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- PDB-5uwz: Protein 12 with aldehyde deformylating oxygenase activity from Gl... -

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Basic information

Entry
Database: PDB / ID: 5uwz
TitleProtein 12 with aldehyde deformylating oxygenase activity from Gloeobacter violaceus
ComponentsAldehyde decarbonylase
KeywordsLYASE / decarbonylase / iron / ferritin
Function / homology
Function and homology information


aldehyde oxygenase (deformylating) activity / 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 speciesGloeobacter violaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.25 Å
AuthorsWilson, D.K.
CitationJournal: To Be Published
Title: Protein 12 with aldehyde deformylating oxygenase activity from Gloeobacter violaceus
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 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8124
Polymers27,4031
Non-polymers4093
Water3,639202
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.842, 95.424, 39.255
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 27402.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gloeobacter violaceus (strain PCC 7421) (bacteria)
Strain: PCC 7421 / Gene: gll3146 / Production host: Escherichia coli (E. coli)
References: UniProt: Q7NGM3, aldehyde oxygenase (deformylating)
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-STE / STEARIC ACID


Mass: 284.477 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H36O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 48.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2 / Details: 10% PEG 3000, 100 mM citrate, 200 mM NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.03317 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 1.25→56.4 Å / Num. obs: 73111 / % possible obs: 99.7 % / Redundancy: 4.01 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 20.6
Reflection shellResolution: 1.25→1.27 Å / Rmerge(I) obs: 0.255 / Mean I/σ(I) obs: 2.5 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 1.25→56.36 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.087 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.036 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16743 3701 5.1 %RANDOM
Rwork0.13869 ---
obs0.14014 69361 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.842 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å2-0 Å2
2--0.94 Å2-0 Å2
3----0.65 Å2
Refinement stepCycle: 1 / Resolution: 1.25→56.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1741 0 28 202 1971
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191846
X-RAY DIFFRACTIONr_bond_other_d0.0010.021759
X-RAY DIFFRACTIONr_angle_refined_deg1.6491.9542492
X-RAY DIFFRACTIONr_angle_other_deg0.88534035
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3255228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.0724.27196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.97815311
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7231514
X-RAY DIFFRACTIONr_chiral_restr0.0950.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022133
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02441
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_it1.3361.336900
X-RAY DIFFRACTIONr_mcbond_other1.2641.333899
X-RAY DIFFRACTIONr_mcangle_it1.6762.0131132
X-RAY DIFFRACTIONr_mcangle_other1.6772.0161133
X-RAY DIFFRACTIONr_scbond_it3.4571.872945
X-RAY DIFFRACTIONr_scbond_other3.4551.873946
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0422.6411361
X-RAY DIFFRACTIONr_long_range_B_refined4.21112.9592408
X-RAY DIFFRACTIONr_long_range_B_other4.2112.9642409
X-RAY DIFFRACTIONr_rigid_bond_restr2.99933604
X-RAY DIFFRACTIONr_sphericity_free32.074572
X-RAY DIFFRACTIONr_sphericity_bonded10.26953700
LS refinement shellResolution: 1.251→1.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 275 -
Rwork0.207 5011 -
obs--98.82 %

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