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

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Basic information

Entry
Database: PDB / ID: 8jhe
TitleHyper-thermostable ancestral L-amino acid oxidase 2 (HTAncLAAO2)
ComponentsHyper thermostable ancestral L-amino acid oxidase
KeywordsOXIDOREDUCTASE / L-amino acid oxidases / FAD-dependent / Ancestral sequence reconstruction
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.201 Å
AuthorsKawamura, Y. / Ishida, C. / Miyata, R. / Miyata, A. / Hayashi, S. / Fujinami, D. / Ito, S. / Nakano, S.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18K14391 Japan
Japan Society for the Promotion of Science (JSPS)21K05395 Japan
Japan Science and TechnologyJPMJPR20AB Japan
CitationJournal: 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
DepositionMay 23, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 4, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)253,8248
Polymers250,6824
Non-polymers3,1424
Water30,3191683
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


Theoretical massNumber of molelcules
Total (without water)507,64916
Polymers501,3648
Non-polymers6,2848
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area30790 Å2
ΔGint-144 kcal/mol
Surface area140660 Å2
MethodPISA
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


Theoretical massNumber of molelcules
Total (without water)507,64916
Polymers501,3648
Non-polymers6,2848
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area30720 Å2
ΔGint-152 kcal/mol
Surface area140270 Å2
MethodPISA
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 number75
Space group name H-MP4
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
32A
42C
53A
63D
74B
84C
95B
105D
116C
126D

NCS domain segments:

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

Dom-IDComponent-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111VALVALAA4 - 5382 - 536
221VALVALBB4 - 5382 - 536
332VALVALAA4 - 5382 - 536
442VALVALCC4 - 5382 - 536
553VALVALAA4 - 5382 - 536
663VALVALDD4 - 5382 - 536
774GLUGLUBB4 - 5392 - 537
884GLUGLUCC4 - 5392 - 537
995GLUGLUBB4 - 5392 - 537
10105GLUGLUDD4 - 5392 - 537
11116GLUGLUCC4 - 5392 - 537
12126GLUGLUDD4 - 5392 - 537

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

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Components

#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 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 1683 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.7 %
Crystal growTemperature: 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

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→48.5 Å / Num. obs: 133518 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 0.999 / Net I/σ(I): 21.5
Reflection shellResolution: 2.2→2.35 Å / Mean I/σ(I) obs: 5.3 / Num. unique obs: 19360 / CC1/2: 0.952

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.201→48.5 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc 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
RfactorNum. reflection% reflection
Rfree0.2001 6626 4.963 %
Rwork0.1674 126892 -
all0.169 --
obs-133518 99.965 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 28.147 Å2
Baniso -1Baniso -2Baniso -3
1--0.001 Å20 Å20 Å2
2---0.001 Å20 Å2
3---0.001 Å2
Refinement stepCycle: LAST / Resolution: 2.201→48.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16068 0 212 1683 17963
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01316708
X-RAY DIFFRACTIONr_bond_other_d0.0010.01715511
X-RAY DIFFRACTIONr_angle_refined_deg1.5181.64122729
X-RAY DIFFRACTIONr_angle_other_deg1.3281.57935809
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.04552012
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.34923.868848
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.777152775
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1091568
X-RAY DIFFRACTIONr_chiral_restr0.0770.22129
X-RAY DIFFRACTIONr_chiral_restr_other0.0460.24
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0218964
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023832
X-RAY DIFFRACTIONr_nbd_refined0.20.23225
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.214610
X-RAY DIFFRACTIONr_nbtor_refined0.1720.28089
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.27443
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.21441
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0440.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0750.213
X-RAY DIFFRACTIONr_nbd_other0.1040.264
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1270.261
X-RAY DIFFRACTIONr_mcbond_it2.5322.7798072
X-RAY DIFFRACTIONr_mcbond_other2.5322.7798071
X-RAY DIFFRACTIONr_mcangle_it3.584.15410076
X-RAY DIFFRACTIONr_mcangle_other3.5794.15510077
X-RAY DIFFRACTIONr_scbond_it3.053.0528636
X-RAY DIFFRACTIONr_scbond_other3.0513.0528633
X-RAY DIFFRACTIONr_scangle_it4.5664.45212653
X-RAY DIFFRACTIONr_scangle_other4.5664.45212654
X-RAY DIFFRACTIONr_lrange_it6.01932.37119621
X-RAY DIFFRACTIONr_lrange_other5.92531.95219171
X-RAY DIFFRACTIONr_ncsr_local_group_10.0520.0517083
X-RAY DIFFRACTIONr_ncsr_local_group_20.0560.0517064
X-RAY DIFFRACTIONr_ncsr_local_group_30.0650.0517065
X-RAY DIFFRACTIONr_ncsr_local_group_40.0560.0517162
X-RAY DIFFRACTIONr_ncsr_local_group_50.0640.0517076
X-RAY DIFFRACTIONr_ncsr_local_group_60.0610.0517097
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.052460.05009
12BX-RAY DIFFRACTIONLocal ncs0.052460.05009
23AX-RAY DIFFRACTIONLocal ncs0.055530.05009
24CX-RAY DIFFRACTIONLocal ncs0.055530.05009
35AX-RAY DIFFRACTIONLocal ncs0.065320.05009
36DX-RAY DIFFRACTIONLocal ncs0.065320.05009
47BX-RAY DIFFRACTIONLocal ncs0.05580.05009
48CX-RAY DIFFRACTIONLocal ncs0.05580.05009
59BX-RAY DIFFRACTIONLocal ncs0.063950.05009
510DX-RAY DIFFRACTIONLocal ncs0.063950.05009
611CX-RAY DIFFRACTIONLocal ncs0.060520.05009
612DX-RAY DIFFRACTIONLocal ncs0.060520.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.201-2.2580.2494790.1919316X-RAY DIFFRACTION99.7048
2.258-2.320.2194860.1769073X-RAY DIFFRACTION100
2.32-2.3870.2074820.1688862X-RAY DIFFRACTION100
2.387-2.460.2134240.1668607X-RAY DIFFRACTION100
2.46-2.5410.2154200.1668361X-RAY DIFFRACTION100
2.541-2.630.2334000.1698076X-RAY DIFFRACTION100
2.63-2.7290.2244160.1647764X-RAY DIFFRACTION100
2.729-2.8410.1934370.1647443X-RAY DIFFRACTION100
2.841-2.9670.1933510.1617236X-RAY DIFFRACTION100
2.967-3.1120.2143550.1656925X-RAY DIFFRACTION100
3.112-3.280.2253480.1726545X-RAY DIFFRACTION100
3.28-3.4790.2033380.1746219X-RAY DIFFRACTION100
3.479-3.7190.2053100.1735806X-RAY DIFFRACTION100
3.719-4.0170.1722890.1545416X-RAY DIFFRACTION100
4.017-4.40.1572510.1435047X-RAY DIFFRACTION100
4.4-4.9190.1532470.1424533X-RAY DIFFRACTION100
4.919-5.6790.1941930.1744056X-RAY DIFFRACTION100
5.679-6.9540.2511830.2063424X-RAY DIFFRACTION100
6.954-9.8270.1621510.1592663X-RAY DIFFRACTION100
9.827-48.50.235660.2361520X-RAY DIFFRACTION98.8778

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