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- PDB-6big: Crystal structure of cobalt-substituted Synechocystis ACO -

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Basic information

Entry
Database: PDB / ID: 6big
TitleCrystal structure of cobalt-substituted Synechocystis ACO
ComponentsApocarotenoid-15,15'-oxygenase
KeywordsOXIDOREDUCTASE / dioxygenase / cobalt / non-heme iron / beta propeller
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: 2.21 Å
AuthorsSui, X. / Shi, W. / Kiser, P.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)EY009339 United States
CitationJournal: J. Biol. Inorg. Chem. / Year: 2018
Title: Preparation and characterization of metal-substituted carotenoid cleavage oxygenases.
Authors: Sui, X. / Farquhar, E.R. / Hill, H.E. / von Lintig, J. / Shi, W. / Kiser, P.D.
History
DepositionNov 2, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 8, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 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 / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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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)217,71911
Polymers217,3774
Non-polymers3427
Water12,268681
1
A: Apocarotenoid-15,15'-oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4744
Polymers54,3441
Non-polymers1303
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Apocarotenoid-15,15'-oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4393
Polymers54,3441
Non-polymers942
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Apocarotenoid-15,15'-oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4032
Polymers54,3441
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Apocarotenoid-15,15'-oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4032
Polymers54,3441
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.074, 124.531, 202.608
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: 0 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 0 / 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. (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-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 681 / 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: 3.43 Å3/Da / Density % sol: 64.1 %
Crystal growTemperature: 281.15 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M Bis-Tris pH 6, 0.2 M NaCl, 22% Sodium polyacrylate 2100

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075, 1.6021, 1.6146
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 2, 2017
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.0751
21.60211
31.61461
ReflectionResolution: 2.21→50 Å / Num. obs: 145134 / % possible obs: 97 % / Redundancy: 6.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.102 / Net I/σ(I): 15.25
Reflection shellResolution: 2.21→2.34 Å / Redundancy: 6 % / Rmerge(I) obs: 1.806 / Mean I/σ(I) obs: 1.15 / Num. unique obs: 21023 / CC1/2: 0.792 / % possible all: 87.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0085refinement
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4OU9

4ou9


Resolution: 2.21→48.39 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.947 / SU B: 17.938 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.179 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22932 6801 4.8 %RANDOM
Rwork0.20818 ---
obs0.20917 135096 94.87 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 59.737 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20 Å2
2---1.75 Å20 Å2
3---1.57 Å2
Refinement stepCycle: 1 / Resolution: 2.21→48.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15064 0 7 681 15752
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01915557
X-RAY DIFFRACTIONr_bond_other_d0.0070.0214469
X-RAY DIFFRACTIONr_angle_refined_deg1.551.95321198
X-RAY DIFFRACTIONr_angle_other_deg1.146333332
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.91651922
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.17123.819741
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.311152388
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5671593
X-RAY DIFFRACTIONr_chiral_restr0.0880.22239
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02117889
X-RAY DIFFRACTIONr_gen_planes_other0.0060.023732
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9732.1737679
X-RAY DIFFRACTIONr_mcbond_other0.9732.1737678
X-RAY DIFFRACTIONr_mcangle_it1.6663.2579598
X-RAY DIFFRACTIONr_mcangle_other1.6663.2579599
X-RAY DIFFRACTIONr_scbond_it1.0222.2687878
X-RAY DIFFRACTIONr_scbond_other1.0222.2687878
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.753.35811598
X-RAY DIFFRACTIONr_long_range_B_refined3.48417.11116939
X-RAY DIFFRACTIONr_long_range_B_other3.45317.09416878
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.01 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A57598
12B57598
21A56746
22C56746
31A56434
32D56434
41B56938
42C56938
51B56472
52D56472
61C57628
62D57628
LS refinement shellResolution: 2.21→2.267 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.648 259 -
Rwork0.637 4847 -
obs--46.6 %
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)
13.59340.1034-0.86281.884-0.34682.4380.1951-0.07740.1519-0.06-0.0902-0.0976-0.1167-0.0569-0.10490.26590.05870.05290.37620.03640.022524.0731.820692.1704
21.8949-0.0594-0.48663.50750.5612.054-0.1720.0136-0.0381-0.06750.1965-0.20610.14780.0001-0.02450.2656-0.04960.06350.357-0.0520.028631.66915.21341.5681
32.2683-0.8774-0.26922.61690.18562.2228-0.1084-0.0211-0.17590.00670.01610.16940.1689-0.17870.09230.20670.01120.02390.40720.01980.12543.4559-43.468285.9677
43.61191.6379-0.24192.0259-0.19281.8176-0.25440.29730.4283-0.19390.24880.3618-0.2884-0.10060.00560.4054-0.0606-0.02490.33870.05970.1599-12.8982-16.900435.6633
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 490
2X-RAY DIFFRACTION2B12 - 490
3X-RAY DIFFRACTION3C12 - 490
4X-RAY DIFFRACTION4D12 - 490

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