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- PDB-5k52: Crystal structures of aldehyde deformylating oxygenase from Limno... -

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Basic information

Entry
Database: PDB / ID: 5k52
TitleCrystal structures of aldehyde deformylating oxygenase from Limnothrix sp. KNUA012
ComponentsAldehyde decarbonylase
KeywordsMETAL BINDING PROTEIN / ferritin-like di-iron protein
Function / homology
Function and homology information


aldehyde oxygenase (deformylating) / : / : / transition metal ion binding
Similarity search - Function
Long-chain fatty aldehyde decarbonylase / Long-chain fatty aldehyde decarbonylase / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
octadecanal / Aldehyde decarbonylase
Similarity search - Component
Biological speciesLimnothrix sp. KNUA012 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPark, A.K. / Kim, H-.W.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Korea Polar Research InstitutePE16070 Korea, Republic Of
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2016
Title: Crystal structures of aldehyde deformylating oxygenase from Limnothrix sp. KNUA012 and Oscillatoria sp. KNUA011.
Authors: Park, A.K. / Kim, I.S. / Jeon, B.W. / Roh, S.J. / Ryu, M.Y. / Baek, H.R. / Jo, S.W. / Kim, Y.S. / Park, H. / Lee, J.H. / Yoon, H.S. / Kim, H.W.
History
DepositionMay 23, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Aldehyde decarbonylase
B: Aldehyde decarbonylase
C: Aldehyde decarbonylase
D: Aldehyde decarbonylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,2066
Polymers117,6694
Non-polymers5372
Water2,126118
1
A: Aldehyde decarbonylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6862
Polymers29,4171
Non-polymers2681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Aldehyde decarbonylase


Theoretical massNumber of molelcules
Total (without water)29,4171
Polymers29,4171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Aldehyde decarbonylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6862
Polymers29,4171
Non-polymers2681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Aldehyde decarbonylase


Theoretical massNumber of molelcules
Total (without water)29,4171
Polymers29,4171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.658, 135.658, 71.795
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: Protein
Aldehyde decarbonylase / AD / Fatty aldehyde decarbonylase


Mass: 29417.166 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Limnothrix sp. KNUA012 (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: A0A193CDY9, aldehyde oxygenase (deformylating)
#2: Chemical ChemComp-OCD / octadecanal


Mass: 268.478 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H36O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA sequence reference for this protein does not currently exist.

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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: 56.18 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: Bis-Tris propane, sodium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 52273 / % possible obs: 99.2 % / Redundancy: 12 % / Rmerge(I) obs: 0.192 / Rpim(I) all: 0.071 / Rrim(I) all: 0.202 / Χ2: 2.423 / Net I/av σ(I): 24.037 / Net I/σ(I): 4.7 / Num. measured all: 628548
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.4-2.4412.925730.6540.5231.369100
2.44-2.4912.926430.710.4481.435100
2.49-2.5312.926070.7680.3971.501100
2.53-2.5912.926470.8020.3811.488100
2.59-2.641325870.7860.3261.556100
2.64-2.712.825930.8570.2641.6951000.9130.951
2.7-2.7712.826310.9330.2191.7961000.7540.786
2.77-2.8512.826460.9080.1971.9081000.6810.709
2.85-2.9312.726050.940.1811.9811000.620.646
2.93-3.0212.626490.9470.1542.1771000.5260.548
3.02-3.1312.526120.9650.1262.3671000.4280.447
3.13-3.2612.426260.9810.1062.5171000.3570.373
3.26-3.4112.226230.9840.0882.7811000.2910.305
3.41-3.5811.826290.9870.0713.1799.90.230.241
3.58-3.8111.326290.9880.0593.4899.50.1850.195
3.81-4.110.725960.9890.053.71798.90.1510.16
4.1-4.529.925860.9880.0443.816970.1260.134
4.52-5.1710.126110.990.0383.70898.30.110.117
5.17-6.5111.826670.9930.0343.37699.80.1080.114
6.51-509.425130.990.0354.47191.50.0930.1

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Processing

Software
NameVersionClassification
REFMACrefinement
HKL-2000data collection
SCALEPACKdata scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QUW

4quw


Resolution: 2.4→50.01 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.928 / SU B: 9.784 / SU ML: 0.213 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.31 / ESU R Free: 0.246 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2615 2496 4.9 %RANDOM
Rwork0.2099 ---
obs0.2125 48373 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 147.05 Å2 / Biso mean: 59.6935 Å2 / Biso min: 28.73 Å2
Baniso -1Baniso -2Baniso -3
1-1.57 Å2-0 Å2-0 Å2
2--1.57 Å2-0 Å2
3----3.13 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6972 0 38 118 7128
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 171 -
Rwork0.293 3567 -
all-3738 -
obs--100 %

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