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- PDB-7og2: Crystal structure of Pseudoalteromonas luteoviolacea L-amino acid... -

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Basic information

Entry
Database: PDB / ID: 7og2
TitleCrystal structure of Pseudoalteromonas luteoviolacea L-amino acid oxidase
ComponentsAmine oxidoreductase
KeywordsOXIDOREDUCTASE / Flavoprotein / L-amino acid
Function / homology: / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain superfamily / oxidoreductase activity / nucleotide binding / FLAVIN-ADENINE DINUCLEOTIDE / : / Amine oxidoreductase
Function and homology information
Biological speciesPseudoalteromonas luteoviolacea DSM 6061 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsRozeboom, H.J. / Savino, S. / Fraaije, M.W.
CitationJournal: Catalysts / Year: 2021
Title: Kinetic and Structural Properties of a Robust Bacterial L-Amino Acid Oxidase
Authors: Savino, S. / Meijer, J.D. / Rozeboom, H.J. / van Beek, H.L. / Fraaije, M.W.
History
DepositionMay 6, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Amine oxidoreductase
B: Amine oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,50616
Polymers148,1232
Non-polymers2,38314
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9560 Å2
ΔGint-117 kcal/mol
Surface area47070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.045, 134.159, 251.920
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Amine oxidoreductase


Mass: 74061.633 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoalteromonas luteoviolacea DSM 6061 (bacteria)
Gene: N475_02295 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A166WMK8

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Non-polymers , 5 types, 113 molecules

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


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Pt
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.63 Å3/Da / Density % sol: 53 % / Description: cubes
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 0.1 M Tris pH 7-8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96862 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96862 Å / Relative weight: 1
ReflectionResolution: 2.8→48.49 Å / Num. obs: 38863 / % possible obs: 100 % / Redundancy: 3.4 % / Biso Wilson estimate: 55.24 Å2 / CC1/2: 0.995 / Rpim(I) all: 0.053 / Net I/σ(I): 8.3
Reflection shellResolution: 2.8→2.92 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 4684 / CC1/2: 0.824 / Rpim(I) all: 0.387

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7C4K

7c4k


Resolution: 2.8→47.17 Å / SU ML: 0.375 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.5101
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2699 1959 5.05 %
Rwork0.2025 36811 -
obs0.2059 38770 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.79 Å2
Refinement stepCycle: LAST / Resolution: 2.8→47.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9872 0 138 99 10109
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007910255
X-RAY DIFFRACTIONf_angle_d1.003213940
X-RAY DIFFRACTIONf_chiral_restr0.05471474
X-RAY DIFFRACTIONf_plane_restr0.00871816
X-RAY DIFFRACTIONf_dihedral_angle_d16.03081350
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.870.40471340.29882573X-RAY DIFFRACTION99.93
2.87-2.950.35751320.26142617X-RAY DIFFRACTION99.96
2.95-3.030.29271450.24412572X-RAY DIFFRACTION99.89
3.03-3.130.27411380.22242615X-RAY DIFFRACTION99.96
3.13-3.240.32761400.21362593X-RAY DIFFRACTION99.89
3.24-3.370.30621300.2142618X-RAY DIFFRACTION99.93
3.37-3.530.2521310.19182623X-RAY DIFFRACTION99.93
3.53-3.710.25591380.18082621X-RAY DIFFRACTION99.93
3.71-3.950.25841460.18282627X-RAY DIFFRACTION99.89
3.95-4.250.28221420.18012609X-RAY DIFFRACTION99.96
4.25-4.680.23631410.16762610X-RAY DIFFRACTION98.81
4.68-5.350.24631440.17982666X-RAY DIFFRACTION100
5.35-6.740.28081530.22512663X-RAY DIFFRACTION99.96
6.74-47.170.24121450.21772804X-RAY DIFFRACTION99.86
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.10939149550.1609757133510.1119204491220.992865809728-0.02203540671320.4986304569210.0354176152537-0.3366358239510.1453640767530.205061939415-0.0425127849212-0.132993937187-0.04648830186420.1102784295410.006838093364250.387639030225-0.02218176110140.007546540925310.488026685232-0.05865936734010.37592779286565.403763957427.062170719235.0213286618
20.921393101791-0.269581426041-0.05398665337020.585624435550.01030070746630.854160297727-0.0275937383903-0.115564687560.1638901773270.0330093397738-0.0206738164780.0809810031609-0.13700168898-0.1997952219720.04709437186670.42340352756-0.009211911842340.002733293278460.517672540079-0.06431570171470.45522512014626.186773684835.325757788627.1294106652
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 10 through 631)AA10 - 6311 - 622
22(chain 'B' and resid 15 through 624)BE15 - 6241 - 610

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