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- PDB-5kk0: Synechocystis ACO mutant - T136A -

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Basic information

Entry
Database: PDB / ID: 5kk0
TitleSynechocystis ACO mutant - T136A
ComponentsApocarotenoid-15,15'-oxygenase
KeywordsOXIDOREDUCTASE / carotenoid cleavage dioxygenase / iron coordination / non-heme iron proteins
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.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Utilization of Dioxygen by Carotenoid Cleavage Oxygenases.
Authors: Sui, X. / Golczak, M. / Zhang, J. / Kleinberg, K.A. / von Lintig, J. / Palczewski, K. / Kiser, P.D.
History
DepositionJun 20, 2016Deposition site: RCSB / Processing site: RCSB
SupersessionJul 13, 2016ID: 5E47
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,55110
Polymers217,2574
Non-polymers2946
Water79344
1
A: Apocarotenoid-15,15'-oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4053
Polymers54,3141
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)54,3702
Polymers54,3141
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)54,3702
Polymers54,3141
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)54,4053
Polymers54,3141
Non-polymers912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.760, 124.961, 203.911
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: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROTHRTHRAA10 - 49010 - 490
21PROPROTHRTHRBB10 - 49010 - 490
12GLNGLNGLNGLNAA12 - 48912 - 489
22GLNGLNGLNGLNCC12 - 48912 - 489
13GLNGLNGLNGLNAA12 - 48912 - 489
23GLNGLNGLNGLNDD12 - 48912 - 489
14GLNGLNGLNGLNBB12 - 48912 - 489
24GLNGLNGLNGLNCC12 - 48912 - 489
15GLNGLNGLNGLNBB12 - 48912 - 489
25GLNGLNGLNGLNDD12 - 48912 - 489
16GLNGLNTHRTHRCC12 - 49012 - 490
26GLNGLNTHRTHRDD12 - 49012 - 490

NCS ensembles :
ID
1
2
3
4
5
6

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.024344, -0.999637, -0.011567), (0.999703, 0.024331, 0.001212), (-0.000931, -0.011593, 0.999932)29.12851, -30.15925, 51.025269
3given(1), (1), (1)
4given(0.393817, 0.212616, -0.894261), (-0.58235, -0.695009, -0.421699), (-0.71118, 0.686845, -0.14989)93.832893, 32.869259, 167.197845
5given(1), (1), (1)
6given(0.220747, -0.361033, -0.90605), (-0.74649, 0.535332, -0.395186), (0.627712, 0.763594, -0.151334)53.570091, 14.85563, 119.593773
7given(1), (1), (1)
8given(-0.571889, -0.690274, -0.443244), (-0.399635, -0.237437, 0.88539), (-0.716404, 0.683481, -0.14007)64.478691, -64.491669, 115.494469
9given(1), (1), (1)
10given(-0.741485, 0.525634, -0.417025), (-0.246136, 0.36511, 0.897837), (0.624194, 0.768377, -0.141346)45.533871, -24.13142, 68.336487
11given(1), (1), (1)
12given(0.075226, -0.996984, -0.019065), (0.996894, 0.075639, -0.021921), (0.023297, -0.017356, 0.999578)28.48933, -28.737949, 50.736881

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Components

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


Mass: 54314.168 Da / Num. of mol.: 4
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.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 44 / 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: 3.48 Å3/Da / Density % sol: 64.68 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Sodium Chloride, BisTris Propane, Sodium Polyacrylate 2100, Triton X-100
PH range: 6.0 - 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-E / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.79→48.61 Å / Num. obs: 75385 / % possible obs: 99.8 % / Redundancy: 3.7 % / Net I/σ(I): 7.1

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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→48.61 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.894 / Cross valid method: THROUGHOUT / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26371 3538 4.7 %RANDOM
Rwork0.22521 ---
obs0.22699 71847 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 62.2 Å2
Refinement stepCycle: 1 / Resolution: 2.8→48.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15090 0 6 44 15140
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01915544
X-RAY DIFFRACTIONr_bond_other_d0.0020.0214454
X-RAY DIFFRACTIONr_angle_refined_deg1.3971.95421174
X-RAY DIFFRACTIONr_angle_other_deg0.824333294
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.57351916
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.49423.838740
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.715152382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8491592
X-RAY DIFFRACTIONr_chiral_restr0.0710.22232
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02117876
X-RAY DIFFRACTIONr_gen_planes_other0.0030.023728
X-RAY DIFFRACTIONr_mcbond_it4.1326.0387676
X-RAY DIFFRACTIONr_mcbond_other4.1326.0377675
X-RAY DIFFRACTIONr_mcangle_it6.649.0479588
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT THERMAL / Weight position: 0.87

Ens-IDAuth asym-IDNumberRms dev position (Å)
1A43225.28
2A42966.31
3A42967.98
4B42967.51
5B42969
6C43086.15
LS refinement shellHighest resolution: 2.8 Å

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