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- PDB-4rc5: Crystal structure of cyanobacterial aldehyde-deformylating oxygenase -

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Basic information

Entry
Database: PDB / ID: 4rc5
TitleCrystal structure of cyanobacterial aldehyde-deformylating oxygenase
Components(Aldehyde decarbonylase) x 2
KeywordsLYASE / 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
: / HEXADECAN-1-OL / Aldehyde decarbonylase
Similarity search - Component
Biological speciesSynechococcus elongatus PCC 7942 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsJia, C.J. / Li, M. / Chang, W.R.
CitationJournal: Protein Cell / Year: 2015
Title: Structural insights into the catalytic mechanism of aldehyde-deformylating oxygenases.
Authors: Jia, C. / Li, M. / Li, J. / Zhang, J. / Zhang, H. / Cao, P. / Pan, X. / Lu, X. / Chang, W.
History
DepositionSep 14, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aldehyde decarbonylase
B: Aldehyde decarbonylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2796
Polymers50,6832
Non-polymers5974
Water3,081171
1
A: Aldehyde decarbonylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6394
Polymers25,2851
Non-polymers3543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Aldehyde decarbonylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6402
Polymers25,3981
Non-polymers2421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.656, 61.833, 124.926
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 25284.721 Da / Num. of mol.: 1 / Fragment: UNP residues 11-231
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus PCC 7942 (bacteria)
Strain: PCC 7942 / Gene: Synpcc7942_1593 / Production host: Escherichia coli (E. coli)
References: UniProt: Q54764, aldehyde oxygenase (deformylating)
#2: Protein Aldehyde decarbonylase / AD / Fatty aldehyde decarbonylase


Mass: 25397.879 Da / Num. of mol.: 1 / Fragment: UNP residues 10-231
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus PCC 7942 (bacteria)
Strain: PCC 7942 / Gene: Synpcc7942_1593 / Production host: Escherichia coli (E. coli)
References: UniProt: Q54764, aldehyde oxygenase (deformylating)
#3: Chemical ChemComp-PL3 / HEXADECAN-1-OL


Mass: 242.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H34O
#4: Chemical ChemComp-FE2 / FE (II) ION


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


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.35 Å3/Da / Density % sol: 47.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: 0.2M L-proline, 0.1M Hepes, 25%(w/v) PEG1500, pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 21892 / Num. obs: 21848 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.3→2.34 Å / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QUW

4quw


Resolution: 2.3→43.944 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.912 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.399 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23789 1112 5.1 %RANDOM
Rwork0.20874 ---
all0.21021 20844 --
obs0.21024 20675 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.051 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å2-0 Å20 Å2
2---1.1 Å20 Å2
3---0.78 Å2
Refinement stepCycle: LAST / Resolution: 2.3→43.944 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3552 0 36 171 3759
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193648
X-RAY DIFFRACTIONr_bond_other_d00.023487
X-RAY DIFFRACTIONr_angle_refined_deg1.441.9584897
X-RAY DIFFRACTIONr_angle_other_deg3.67338007
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9125441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69824.536194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.67515648
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1941526
X-RAY DIFFRACTIONr_chiral_restr0.1160.2520
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024161
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02865
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_it1.2792.4521770
X-RAY DIFFRACTIONr_mcbond_other1.2762.451769
X-RAY DIFFRACTIONr_mcangle_it1.9443.6692209
X-RAY DIFFRACTIONr_mcangle_other1.9453.6712210
X-RAY DIFFRACTIONr_scbond_it2.1922.721878
X-RAY DIFFRACTIONr_scbond_other2.1922.721878
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3793.9732689
X-RAY DIFFRACTIONr_long_range_B_refined4.18519.7864428
X-RAY DIFFRACTIONr_long_range_B_other4.15819.7184380
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.297→2.356 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 71 -
Rwork0.214 1391 -
obs--92.65 %

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