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- PDB-4ou8: Crystal structure of apocarotenoid oxygenase in the presence of C8E6 -

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Basic information

Entry
Database: PDB / ID: 4ou8
TitleCrystal structure of apocarotenoid oxygenase in the presence of C8E6
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 / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSui, X. / Shi, W. / 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 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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)217,70711
Polymers217,3774
Non-polymers3307
Water1,56787
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)54,4714
Polymers54,3441
Non-polymers1273
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)118.561, 125.122, 203.012
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: THR / End label comp-ID: THR / Refine code: _ / Auth seq-ID: 12 - 490 / Label seq-ID: 12 - 490

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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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.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 3.46 Å3/Da / Density % sol: 64.49 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 3350, BTP, NH4Cl, C8E6 , VAPOR DIFFUSION, HANGING DROP, temperature 281K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.7308 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 26, 2013
RadiationMonochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7308 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 75329 / Num. obs: 75053 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.8.0049refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BIW

2biw


Resolution: 2.8→48.58 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.902 / SU B: 35.157 / SU ML: 0.287 / Cross valid method: THROUGHOUT / ESU R: 0.711 / ESU R Free: 0.309 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23554 3609 4.8 %RANDOM
Rwork0.21103 ---
obs0.21219 71479 99.68 %-
all-75329 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.077 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å2-0 Å20 Å2
2---0.98 Å20 Å2
3---0.48 Å2
Refinement stepCycle: LAST / Resolution: 2.8→48.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15072 0 7 87 15166
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01915524
X-RAY DIFFRACTIONr_bond_other_d0.0060.0214436
X-RAY DIFFRACTIONr_angle_refined_deg1.4131.95421148
X-RAY DIFFRACTIONr_angle_other_deg0.988333252
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.39251912
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.79823.838740
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.446152384
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3221592
X-RAY DIFFRACTIONr_chiral_restr0.0750.22232
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02117848
X-RAY DIFFRACTIONr_gen_planes_other0.0050.023724
X-RAY DIFFRACTIONr_mcbond_it1.2392.1477660
X-RAY DIFFRACTIONr_mcbond_other1.2392.1477659
X-RAY DIFFRACTIONr_mcangle_it2.1093.2199568
X-RAY DIFFRACTIONr_mcangle_other2.1093.2199569
X-RAY DIFFRACTIONr_scbond_it1.3232.2557864
X-RAY DIFFRACTIONr_scbond_other1.3232.2557864
X-RAY DIFFRACTIONr_scangle_other2.2343.33111580
X-RAY DIFFRACTIONr_long_range_B_refined3.66717.00316353
X-RAY DIFFRACTIONr_long_range_B_other3.66717.00316353
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A293510.05
12B293510.05
21A290840.06
22C290840.06
31A292880.05
32D292880.05
41B291160.05
42C291160.05
51B293040.05
52D293040.05
61C293140.04
62D293140.04
LS refinement shellResolution: 2.796→2.869 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 276 -
Rwork0.399 4996 -
obs--96.05 %
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)
11.52690.3839-0.59552.1483-0.51422.4420.0793-0.01070.0083-0.2036-0.1405-0.08890.0828-0.10160.06120.28260.07190.03540.13390.02230.009124.38621.333492.2185
21.8256-0.2885-0.49661.70530.67742.1205-0.15930.0981-0.00470.0780.04860.11880.0947-0.09830.11080.3047-0.0520.04580.1199-0.01850.018331.26944.952841.5382
31.8647-0.844-0.38992.23070.50622.2324-0.0424-0.01-0.24330.0548-0.07740.37770.1334-0.22330.11980.25530.03320.02310.15390.01710.157843.8385-44.091185.72
42.71751.31530.06182.31540.05151.8491-0.23860.16050.4305-0.21930.22610.367-0.2335-0.02630.01250.3993-0.0807-0.04750.09570.03850.1721-13.2028-17.337535.3838
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 632
2X-RAY DIFFRACTION2B12 - 622
3X-RAY DIFFRACTION3C12 - 620
4X-RAY DIFFRACTION4D12 - 613

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