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- PDB-4z5s: Crystal structure of apo-form of aldehyde deformylating oxygenase... -

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Basic information

Entry
Database: PDB / ID: 4z5s
TitleCrystal structure of apo-form of aldehyde deformylating oxygenase from Synechocystis sp.PCC 6803
ComponentsAldehyde decarbonylase
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
Aldehyde decarbonylase
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.582 Å
AuthorsJia, C. / Li, M. / Chang, W.
CitationJournal: BMC Biotechnol. / Year: 2017
Title: Identification of residues important for the activity of aldehyde-deformylating oxygenase through investigation into the structure-activity relationship
Authors: Wang, Q. / Bao, L. / Jia, C. / Li, M. / Li, J.J. / Lu, X.
History
DepositionApr 3, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Database references
Revision 1.2Nov 8, 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


Theoretical massNumber of molelcules
Total (without water)26,2031
Polymers26,2031
Non-polymers00
Water5,080282
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10730 Å2
Unit cell
Length a, b, c (Å)68.519, 88.027, 36.251
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 26202.646 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / Gene: sll0208 / Production host: Escherichia coli (E. coli)
References: UniProt: Q55688, aldehyde oxygenase (deformylating)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.04 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: 19%(v/v) 2-Propanol, 0.2M Ammonium sulfate, 0.1M Sodium citrate tribasic dehydrate pH5.2, 18% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 8, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.582→44.014 Å / Num. obs: 29825 / % possible obs: 99.6 % / Redundancy: 8.5 % / Net I/σ(I): 22.2
Reflection shellResolution: 1.58→1.61 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 4.75 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
ADSCdata collection
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OC5

2oc5


Resolution: 1.582→44.014 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.55 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2128 1491 5 %
Rwork0.173 --
obs0.175 29825 97.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.582→44.014 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1787 0 0 282 2069
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071873
X-RAY DIFFRACTIONf_angle_d1.0022535
X-RAY DIFFRACTIONf_dihedral_angle_d13.616712
X-RAY DIFFRACTIONf_chiral_restr0.07270
X-RAY DIFFRACTIONf_plane_restr0.005333
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5818-1.63290.22431020.17822023X-RAY DIFFRACTION78
1.6329-1.69130.24961260.18012438X-RAY DIFFRACTION94
1.6913-1.7590.23321460.18292587X-RAY DIFFRACTION99
1.759-1.8390.2131370.18142611X-RAY DIFFRACTION100
1.839-1.9360.21191250.17552626X-RAY DIFFRACTION100
1.936-2.05730.18441340.16082625X-RAY DIFFRACTION100
2.0573-2.21610.19761430.15662649X-RAY DIFFRACTION100
2.2161-2.43910.21961420.16572646X-RAY DIFFRACTION100
2.4391-2.7920.20441490.17752664X-RAY DIFFRACTION100
2.792-3.51740.22711470.17662670X-RAY DIFFRACTION100
3.5174-44.03050.20821400.17642795X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 14.2667 Å / Origin y: 102.1311 Å / Origin z: 46.6198 Å
111213212223313233
T0.0686 Å2-0.016 Å2-0.0021 Å2-0.0722 Å20.012 Å2--0.0587 Å2
L1.2215 °2-0.7584 °2-0.3012 °2-1.1979 °20.2945 °2--0.5045 °2
S-0.0315 Å °-0.027 Å °-0.1187 Å °-0.0712 Å °-0.008 Å °0.095 Å °0.0184 Å °-0.0073 Å °0.0235 Å °
Refinement TLS groupSelection details: all

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