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- PDB-7fgp: Crystal structure of Aureimonas altamirenisis flavin-containing o... -

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Basic information

Entry
Database: PDB / ID: 7fgp
TitleCrystal structure of Aureimonas altamirenisis flavin-containing opine dehydrogenase (FAD-bound form)
ComponentsGlycine/D-amino acid oxidase
KeywordsFLAVOPROTEIN / Opine / Nopaline / Glycine oxidase family
Function / homologyFAD dependent oxidoreductase / FAD dependent oxidoreductase / FAD/NAD(P)-binding domain superfamily / oxidoreductase activity / FLAVIN-ADENINE DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / Glycine/D-amino acid oxidase
Function and homology information
Biological speciesAureimonas altamirensis DSM 21988 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.47 Å
AuthorsYoshiwara, K. / Watanabe, Y. / Watanabe, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structural basis for Flavin-containing opine dehydrogenase from Aureimonas altamirensis
Authors: Yoshiwara, K. / Watanabe, S. / Watanabe, Y.
History
DepositionJul 27, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycine/D-amino acid oxidase
B: Glycine/D-amino acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,81116
Polymers84,1012
Non-polymers2,71014
Water16,664925
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8960 Å2
ΔGint-69 kcal/mol
Surface area26510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.727, 105.727, 261.837
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-855-

HOH

21A-891-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glycine/D-amino acid oxidase


Mass: 42050.539 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aureimonas altamirensis DSM 21988 (bacteria)
Gene: SAMN02745911_3969 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1M6P181

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Non-polymers , 5 types, 939 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 925 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.52 Å3/Da / Density % sol: 51.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Lithium sulfate, 0.1 M Bis-tris pH 5.5, 24.5% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.47→49.02 Å / Num. obs: 146819 / % possible obs: 100 % / Redundancy: 68.7 % / CC1/2: 0.987 / Rmerge(I) obs: 0.635 / Rpim(I) all: 0.076 / Rrim(I) all: 0.64 / Net I/σ(I): 10.1 / Num. measured all: 10079189 / Scaling rejects: 95628
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.47-1.543.62.11531296471750.8420.3212.1392.3100
8.05-49.0264.50.3277112311030.9870.040.32918.199.6

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
Aimless0.7.4data scaling
PHENIXmodel building
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.47→49.018 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1853 7341 5.01 %
Rwork0.1736 139315 -
obs0.1742 146656 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 59.05 Å2 / Biso mean: 20.9636 Å2 / Biso min: 6.31 Å2
Refinement stepCycle: final / Resolution: 1.47→49.018 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5584 0 174 925 6683
Biso mean--22.3 30.71 -
Num. residues----743
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.47-1.48670.25862380.23484586
1.4867-1.50420.25662420.21754539
1.5042-1.52260.24272360.20834585
1.5226-1.54180.22832520.2034571
1.5418-1.56210.2332310.19734581
1.5621-1.58350.22292460.19094577
1.5835-1.60610.20532410.18464587
1.6061-1.63010.21052460.18074580
1.6301-1.65560.19972390.1884585
1.6556-1.68270.21112480.18674577
1.6827-1.71170.20522410.18484604
1.7117-1.74290.20262360.17874578
1.7429-1.77640.18042300.1764606
1.7764-1.81270.2022430.17264600
1.8127-1.85210.18612220.17784640
1.8521-1.89520.19142440.16944604
1.8952-1.94260.19822440.17274608
1.9426-1.99510.17852190.17874671
1.9951-2.05380.20512200.17244623
2.0538-2.12010.1842700.1694628
2.1201-2.19590.16962270.16624620
2.1959-2.28380.16622620.174656
2.2838-2.38770.17372640.1714631
2.3877-2.51360.19222620.17524668
2.5136-2.67110.22410.18394678
2.6711-2.87730.19242580.17834697
2.8773-3.16680.1832390.17274746
3.1668-3.62490.17382420.16264764
3.6249-4.56650.15162620.14854839
4.5665-49.0180.18112960.17975086

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