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

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Basic information

Entry
Database: PDB / ID: 4pgk
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
: / 11-[2-(2-ethoxyethoxy)ethoxy]undecanal / Aldehyde decarbonylase
Similarity search - Component
Biological speciesProchlorococcus marinus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.17 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
DepositionMay 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Derived calculations
Revision 1.2Nov 22, 2017Group: Derived calculations / Other ...Derived calculations / Other / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_database_status ...entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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)27,6354
Polymers27,2211
Non-polymers4143
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.340, 77.340, 116.960
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Detailsbiological unit is the same as asym.

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Components

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


Mass: 27221.006 Da / Num. of mol.: 1 / Fragment: UNP residues 1-243 / Mutation: E90K, R191L
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-Y69 / 11-[2-(2-ethoxyethoxy)ethoxy]undecanal


Mass: 302.449 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H34O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 3.5 Å3/Da / Density % sol: 64.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 20% PEG3350, 0.3 M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 11, 2012
RadiationMonochromator: Si[111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.17→22.13 Å / Num. obs: 19412 / % possible obs: 100 % / Redundancy: 14.4 % / Biso Wilson estimate: 40.59 Å2 / Net I/σ(I): 20

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PDB_EXTRACT3.14data extraction
Cootmodel building
BUSTER2.10.0refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TW3

4tw3


Resolution: 2.17→22.13 Å / Cor.coef. Fo:Fc: 0.9379 / Cor.coef. Fo:Fc free: 0.9249 / SU R Cruickshank DPI: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.211 / SU Rfree Blow DPI: 0.159 / SU Rfree Cruickshank DPI: 0.156
RfactorNum. reflection% reflectionSelection details
Rfree0.2234 995 5.12 %RANDOM
Rwork0.2189 ---
obs0.2191 19412 99.98 %-
Displacement parametersBiso max: 110.19 Å2 / Biso mean: 41.51 Å2 / Biso min: 22.59 Å2
Baniso -1Baniso -2Baniso -3
1-2.8921 Å20 Å20 Å2
2--2.8921 Å20 Å2
3----5.7841 Å2
Refine analyzeLuzzati coordinate error obs: 0.334 Å
Refinement stepCycle: final / Resolution: 2.17→22.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1732 0 44 86 1862
Biso mean--41.86 47.19 -
Num. residues----221
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d687SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes56HARMONIC2
X-RAY DIFFRACTIONt_gen_planes286HARMONIC5
X-RAY DIFFRACTIONt_it1949HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion256SEMIHARMONIC5
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_contact2374SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1949HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg2636HARMONIC20.97
X-RAY DIFFRACTIONt_omega_torsion2.02
X-RAY DIFFRACTIONt_other_torsion18.47
LS refinement shellResolution: 2.17→2.29 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2727 156 5.6 %
Rwork0.2282 2628 -
all0.2307 2784 -
obs--99.98 %
Refinement TLS params.Method: refined / Origin x: -20.2646 Å / Origin y: 2.4129 Å / Origin z: -9.657 Å
111213212223313233
T-0.025 Å2-0.0162 Å2-0.0437 Å2--0.1175 Å20.0604 Å2---0.0545 Å2
L1.1716 °2-0.2117 °2-0.3839 °2-1.6156 °2-0.2333 °2--1.0505 °2
S-0.0095 Å °-0.033 Å °-0.0201 Å °0.0525 Å °0.0114 Å °0.0372 Å °-0.0348 Å °0.0037 Å °-0.0019 Å °
Refinement TLS groupSelection details: { A|* }

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