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- PDB-4pg1: Insights into Substrate and Metal Binding from the Crystal Struct... -

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Basic information

Entry
Database: PDB / ID: 4pg1
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) / : / : / 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
: / (1S,2S)-2-nonylcyclopropanecarboxylic acid / Aldehyde decarbonylase
Similarity search - Component
Biological speciesProchlorococcus marinus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 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 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Database references
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 ...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_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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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)27,8796
Polymers27,2651
Non-polymers6145
Water3,423190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.122, 77.122, 116.197
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: 27264.975 Da / Num. of mol.: 1 / Fragment: UNP residues 2-243
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-Y39 / (1S,2S)-2-nonylcyclopropanecarboxylic acid


Mass: 212.328 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H24O2
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 3.44 Å3/Da / Density % sol: 64.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 35% PEG400, 0.1M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0781 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 24, 2013
RadiationMonochromator: Si[111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 1.7→36.6 Å / Num. obs: 39033 / % possible obs: 99.9 % / Redundancy: 14.2 % / Biso Wilson estimate: 28.73 Å2 / Net I/σ(I): 20

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
BUSTER-TNTBUSTER 2.8.0refinement
PDB_EXTRACT3.14data extraction
Cootmodel building
BUSTER2.8.0refinement
PHASERphasing
MD2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TW3

4tw3


Resolution: 1.7→24.58 Å / Cor.coef. Fo:Fc: 0.9609 / Cor.coef. Fo:Fc free: 0.9567 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.1914 1960 5.02 %RANDOM
Rwork0.1803 ---
obs0.1808 39022 99.9 %-
Displacement parametersBiso max: 92.68 Å2 / Biso mean: 29.95 Å2 / Biso min: 15.94 Å2
Baniso -1Baniso -2Baniso -3
1-0.4765 Å20 Å20 Å2
2--0.4765 Å20 Å2
3----0.953 Å2
Refine analyzeLuzzati coordinate error obs: 0.212 Å
Refinement stepCycle: final / Resolution: 1.7→24.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1741 0 36 190 1967
Biso mean--44.42 39.95 -
Num. residues----222
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d659SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes49HARMONIC2
X-RAY DIFFRACTIONt_gen_planes277HARMONIC5
X-RAY DIFFRACTIONt_it1855HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion245SEMIHARMONIC5
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_contact2379SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1855HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2515HARMONIC20.87
X-RAY DIFFRACTIONt_omega_torsion2.56
X-RAY DIFFRACTIONt_other_torsion16.43
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.221 131 4.96 %
Rwork0.2009 2509 -
all0.2019 2640 -
Refinement TLS params.Method: refined / Origin x: 1.9545 Å / Origin y: -20.257 Å / Origin z: 9.4871 Å
111213212223313233
T-0.069 Å2-0.0072 Å2-0.0385 Å2--0.0206 Å20.028 Å2---0.0409 Å2
L1.5574 °2-0.1229 °2-0.1961 °2-0.5756 °2-0.0002 °2--0.8284 °2
S0.0086 Å °0.0757 Å °-0.0203 Å °-0.0198 Å °-0.0004 Å °0.0248 Å °-0.0132 Å °-0.0415 Å °-0.0081 Å °
Refinement TLS groupSelection details: { A|21 - A|242 }

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