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- PDB-5k53: Crystal structures of aldehyde deformylating oxygenase from Oscil... -

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Basic information

Entry
Database: PDB / ID: 5k53
TitleCrystal structures of aldehyde deformylating oxygenase from Oscillatoria sp. KNUA011
Componentsaldehyde deformylating oxygenase
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
: / STEARIC ACID / Aldehyde decarbonylase
Similarity search - Component
Biological speciesOscillatoria sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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: RCSB / Processing site: PDBJ
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: aldehyde deformylating oxygenase
B: aldehyde deformylating oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3178
Polymers58,5242
Non-polymers7926
Water1,72996
1
A: aldehyde deformylating oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6584
Polymers29,2621
Non-polymers3963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: aldehyde deformylating oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6584
Polymers29,2621
Non-polymers3963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.012, 78.265, 108.861
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 aldehyde deformylating oxygenase


Mass: 29262.240 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oscillatoria sp. (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1D5B390*PLUS
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-STE / STEARIC ACID


Mass: 284.477 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H36O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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 Å3/Da / Density % sol: 38.57 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: Tris, Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97953 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97953 Å / Relative weight: 1
ReflectionResolution: 1.8→50.01 Å / Num. obs: 43714 / % possible obs: 97.4 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.077 / Net I/av σ(I): 45.061 / Net I/σ(I): 12
Reflection shell
Resolution (Å)Redundancy (%)Diffraction-ID% possible allRmerge(I) obs
1.8-1.838197.7
1.83-1.868197.7
1.86-1.97.9198.20.861
1.9-1.948198.40.639
1.94-1.988198.30.525
1.98-2.038198.20.439
2.03-2.088198.30.345
2.08-2.138198.50.277
2.13-2.28198.70.208
2.2-2.278198.80.174
2.27-2.3581990.146
2.35-2.448198.70.131
2.44-2.557.91990.107
2.55-2.697.9199.40.093
2.69-2.867.9199.10.079
2.86-3.087.7199.30.067
3.08-3.397.6199.50.059
3.39-3.887.21990.055
3.88-4.886.4193.20.056
4.88-505.6180.60.06

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
REFMAC5.8.0103refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QUW

4quw


Resolution: 1.8→50.01 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.137 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.128 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2341 2096 4.9 %RANDOM
Rwork0.1929 ---
obs0.1949 41104 97.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 101.18 Å2 / Biso mean: 41.613 Å2 / Biso min: 23.57 Å2
Baniso -1Baniso -2Baniso -3
1-1.81 Å20 Å20 Å2
2---0.56 Å20 Å2
3----1.26 Å2
Refinement stepCycle: final / Resolution: 1.8→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3456 0 42 96 3594
Biso mean--45.85 44.83 -
Num. residues----436
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193581
X-RAY DIFFRACTIONr_bond_other_d0.0040.023470
X-RAY DIFFRACTIONr_angle_refined_deg1.841.954819
X-RAY DIFFRACTIONr_angle_other_deg1.1793.0077971
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1325440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.24525.301183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.88915635
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3551517
X-RAY DIFFRACTIONr_chiral_restr0.1240.2527
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024102
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02839
X-RAY DIFFRACTIONr_mcbond_it3.2613.7221754
X-RAY DIFFRACTIONr_mcbond_other3.2523.7181753
X-RAY DIFFRACTIONr_mcangle_it3.9875.5582193
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 144 -
Rwork0.297 3018 -
all-3162 -
obs--97.8 %

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