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- PDB-7c4m: Ancestral L-amino acid oxidase (AncLAAO-N5) L-Trp binding form -

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Basic information

Entry
Database: PDB / ID: 7c4m
TitleAncestral L-amino acid oxidase (AncLAAO-N5) L-Trp binding form
ComponentsAncestral L-amino acid oxidase
KeywordsOXIDOREDUCTASE / L-amino acid oxidase
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE / TRYPTOPHAN
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsNakano, S. / Minamino, Y. / Karasuda, H. / Ito, S.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)16K18688 Japan
Japan Society for the Promotion of Science (JSPS)18K14391 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: Ancestral L-amino acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,9543
Polymers74,9641
Non-polymers9902
Water3,873215
1
A: Ancestral L-amino acid oxidase
hetero molecules

A: Ancestral L-amino acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,9086
Polymers149,9282
Non-polymers1,9804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area6790 Å2
ΔGint-33 kcal/mol
Surface area46210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.499, 132.499, 191.732
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 Ancestral 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 / 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-TRP / TRYPTOPHAN / Tryptophan


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12N2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 56.17 %
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: 2.4→47.93 Å / Num. obs: 33554 / % possible obs: 100 % / Redundancy: 26.8 % / Biso Wilson estimate: 35.47 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.107 / Net I/σ(I): 30.8
Reflection shellResolution: 2.4→2.53 Å / Rmerge(I) obs: 0.596 / Num. unique obs: 4819 / CC1/2: 0.966

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.14_3260refinement
SCALAdata scaling
AutoSolphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.4→47.93 Å / SU ML: 0.3172 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.2419 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2696 1617 4.82 %
Rwork0.2083 31935 -
obs0.2112 33552 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.95 Å2
Refinement stepCycle: LAST / Resolution: 2.4→47.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4898 0 68 215 5181
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00765097
X-RAY DIFFRACTIONf_angle_d0.91736929
X-RAY DIFFRACTIONf_chiral_restr0.0506730
X-RAY DIFFRACTIONf_plane_restr0.0059901
X-RAY DIFFRACTIONf_dihedral_angle_d5.68862979
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.470.29781260.21542598X-RAY DIFFRACTION99.85
2.47-2.550.33511270.23222620X-RAY DIFFRACTION100
2.55-2.640.36281340.23892624X-RAY DIFFRACTION100
2.64-2.750.31461320.22912634X-RAY DIFFRACTION100
2.75-2.880.30211290.22332640X-RAY DIFFRACTION100
2.88-3.030.24411400.22992633X-RAY DIFFRACTION100
3.03-3.220.28511200.24292644X-RAY DIFFRACTION100
3.22-3.460.32951350.22812653X-RAY DIFFRACTION100
3.46-3.810.24511590.20152644X-RAY DIFFRACTION100
3.81-4.360.25671390.19022682X-RAY DIFFRACTION100
4.36-5.50.21651230.18742723X-RAY DIFFRACTION100
5.5-47.930.24381530.18562840X-RAY DIFFRACTION99.93

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