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- PDB-4ou9: Crystal structure of apocarotenoid oxygenase in the presence of T... -

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Basic information

Entry
Database: PDB / ID: 4ou9
TitleCrystal structure of apocarotenoid oxygenase in the presence of Triton X-100
ComponentsApocarotenoid-15,15'-oxygenase
KeywordsOXIDOREDUCTASE / monotopic membrane protein / non-heme iron / metalloenzyme / 4-His iron center / beta propeller / carotenoid oxygenase
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 / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsSui, X. / Palczewski, K. / Kiser, P.D.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Analysis of Carotenoid Isomerase Activity in a Prototypical Carotenoid Cleavage Enzyme, Apocarotenoid Oxygenase (ACO).
Authors: Sui, X. / Kiser, P.D. / Che, T. / Carey, P.R. / Golczak, M. / Shi, W. / von Lintig, J. / Palczewski, K.
History
DepositionFeb 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2014Group: Database references
Revision 1.2May 21, 2014Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Apocarotenoid-15,15'-oxygenase
B: Apocarotenoid-15,15'-oxygenase
C: Apocarotenoid-15,15'-oxygenase
D: Apocarotenoid-15,15'-oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,67110
Polymers217,3774
Non-polymers2946
Water15,763875
1
A: Apocarotenoid-15,15'-oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4353
Polymers54,3441
Non-polymers912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Apocarotenoid-15,15'-oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4353
Polymers54,3441
Non-polymers912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Apocarotenoid-15,15'-oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4002
Polymers54,3441
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Apocarotenoid-15,15'-oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4002
Polymers54,3441
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.470, 125.390, 202.540
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
Apocarotenoid-15,15'-oxygenase / ACO / 8'-apo-beta-carotenal 15 / 15'-oxygenase / Diox1


Mass: 54344.191 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Gene: Diox1, sll1541 / Production host: Escherichia coli (E. coli)
References: UniProt: P74334, all-trans-8'-apo-beta-carotenal 15,15'-oxygenase
#2: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 875 / 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: 3.46 Å3/Da / Density % sol: 64.45 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 3350, NH4Cl, Triton X-100, BTP, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 281K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 10, 2013
RadiationMonochromator: Silicon(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 203162 / Num. obs: 200469 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3

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Processing

Software
NameClassification
XDSdata scaling
REFMACrefinement
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2→48.61 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / SU B: 8.364 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20467 9860 4.9 %RANDOM
Rwork0.17717 ---
obs0.17849 190607 98.67 %-
all-203162 --
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.673 Å2
Baniso -1Baniso -2Baniso -3
1--0.9 Å2-0 Å2-0 Å2
2--0.56 Å2-0 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 2→48.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15098 0 6 875 15979
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01915616
X-RAY DIFFRACTIONr_bond_other_d0.0010.0214528
X-RAY DIFFRACTIONr_angle_refined_deg1.4421.95421287
X-RAY DIFFRACTIONr_angle_other_deg0.746333471
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.58551932
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.04823.836743
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.048152401
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3841593
X-RAY DIFFRACTIONr_chiral_restr0.0860.22247
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02117986
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023747
X-RAY DIFFRACTIONr_mcbond_it1.6912.6057707
X-RAY DIFFRACTIONr_mcbond_other1.6912.6057706
X-RAY DIFFRACTIONr_mcangle_it2.5543.8969637
X-RAY DIFFRACTIONr_mcangle_other2.5543.8979638
X-RAY DIFFRACTIONr_scbond_it2.2222.8927909
X-RAY DIFFRACTIONr_scbond_other2.2222.8927909
X-RAY DIFFRACTIONr_scangle_other3.5734.22611647
X-RAY DIFFRACTIONr_long_range_B_refined5.24221.37717440
X-RAY DIFFRACTIONr_long_range_B_other5.22921.34717375
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 742 -
Rwork0.29 14104 -
obs--99.78 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.27950.3031-0.32311.5175-0.39111.73580.07780.04260.0131-0.1642-0.0874-0.08050.0451-0.09230.00960.20810.04070.02270.02140.00940.006324.46891.141992.0547
21.4372-0.199-0.60261.40240.49761.6491-0.11650.0826-0.0190.07720.06730.0830.0777-0.03990.04920.2165-0.02830.02670.0194-0.00190.008331.13094.854341.3926
31.2288-0.5858-0.25341.45680.23861.7023-0.0344-0.0288-0.16090.034-0.05070.19840.0967-0.14590.08510.18640.01890.01110.0344-0.00090.094444.0392-44.082885.5048
41.87310.8153-0.03061.490.01881.329-0.12360.12090.2057-0.12970.14540.1879-0.1647-0.0204-0.02180.2731-0.0605-0.01010.02680.02830.0937-12.9716-17.584435.2633
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 848
2X-RAY DIFFRACTION2B10 - 824
3X-RAY DIFFRACTION3C12 - 809
4X-RAY DIFFRACTION4D12 - 794

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