by author&software
508 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	180.896, 180.896, 81.410
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	75
Space group name H-M	P4

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	2	A
4	2	C
5	3	A
6	3	D
7	4	B
8	4	C
9	5	B
10	5	D
11	6	C
12	6	D

NCS domain segments:

Beg auth comp-ID: GLU / Beg label comp-ID: GLU

Dom-ID	Component-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	VAL	VAL	A	A	4 - 538	2 - 536
2	2	1	VAL	VAL	B	B	4 - 538	2 - 536
3	3	2	VAL	VAL	A	A	4 - 538	2 - 536
4	4	2	VAL	VAL	C	C	4 - 538	2 - 536
5	5	3	VAL	VAL	A	A	4 - 538	2 - 536
6	6	3	VAL	VAL	D	D	4 - 538	2 - 536
7	7	4	GLU	GLU	B	B	4 - 539	2 - 537
8	8	4	GLU	GLU	C	C	4 - 539	2 - 537
9	9	5	GLU	GLU	B	B	4 - 539	2 - 537
10	10	5	GLU	GLU	D	D	4 - 539	2 - 537
11	11	6	GLU	GLU	C	C	4 - 539	2 - 537
12	12	6	GLU	GLU	D	D	4 - 539	2 - 537

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12

#1: Protein	Hyper thermostable ancestral L-amino acid oxidase Mass: 62670.539 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli B (bacteria)
#2: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE Mass: 785.550 Da / Num. of mol.: 4 / 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.: 1683 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 53.7 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 10% PEG3350, 0.2 M ammonium citrate tribasic, and 4%(v/v) 1,1,1,3,3,3-Hexafluoro-2-propanol

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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 PILATUS 2M-F / Detector: PIXEL / Date: May 26, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.2→48.5 Å / Num. obs: 133518 / % possible obs: 100 % / Redundancy: 20 % / CC_1/2: 0.999 / Net I/σ(I): 21.5
Reflection shell	Resolution: 2.2→2.35 Å / Mean I/σ(I) obs: 5.3 / Num. unique obs: 19360 / CC_1/2: 0.952

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.201→48.5 Å / Cor.coef. F_o:F_c: 0.958 / Cor.coef. F_o:F_c free: 0.947 / SU B: 4.33 / SU ML: 0.11 / Cross valid method: FREE R-VALUE / ESU R: 0.214 / ESU R Free: 0.169
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2001	6626	4.963 %
R_work	0.1674	126892	-
all	0.169	-	-
obs	-	133518	99.965 %

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: 28.147 Å²

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

Refinement step

Cycle: LAST / Resolution: 2.201→48.5 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16068	0	212	1683	17963

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.013	16708
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	15511
X-RAY DIFFRACTION	r_angle_refined_deg	1.518	1.641	22729
X-RAY DIFFRACTION	r_angle_other_deg	1.328	1.579	35809
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.045	5	2012
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.349	23.868	848
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.777	15	2775
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.109	15	68
X-RAY DIFFRACTION	r_chiral_restr	0.077	0.2	2129
X-RAY DIFFRACTION	r_chiral_restr_other	0.046	0.2	4
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	18964
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3832
X-RAY DIFFRACTION	r_nbd_refined	0.2	0.2	3225
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.179	0.2	14610
X-RAY DIFFRACTION	r_nbtor_refined	0.172	0.2	8089
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	7443
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.183	0.2	1441
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.044	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.075	0.2	13
X-RAY DIFFRACTION	r_nbd_other	0.104	0.2	64
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.127	0.2	61
X-RAY DIFFRACTION	r_mcbond_it	2.532	2.779	8072
X-RAY DIFFRACTION	r_mcbond_other	2.532	2.779	8071
X-RAY DIFFRACTION	r_mcangle_it	3.58	4.154	10076
X-RAY DIFFRACTION	r_mcangle_other	3.579	4.155	10077
X-RAY DIFFRACTION	r_scbond_it	3.05	3.052	8636
X-RAY DIFFRACTION	r_scbond_other	3.051	3.052	8633
X-RAY DIFFRACTION	r_scangle_it	4.566	4.452	12653
X-RAY DIFFRACTION	r_scangle_other	4.566	4.452	12654
X-RAY DIFFRACTION	r_lrange_it	6.019	32.371	19621
X-RAY DIFFRACTION	r_lrange_other	5.925	31.952	19171
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.052	0.05	17083
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.056	0.05	17064
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.065	0.05	17065
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.056	0.05	17162
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.064	0.05	17076
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.061	0.05	17097

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.05246	0.05009
1	2	B	X-RAY DIFFRACTION	Local ncs	0.05246	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.05553	0.05009
2	4	C	X-RAY DIFFRACTION	Local ncs	0.05553	0.05009
3	5	A	X-RAY DIFFRACTION	Local ncs	0.06532	0.05009
3	6	D	X-RAY DIFFRACTION	Local ncs	0.06532	0.05009
4	7	B	X-RAY DIFFRACTION	Local ncs	0.0558	0.05009
4	8	C	X-RAY DIFFRACTION	Local ncs	0.0558	0.05009
5	9	B	X-RAY DIFFRACTION	Local ncs	0.06395	0.05009
5	10	D	X-RAY DIFFRACTION	Local ncs	0.06395	0.05009
6	11	C	X-RAY DIFFRACTION	Local ncs	0.06052	0.05009
6	12	D	X-RAY DIFFRACTION	Local ncs	0.06052	0.05009

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 (%)
2.201-2.258	0.249	479	0.191	9316	X-RAY DIFFRACTION	99.7048
2.258-2.32	0.219	486	0.176	9073	X-RAY DIFFRACTION	100
2.32-2.387	0.207	482	0.168	8862	X-RAY DIFFRACTION	100
2.387-2.46	0.213	424	0.166	8607	X-RAY DIFFRACTION	100
2.46-2.541	0.215	420	0.166	8361	X-RAY DIFFRACTION	100
2.541-2.63	0.233	400	0.169	8076	X-RAY DIFFRACTION	100
2.63-2.729	0.224	416	0.164	7764	X-RAY DIFFRACTION	100
2.729-2.841	0.193	437	0.164	7443	X-RAY DIFFRACTION	100
2.841-2.967	0.193	351	0.161	7236	X-RAY DIFFRACTION	100
2.967-3.112	0.214	355	0.165	6925	X-RAY DIFFRACTION	100
3.112-3.28	0.225	348	0.172	6545	X-RAY DIFFRACTION	100
3.28-3.479	0.203	338	0.174	6219	X-RAY DIFFRACTION	100
3.479-3.719	0.205	310	0.173	5806	X-RAY DIFFRACTION	100
3.719-4.017	0.172	289	0.154	5416	X-RAY DIFFRACTION	100
4.017-4.4	0.157	251	0.143	5047	X-RAY DIFFRACTION	100
4.4-4.919	0.153	247	0.142	4533	X-RAY DIFFRACTION	100
4.919-5.679	0.194	193	0.174	4056	X-RAY DIFFRACTION	100
5.679-6.954	0.251	183	0.206	3424	X-RAY DIFFRACTION	100
6.954-9.827	0.162	151	0.159	2663	X-RAY DIFFRACTION	100
9.827-48.5	0.235	66	0.236	1520	X-RAY DIFFRACTION	98.8778

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