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- PDB-4rc7: Crystal structure of cyanobacterial aldehyde-deformylating oxygen... -

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Basic information

Entry
Database: PDB / ID: 4rc7
TitleCrystal structure of cyanobacterial aldehyde-deformylating oxygenase F86YF87Y mutant
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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_ref_seq_dif / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)51,3568
Polymers50,6472
Non-polymers7086
Water2,846158
1
A: Aldehyde decarbonylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5724
Polymers25,2181
Non-polymers3543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Aldehyde decarbonylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7844
Polymers25,4301
Non-polymers3543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.014, 62.109, 125.003
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: 25217.592 Da / Num. of mol.: 1 / Fragment: UNP residues 11-230 / Mutation: F86Y, F87Y
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: 25429.879 Da / Num. of mol.: 1 / Fragment: UNP residues 10-231 / Mutation: F86Y, F87Y
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.: 4 / Source method: obtained synthetically / Formula: Fe
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.38 Å3/Da / Density % sol: 48.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: 0.02M adenosine-5'-triphosphate disodium salt hydrate, 0.2M L-proline, 0.1M Hepes pH 7.1, 25%(w/v) PEG1500 , VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.7382 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7382 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 25089 / Num. obs: 24713 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.2→2.28 Å / % possible all: 99.1

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Processing

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

4quw


Resolution: 2.2→41.407 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.901 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.309 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23763 1252 5.1 %RANDOM
Rwork0.20514 ---
obs0.20676 23389 98.21 %-
all-23815 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.482 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å2-0 Å20 Å2
2---0.41 Å20 Å2
3---0.96 Å2
Refinement stepCycle: LAST / Resolution: 2.2→41.407 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3549 0 38 158 3745
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193645
X-RAY DIFFRACTIONr_bond_other_d00.023470
X-RAY DIFFRACTIONr_angle_refined_deg1.1451.964895
X-RAY DIFFRACTIONr_angle_other_deg3.60437969
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3015440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.29724.536194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.96115647
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2941526
X-RAY DIFFRACTIONr_chiral_restr0.0820.2518
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024158
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02860
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_it1.3532.4051766
X-RAY DIFFRACTIONr_mcbond_other1.3532.4031765
X-RAY DIFFRACTIONr_mcangle_it2.0483.5992204
X-RAY DIFFRACTIONr_mcangle_other2.0473.6012205
X-RAY DIFFRACTIONr_scbond_it2.4812.8131879
X-RAY DIFFRACTIONr_scbond_other2.6772.8121880
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9224.0662692
X-RAY DIFFRACTIONr_long_range_B_refined5.07419.9514417
X-RAY DIFFRACTIONr_long_range_B_other5.06219.8984385
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.261 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 83 -
Rwork0.267 1631 -
obs--94.91 %

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