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- PDB-2bix: Crystal structure of apocarotenoid cleavage oxygenase from Synech... -

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Basic information

Entry
Database: PDB / ID: 2bix
TitleCrystal structure of apocarotenoid cleavage oxygenase from Synechocystis, Fe-free apoenzyme
ComponentsAPOCAROTENOID-CLEAVING OXYGENASE
KeywordsOXIDOREDUCTASE / OXYGENASE / NON-HEME IRON / CAROTENOID CLEAVAGE / RETINAL FORMATION / DIOXYGENASE
Function / homologyall-trans-8'-apo-beta-carotenal 15,15'-oxygenase / all-trans-8'-apo-beta-carotenal 15,15'-oxygenase activity / carotenoid dioxygenase activity / carotene catabolic process / Carotenoid oxygenase / Retinal pigment epithelial membrane protein / metal ion binding / Apocarotenoid-15,15'-oxygenase
Function and homology information
Biological speciesSYNECHOCYSTIS SP. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.68 Å
AuthorsKloer, D.P. / Ruch, S. / Al-Babili, S. / Beyer, P. / Schulz, G.E.
CitationJournal: Science / Year: 2005
Title: The Structure of a Retinal-Forming Carotenoid Oxygenase
Authors: Kloer, D.P. / Ruch, S. / Al-Babili, S. / Beyer, P. / Schulz, G.E.
History
DepositionJan 26, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: APOCAROTENOID-CLEAVING OXYGENASE
B: APOCAROTENOID-CLEAVING OXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,4856
Polymers108,6882
Non-polymers7974
Water2,054114
1
A: APOCAROTENOID-CLEAVING OXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8354
Polymers54,3441
Non-polymers4913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: APOCAROTENOID-CLEAVING OXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6512
Polymers54,3441
Non-polymers3061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)122.928, 122.928, 205.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.35963, -0.20798, 0.90962), (-0.55265, 0.73799, 0.38724), (-0.75182, -0.64197, 0.15046)
Vector: -107.3935, 36.9829, 140.2682)

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Components

#1: Protein APOCAROTENOID-CLEAVING OXYGENASE / LIGNOSTILBENE-ALPHA / BETA-DIOXYGENASE


Mass: 54344.191 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNECHOCYSTIS SP. (bacteria) / Strain: PCC 6803 / Plasmid: PET3B-ACO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: P74334
#2: Chemical ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE NAME OF THE MOLECULE IN THE UNIPROT DATABASE WITH ACCESSION NUMBER P74334 IS LIGNOSTILBENE- ...THE NAME OF THE MOLECULE IN THE UNIPROT DATABASE WITH ACCESSION NUMBER P74334 IS LIGNOSTILBENE-ALPHA,BETA- DIOXYGENASE BUT THE DEPOSITOR MAINTAINS THAT THIS IS A DATABASE ERROR

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.6 Å3/Da / Density % sol: 65.57 %
Crystal growpH: 5.7 / Details: pH 5.70

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0716
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0716 Å / Relative weight: 1
ReflectionResolution: 2.68→45.8 Å / Num. obs: 44859 / % possible obs: 98.6 % / Redundancy: 8.7 % / Biso Wilson estimate: 55.8 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 24.5
Reflection shellResolution: 2.68→2.85 Å / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 7.2 / % possible all: 92.6

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Processing

Software
NameVersionClassification
TNT5.6.1refinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.68→47.14 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflectionSelection details
Rfree0.243 2248 5.1 %0.211
Rwork0.21 ---
all0.211 44422 --
obs0.21 44422 --
Solvent computationSolvent model: BABINET MODEL WITH MASK / Bsol: 188 Å2 / ksol: 0.92 e/Å3
Refinement stepCycle: LAST / Resolution: 2.68→47.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7534 0 54 114 7702
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.00778102
X-RAY DIFFRACTIONt_angle_deg1.173105442
X-RAY DIFFRACTIONt_dihedral_angle_d20.23744762
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0111882
X-RAY DIFFRACTIONt_gen_planes0.01911445
X-RAY DIFFRACTIONt_it1.499781020
X-RAY DIFFRACTIONt_nbd0.0491495
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
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_contact

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