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- PDB-7c4l: Anncestral L-amino acid oxidase (AncLAAO-N5) L-Gln binding form -

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Basic information

Entry
Database: PDB / ID: 7c4l
TitleAnncestral L-amino acid oxidase (AncLAAO-N5) L-Gln binding form
ComponentsL-amino acid oxidase
KeywordsOXIDOREDUCTASE / L-amino acid oxidase
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE / GLUTAMINE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsNakano, S. / Minamino, Y. / Karasuda, H. / Ito, S.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18K14391 Japan
Japan Society for the Promotion of Science (JSPS)16K18688 Japan
CitationJournal: Commun Chem / Year: 2020
Title: Ancestral L-amino acid oxidases for deracemization and stereoinversion of amino acids
Authors: Nakano, S. / Kozuka, K. / Minamino, Y. / Karasuda, H. / Hasebe, F. / Ito, S.
History
DepositionMay 18, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 6, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-amino acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8963
Polymers74,9641
Non-polymers9322
Water2,198122
1
A: L-amino acid oxidase
hetero molecules

A: L-amino acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,7916
Polymers149,9282
Non-polymers1,8634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
Buried area6780 Å2
ΔGint-33 kcal/mol
Surface area46140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.558, 132.558, 191.806
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

#1: Protein L-amino acid oxidase


Mass: 74963.977 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-GLN / GLUTAMINE


Type: L-peptide linking / Mass: 146.144 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10N2O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.81 Å3/Da / Density % sol: 56.23 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 3.5 / Details: 1.0M NaCl, 0.1M citric acid pH 3.5

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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 PILATUS3 2M / Detector: PIXEL / Date: Dec 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→48 Å / Num. obs: 26591 / % possible obs: 100 % / Redundancy: 26.5 % / Biso Wilson estimate: 43.21 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.119 / Net I/σ(I): 26.5
Reflection shellResolution: 2.6→2.74 Å / Rmerge(I) obs: 0.687 / Num. unique obs: 3823 / CC1/2: 0.953

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.14_3260refinement
SCALAdata scaling
AutoSolphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.6→47.95 Å / SU ML: 0.3796 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 27.3083 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2772 1282 4.82 %
Rwork0.2077 25307 -
obs0.2111 26589 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.12 Å2
Refinement stepCycle: LAST / Resolution: 2.6→47.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4875 0 63 122 5060
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00845067
X-RAY DIFFRACTIONf_angle_d1.01646886
X-RAY DIFFRACTIONf_chiral_restr0.052727
X-RAY DIFFRACTIONf_plane_restr0.0068895
X-RAY DIFFRACTIONf_dihedral_angle_d5.71432965
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.710.34811020.26912802X-RAY DIFFRACTION99.9
2.71-2.830.3061610.25222736X-RAY DIFFRACTION100
2.83-2.980.32621500.24382757X-RAY DIFFRACTION100
2.98-3.160.31191620.25862758X-RAY DIFFRACTION100
3.16-3.410.36311500.25142770X-RAY DIFFRACTION100
3.41-3.750.28151260.21812818X-RAY DIFFRACTION100
3.75-4.290.26061400.18772820X-RAY DIFFRACTION100
4.29-5.410.24141360.17052859X-RAY DIFFRACTION100
5.41-47.950.21851550.17432987X-RAY DIFFRACTION99.94

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