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- PDB-7eme: Putative Leptospira interrogans recombinant L-amino acid oxidase -

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Basic information

Entry
Database: PDB / ID: 7eme
TitlePutative Leptospira interrogans recombinant L-amino acid oxidase
ComponentsNAD(P)/FAD-dependent oxidoreductase
KeywordsOXIDOREDUCTASE / Leptospira interrogans / L-amino acid oxidase / FAD-dependent oxidoreductase / Flavoprotein / Putative amine oxidase
Function / homologyFlavin amine oxidase / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain superfamily / oxidoreductase activity / FLAVIN-ADENINE DINUCLEOTIDE / NAD(P)/FAD-dependent oxidoreductase
Function and homology information
Biological speciesLeptospira interrogans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.78 Å
AuthorsVaigundan, D. / Yuvaraj, I. / Krishnaswamy, P.R. / Sekar, K. / Murthy, M.R.N. / Sunita, P.
Citation
Journal: Curr.Sci. / Year: 2022
Title: Structural characterization of a putative recombinant L-amino acid oxidase from Leptospira interrogans
Authors: Vaigundan, D. / Yuvaraj, I. / Sunita, P. / Sekar, K. / Murthy, M.R.N. / Krishnaswamy, P.R.
#1: Journal: To Be Published
Title: Structural characterization of a putative recombinant L-amino acid oxidase from Leptospira interrogans
Authors: Vaigundan, D. / Krishnaswamy, P.R.
History
DepositionApr 13, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2023Group: Database references / Category: citation / citation_author
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NAD(P)/FAD-dependent oxidoreductase
B: NAD(P)/FAD-dependent oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,0914
Polymers98,5202
Non-polymers1,5712
Water13,277737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6460 Å2
ΔGint-31 kcal/mol
Surface area30100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.756, 106.229, 139.916
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein NAD(P)/FAD-dependent oxidoreductase


Mass: 49260.070 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptospira interrogans (bacteria) / Gene: E4414_19605 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: A0A4D8SV19
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 737 / 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: 1.95 Å3/Da / Density % sol: 36.99 %
Crystal growTemperature: 298 K / Method: microbatch
Details: 0.1 M Potassium thiocyanate, 30% w/v Polyethylene glycol monomethyl ether 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0723 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 1.78→84.61 Å / Num. obs: 74369 / % possible obs: 99.1 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.037 / Rrim(I) all: 0.124 / Net I/σ(I): 14.3
Reflection shellResolution: 1.78→1.81 Å / Rmerge(I) obs: 0.39 / Num. unique obs: 4197 / CC1/2: 0.978 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.78→70.06 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.916 / SU B: 2.573 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.133 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2195 3634 5 %RANDOM
Rwork0.1744 ---
obs0.1767 69277 97.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 73.44 Å2 / Biso mean: 15.409 Å2 / Biso min: 6.51 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å2-0 Å20 Å2
2--0.36 Å2-0 Å2
3---0.06 Å2
Refinement stepCycle: final / Resolution: 1.78→70.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6234 0 106 737 7077
Biso mean--9.19 24.79 -
Num. residues----825
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0136508
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176115
X-RAY DIFFRACTIONr_angle_refined_deg1.6431.6358856
X-RAY DIFFRACTIONr_angle_other_deg1.4931.57414021
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4265839
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.76322.238286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.718151075
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6311536
X-RAY DIFFRACTIONr_chiral_restr0.0780.2906
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027410
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021492
LS refinement shellResolution: 1.78→1.824 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.216 227 -
Rwork0.162 5200 -
obs--99.71 %

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