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- PDB-5kja: Synechocystis apocarotenoid oxygenase (ACO) mutant - Trp149Ala -

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Basic information

Entry
Database: PDB / ID: 5kja
TitleSynechocystis apocarotenoid oxygenase (ACO) mutant - Trp149Ala
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: 2.8 Å
AuthorsSui, X. / Kiser, P.D. / Palczewski, K.
Funding support United States, 4items
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
National Institutes of Health/National Eye Institute (NIH/NEI)EY023948 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 / diffrn_radiation_wavelength / 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)271,49512
Polymers271,1455
Non-polymers3507
Water2,774154
1
A: Apocarotenoid-15,15'-oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3203
Polymers54,2291
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)54,3203
Polymers54,2291
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)54,2852
Polymers54,2291
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)54,2852
Polymers54,2291
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)54,2852
Polymers54,2291
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.140, 125.260, 203.570
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: 0 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNAA12 - 48912 - 489
21GLNGLNBB12 - 48912 - 489
12GLNGLNAA12 - 48912 - 489
22GLNGLNCC12 - 48912 - 489
13GLNGLNAA12 - 48912 - 489
23GLNGLNDD12 - 48912 - 489
14GLNGLNAA12 - 48912 - 489
24GLNGLNEE12 - 48912 - 489
15THRTHRBB12 - 49012 - 490
25THRTHRCC12 - 49012 - 490
16THRTHRBB12 - 49012 - 490
26THRTHRDD12 - 49012 - 490
17THRTHRBB12 - 49012 - 490
27THRTHREE12 - 49012 - 490
18THRTHRCC12 - 49012 - 490
28THRTHRDD12 - 49012 - 490
19THRTHRCC12 - 49012 - 490
29THRTHREE12 - 49012 - 490
110THRTHRDD12 - 49012 - 490
210THRTHREE12 - 49012 - 490

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: 54229.062 Da / Num. of mol.: 5 / Mutation: W149A
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-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cl
#3: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: Fe
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.78 Å3/Da / Density % sol: 55.72 %
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: 0.97921 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2.8→48.62 Å / Num. obs: 75013 / % possible obs: 100 % / Redundancy: 8.2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.19 / Net I/σ(I): 11
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 3.77 % / Rmerge(I) obs: 0.2043 / Mean I/σ(I) obs: 1.1 / % possible all: 100

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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: 2.8→48.62 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.914 / SU B: 18.206 / SU ML: 0.33 / Cross valid method: THROUGHOUT / ESU R Free: 0.351 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23905 3595 4.8 %RANDOM
Rwork0.19804 ---
obs0.19998 71417 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.01 Å20 Å2-0 Å2
2---2.03 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.8→48.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18814 0 7 154 18975
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01919370
X-RAY DIFFRACTIONr_bond_other_d0.0060.0218035
X-RAY DIFFRACTIONr_angle_refined_deg1.3751.95626383
X-RAY DIFFRACTIONr_angle_other_deg1.034341548
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4152393
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.99223.859920
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.651152977
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.51815115
X-RAY DIFFRACTIONr_chiral_restr0.0730.22793
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02122282
X-RAY DIFFRACTIONr_gen_planes_other0.0060.024627
X-RAY DIFFRACTIONr_mcbond_it5.8557.3639587
X-RAY DIFFRACTIONr_mcbond_other5.8547.3639586
X-RAY DIFFRACTIONr_mcangle_it9.1211.0411975
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A291320.05
12B291320.05
21A288690.06
22C288690.06
31A287770.06
32D287770.06
41A290130.05
42E290130.05
51B288080.06
52C288080.06
61B290170.05
62D290170.05
71B291710.04
72E291710.04
81C290070.05
82D290070.05
91C287710.06
92E287710.06
101D289590.05
102E289590.05
LS refinement shellHighest resolution: 2.8 Å

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