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- PDB-4kvs: Crystal Structure of Prochlorococcus marinus aldehyde-deformylati... -

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Basic information

Entry
Database: PDB / ID: 4kvs
TitleCrystal Structure of Prochlorococcus marinus aldehyde-deformylating oxygenase (mutant A134F)
ComponentsAldehyde decarbonylase
KeywordsOXIDOREDUCTASE / Propane production / Aldehyde-deformylating oxygenase
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
HEXANOIC ACID / : / Aldehyde decarbonylase
Similarity search - Component
Biological speciesProchlorococcus marinus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsLevy, C.W. / Khara, B. / Menon, N. / Mansell, D. / Das, D. / Marsh, E.N.G. / Leys, D. / Scrutton, N.S.
CitationJournal: Chembiochem / Year: 2013
Title: Production of propane and other short-chain alkanes by structure-based engineering of ligand specificity in aldehyde-deformylating oxygenase.
Authors: Khara, B. / Menon, N. / Levy, C. / Mansell, D. / Das, D. / Marsh, E.N. / Leys, D. / Scrutton, N.S.
History
DepositionMay 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aldehyde decarbonylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5694
Polymers27,3411
Non-polymers2283
Water5,098283
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Aldehyde decarbonylase
hetero molecules

A: Aldehyde decarbonylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1388
Polymers54,6822
Non-polymers4566
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area1840 Å2
ΔGint0 kcal/mol
Surface area18270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.060, 77.060, 115.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-582-

HOH

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Components

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


Mass: 27341.070 Da / Num. of mol.: 1 / Mutation: A134F
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) / Strain (production host): BL21 DE3
References: UniProt: Q7V6D4, aldehyde oxygenase (deformylating)
#2: Chemical ChemComp-6NA / HEXANOIC ACID


Mass: 116.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O2
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 3.15 Å3/Da / Density % sol: 60.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 0.1 M SPG buffer, and 25 % w/v PEG 1500 Drop size 200nl plus 200nl , pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 30, 2012
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.67→54.49 Å / Num. obs: 41207
Reflection shellResolution: 1.67→1.73 Å / Num. unique all: 4059 / % possible all: 99.98

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Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.67→54.49 Å / SU ML: 0.15 / σ(F): 1.91 / Phase error: 17.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1855 2071 5.03 %Random
Rwork0.1792 ---
obs0.1796 41207 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.67→54.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1761 0 10 283 2054
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0191842
X-RAY DIFFRACTIONf_angle_d1.0312504
X-RAY DIFFRACTIONf_dihedral_angle_d12.89699
X-RAY DIFFRACTIONf_chiral_restr0.068274
X-RAY DIFFRACTIONf_plane_restr0.004325
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.70890.23111280.22212586X-RAY DIFFRACTION100
1.7089-1.75160.22621390.21242560X-RAY DIFFRACTION100
1.7516-1.7990.28271320.21662549X-RAY DIFFRACTION100
1.799-1.85190.23351580.2012544X-RAY DIFFRACTION100
1.8519-1.91170.2561490.19792562X-RAY DIFFRACTION100
1.9117-1.980.21071260.19532587X-RAY DIFFRACTION100
1.98-2.05930.24351280.18872571X-RAY DIFFRACTION100
2.0593-2.1530.19211300.18172606X-RAY DIFFRACTION100
2.153-2.26650.16921510.17022584X-RAY DIFFRACTION100
2.2665-2.40850.16381420.1742595X-RAY DIFFRACTION100
2.4085-2.59450.20841420.17712588X-RAY DIFFRACTION100
2.5945-2.85560.20691320.17962625X-RAY DIFFRACTION100
2.8556-3.26870.1891420.18282640X-RAY DIFFRACTION100
3.2687-4.11810.16161370.16882686X-RAY DIFFRACTION100
4.1181-54.51860.16191350.17452853X-RAY DIFFRACTION100

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