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- PDB-5ux2: Protein 19 with aldehyde deformylating oxidase activity from Syne... -

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Basic information

Entry
Database: PDB / ID: 5ux2
TitleProtein 19 with aldehyde deformylating oxidase activity from Synechococcus
ComponentsAldehyde decarbonylase
KeywordsLYASE / decarbonylase / iron / ferritin
Function / homology
Function and homology information


aldehyde oxygenase (deformylating) / octadecanal decarbonylase activity / aldehyde oxygenase (deformylating) activity / 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
: / PROPANOIC ACID / Aldehyde decarbonylase
Similarity search - Component
Biological speciesSynechococcus sp. RS9917 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsWilson, D.K. / Mak, W.S. / Siegel, J.B.
CitationJournal: To Be Published
Title: Protein 19 with aldehyde deformylating oxidase activity from Synechococcus
Authors: Wilson, D.K. / Mak, W.S. / Siegel, J.B.
History
DepositionFeb 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Oct 4, 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 / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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 decarbonylase
B: Aldehyde decarbonylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9428
Polymers52,5702
Non-polymers3726
Water79344
1
A: Aldehyde decarbonylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4714
Polymers26,2851
Non-polymers1863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Aldehyde decarbonylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4714
Polymers26,2851
Non-polymers1863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.986, 90.227, 109.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 26285.074 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus sp. RS9917 (bacteria) / Gene: RS9917_12945 / Production host: Escherichia coli (E. coli)
References: UniProt: A3Z6M0, aldehyde oxygenase (deformylating)
#2: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-PPI / PROPANOIC ACID / Propionic acid


Mass: 74.079 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O

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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: 2.39 Å3/Da / Density % sol: 48.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25.9 mg/ml 17% PEG 4000, 8.5 isopropanol, 85 mM Hepes

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.99→109.06 Å / Num. obs: 33222 / % possible obs: 95.3 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 11.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UW2

5uw2


Resolution: 1.99→109.06 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.926 / SU B: 5.522 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.172 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25355 1024 3.1 %RANDOM
Rwork0.21106 ---
obs0.21238 31991 94.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.704 Å2
Baniso -1Baniso -2Baniso -3
1--1.61 Å20 Å2-0 Å2
2---1.08 Å20 Å2
3---2.69 Å2
Refinement stepCycle: 1 / Resolution: 1.99→109.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3438 0 14 44 3496
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193510
X-RAY DIFFRACTIONr_bond_other_d0.0010.023392
X-RAY DIFFRACTIONr_angle_refined_deg1.3551.9554746
X-RAY DIFFRACTIONr_angle_other_deg0.81937714
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0085436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.47322.333180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.00715576
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9341544
X-RAY DIFFRACTIONr_chiral_restr0.0750.2526
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024042
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02874
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4453.7541750
X-RAY DIFFRACTIONr_mcbond_other2.4463.7521749
X-RAY DIFFRACTIONr_mcangle_it3.4095.6132184
X-RAY DIFFRACTIONr_mcangle_other3.4085.6152185
X-RAY DIFFRACTIONr_scbond_it3.0574.2911760
X-RAY DIFFRACTIONr_scbond_other3.0564.291761
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7976.2572563
X-RAY DIFFRACTIONr_long_range_B_refined6.19530.3484125
X-RAY DIFFRACTIONr_long_range_B_other6.19530.354112
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.994→2.046 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 58 -
Rwork0.29 2084 -
obs--83.64 %

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