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- PDB-7c4k: Ancestral L-amino acid oxidase (AncLAAO-N5) ligand free form -

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Basic information

Entry
Database: PDB / ID: 7c4k
TitleAncestral L-amino acid oxidase (AncLAAO-N5) ligand free form
ComponentsAncestral L-amino acid oxidase
KeywordsOXIDOREDUCTASE / L-amino acid oxidase
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE
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)75,7502
Polymers74,9641
Non-polymers7861
Water5,296294
1
A: Ancestral L-amino acid oxidase
hetero molecules

A: Ancestral L-amino acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,4994
Polymers149,9282
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area6790 Å2
ΔGint-32 kcal/mol
Surface area46320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.897, 131.897, 191.225
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 294 / 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: 2.77 Å3/Da / Density % sol: 55.65 %
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: Mar 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→47.81 Å / Num. obs: 33315 / % possible obs: 100 % / Redundancy: 26.4 % / Biso Wilson estimate: 34.07 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.125 / Net I/σ(I): 25.9
Reflection shellResolution: 2.4→2.53 Å / Rmerge(I) obs: 0.674 / Num. unique obs: 4796 / CC1/2: 0.967

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Processing

Software
NameVersionClassification
BSSdata collection
PHENIX1.14_3260refinement
XDSdata reduction
SCALAdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→47.8 Å / SU ML: 0.2586 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.4428 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2305 1587 4.76 %
Rwork0.1706 31723 -
obs0.1734 33310 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.66 Å2
Refinement stepCycle: LAST / Resolution: 2.4→47.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4898 0 53 294 5245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00785081
X-RAY DIFFRACTIONf_angle_d0.92336907
X-RAY DIFFRACTIONf_chiral_restr0.0519729
X-RAY DIFFRACTIONf_plane_restr0.0055899
X-RAY DIFFRACTIONf_dihedral_angle_d5.78022974
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.480.24251350.18952845X-RAY DIFFRACTION99.87
2.48-2.570.29131350.19072827X-RAY DIFFRACTION100
2.57-2.670.24811370.18972862X-RAY DIFFRACTION100
2.67-2.790.25861470.18952834X-RAY DIFFRACTION100
2.79-2.940.25481370.19642858X-RAY DIFFRACTION100
2.94-3.120.25961430.20262849X-RAY DIFFRACTION99.97
3.12-3.360.2511370.18882884X-RAY DIFFRACTION100
3.36-3.70.23841660.16572869X-RAY DIFFRACTION100
3.7-4.230.2031530.14912882X-RAY DIFFRACTION100
4.23-5.330.19921270.13772966X-RAY DIFFRACTION100
5.33-47.80.21221700.17173047X-RAY DIFFRACTION99.88

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