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- PDB-4tw3: Insights into Substrate and Metal Binding from the Crystal Struct... -

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Basic information

Entry
Database: PDB / ID: 4tw3
TitleInsights into Substrate and Metal Binding from the Crystal Structure of Cyanobacterial Aldehyde Deformylating Oxygenase with Substrate Bound
ComponentsAldehyde decarbonylase
KeywordsOXIDOREDUCTASE / non-heme di-iron protein / hydrocarbon production / alpha-helix
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 speciesProchlorococcus marinus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsBuer, B.C. / Paul, B. / Das, D. / Stuckey, J.A. / Marsh, E.N.G.
CitationJournal: Acs Chem.Biol. / Year: 2014
Title: Insights into substrate and metal binding from the crystal structure of cyanobacterial aldehyde deformylating oxygenase with substrate bound.
Authors: Buer, B.C. / Paul, B. / Das, D. / Stuckey, J.A. / Marsh, E.N.
History
DepositionJun 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Database references
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid

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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)25,6505
Polymers25,1921
Non-polymers4584
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.215, 77.215, 116.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 25191.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Prochlorococcus marinus (bacteria) / Strain: MIT 9313 / Gene: PMT_1231 / Production host: Escherichia coli (E. coli)
References: UniProt: Q7V6D4, aldehyde oxygenase (deformylating)
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-STE / STEARIC ACID


Mass: 284.477 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H36O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.46 Å3/Da / Density % sol: 64.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 25% PEG 1000, 0.1 M HEPES / PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.6→38.61 Å / Num. obs: 47171 / % possible obs: 100 % / Redundancy: 14.4 % / Biso Wilson estimate: 20.98 Å2 / Net I/σ(I): 20
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 14.3 % / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

SoftwareName: BUSTER / Version: 2.10.0 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OC5

2oc5


Resolution: 1.6→38.61 Å / Cor.coef. Fo:Fc: 0.9577 / Cor.coef. Fo:Fc free: 0.9559 / SU R Cruickshank DPI: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.071 / SU Rfree Blow DPI: 0.068 / SU Rfree Cruickshank DPI: 0.064
RfactorNum. reflection% reflectionSelection details
Rfree0.1897 2386 5.06 %RANDOM
Rwork0.175 ---
obs0.1757 47171 99.97 %-
Displacement parametersBiso mean: 22.29 Å2
Baniso -1Baniso -2Baniso -3
1-0.3898 Å20 Å20 Å2
2--0.3898 Å20 Å2
3----0.7795 Å2
Refine analyzeLuzzati coordinate error obs: 0.172 Å
Refinement stepCycle: 1 / Resolution: 1.6→38.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1815 0 26 293 2134
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011878HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.92548HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d681SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes53HARMONIC2
X-RAY DIFFRACTIONt_gen_planes283HARMONIC5
X-RAY DIFFRACTIONt_it1878HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.64
X-RAY DIFFRACTIONt_other_torsion14.93
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion250SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2558SEMIHARMONIC4
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.1801 159 4.63 %
Rwork0.1718 3273 -
all0.1722 3432 -
obs--99.97 %
Refinement TLS params.Method: refined / Origin x: -20.4648 Å / Origin y: 1.8418 Å / Origin z: -9.5515 Å
111213212223313233
T-0.0313 Å20.0011 Å2-0.0103 Å2--0.0534 Å20.0304 Å2---0.0304 Å2
L0.5135 °2-0.018 °2-0.0239 °2-1.0149 °2-0.0565 °2--0.7513 °2
S0.0077 Å °-0.0045 Å °0.0003 Å °0.0221 Å °0.0028 Å °0.0129 Å °0.0131 Å °0.0013 Å °-0.0106 Å °
Refinement TLS groupSelection details: { A|21 - A|242 }

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