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- PDB-5kjd: Synechocystis apocarotenoid oxygenase (ACO) mutant - Glu150Gln -

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Basic information

Entry
Database: PDB / ID: 5kjd
TitleSynechocystis apocarotenoid oxygenase (ACO) mutant - Glu150Gln
ComponentsApocarotenoid-15,15'-oxygenase
KeywordsOXIDOREDUCTASE / iron-coordination / active site / carotenoid binding / ligand interaction / non-heme iron / mutagenesis
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: 2.75 Å
AuthorsSui, X. / Kiser, P.D. / Palczewski, K.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)EY009339 United States
National Institutes of Health/National Eye Institute (NIH/NEI)EY020551 United States
Department of Veterans AffairsIK2BX002683 United States
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Key Residues for Catalytic Function and Metal Coordination in a Carotenoid Cleavage Dioxygenase.
Authors: Sui, X. / Zhang, J. / Golczak, M. / Palczewski, K. / Kiser, P.D.
History
DepositionJun 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Sep 21, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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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
E: Apocarotenoid-15,15'-oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)271,99510
Polymers271,7165
Non-polymers2795
Water1,928107
1
A: Apocarotenoid-15,15'-oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3992
Polymers54,3431
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Apocarotenoid-15,15'-oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3992
Polymers54,3431
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Apocarotenoid-15,15'-oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3992
Polymers54,3431
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)54,3992
Polymers54,3431
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Apocarotenoid-15,15'-oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3992
Polymers54,3431
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.530, 125.500, 203.600
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
14A
24E
15B
25C
16B
26D
17B
27E
18C
28D
19C
29E
110D
210E

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
14AA
24EE
15BB
25CC
16BB
26DD
17BB
27EE
18CC
28DD
19CC
29EE
110DD
210EE

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10

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Components

#1: Protein
Apocarotenoid-15,15'-oxygenase / ACO / 8'-apo-beta-carotenal 15 / 15'-oxygenase / Diox1


Mass: 54343.207 Da / Num. of mol.: 5 / Mutation: E150Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / Gene: 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.: 5 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.79 Å3/Da / Density % sol: 55.86 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 6
Details: BisTris Propane, Sodium Polyacrylate 2100, Sodium Chloride
PH range: 6.0 - 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97919 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.75→47.42 Å / Num. obs: 75683 / % possible obs: 95 % / Redundancy: 3.8 % / Net I/σ(I): 7.6
Reflection shellHighest resolution: 2.75 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OU9

4ou9


Resolution: 2.75→47.42 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.907 / Cross valid method: THROUGHOUT / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2467 3560 4.7 %USED AS IN 4OU9
Rwork0.21176 ---
obs0.21338 72122 95.04 %-
Displacement parametersBiso mean: 70.019 Å2
Refinement stepCycle: 1 / Resolution: 2.75→47.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18840 0 5 107 18952
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01919405
X-RAY DIFFRACTIONr_bond_other_d0.0060.0218055
X-RAY DIFFRACTIONr_angle_refined_deg1.2681.95326435
X-RAY DIFFRACTIONr_angle_other_deg0.942341580
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.27652390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.57723.838925
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.02152980
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.00715115
X-RAY DIFFRACTIONr_chiral_restr0.0690.22790
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02122320
X-RAY DIFFRACTIONr_gen_planes_other0.0050.024665
X-RAY DIFFRACTIONr_mcbond_it5.0346.8799575
X-RAY DIFFRACTIONr_mcbond_other5.0336.8799574
X-RAY DIFFRACTIONr_mcangle_it7.98610.31311960
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A294920.04
12B294920.04
21A294030.04
22C294030.04
31A293650.05
32D293650.05
41A294030.04
42E294030.04
51B294740.04
52C294740.04
61B294130.05
62D294130.05
71B294980.04
72E294980.04
81C295650.04
82D295650.04
91C295060.04
92E295060.04
101D295410.04
102E295410.04
LS refinement shellHighest resolution: 2.75 Å

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