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- PDB-6c7k: Crystal structure of an ACO/RPE65 chimera -

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Basic information

Entry
Database: PDB / ID: 6c7k
TitleCrystal structure of an ACO/RPE65 chimera
ComponentsApocarotenoid-15,15'-oxygenase
KeywordsOXIDOREDUCTASE / non-heme iron / chimera / 7-bladed 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: 2.5 Å
AuthorsKiser, P.D. / Shi, W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)EY009339 United States
Department of Veterans AffairsIK2BX002683 United States
CitationJournal: Hum.Mol.Genet. / Year: 2018
Title: Insights into the pathogenesis of dominant retinitis pigmentosa associated with a D477G mutation in RPE65.
Authors: Choi, E.H. / Suh, S. / Sander, C.L. / Hernandez, C.J.O. / Bulman, E.R. / Khadka, N. / Dong, Z. / Shi, W. / Palczewski, K. / Kiser, P.D.
History
DepositionJan 22, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2May 8, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,13210
Polymers217,8384
Non-polymers2946
Water13,061725
1
A: Apocarotenoid-15,15'-oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5513
Polymers54,4591
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)54,5513
Polymers54,4591
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)54,5152
Polymers54,4591
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)54,5152
Polymers54,4591
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)119.346, 125.663, 204.412
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: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNTHRTHRAA12 - 49012 - 490
21GLNGLNTHRTHRBB12 - 49012 - 490
12ARGARGGLNGLNAA13 - 48913 - 489
22ARGARGGLNGLNCC13 - 48913 - 489
13ARGARGGLNGLNAA13 - 48913 - 489
23ARGARGGLNGLNDD13 - 48913 - 489
14ARGARGGLNGLNBB13 - 48913 - 489
24ARGARGGLNGLNCC13 - 48913 - 489
15ARGARGGLNGLNBB13 - 48913 - 489
25ARGARGGLNGLNDD13 - 48913 - 489
16ARGARGTHRTHRCC13 - 49013 - 490
26ARGARGTHRTHRDD13 - 49013 - 490

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: 54459.379 Da / Num. of mol.: 4
Mutation: P44L, D45W, P431S, R432H, G434D, G435A, V436L, A437E, W442V, D461N, Q463K
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


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


Mass: 18.015 Da / Num. of mol.: 725 / 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: 3.52 Å3/Da / Density % sol: 65.04 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M Bis-Tris propane, pH 6 and 21% w/v sodium polyacrylate 2100

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.979357 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979357 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 106564 / % possible obs: 99.8 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.196 / Net I/σ(I): 9.5
Reflection shellResolution: 2.5→2.65 Å / Rmerge(I) obs: 1.752 / Num. unique obs: 16940 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4OU9

4ou9


Resolution: 2.5→48.84 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / Cross valid method: THROUGHOUT / ESU R: 0.297 / ESU R Free: 0.217 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21651 5100 4.8 %RANDOM
Rwork0.18135 ---
obs0.18299 101462 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 60.379 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å2-0 Å2-0 Å2
2---2.05 Å20 Å2
3---1.33 Å2
Refinement stepCycle: 1 / Resolution: 2.5→48.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15082 0 6 725 15813
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01915530
X-RAY DIFFRACTIONr_bond_other_d00.0213998
X-RAY DIFFRACTIONr_angle_refined_deg1.5311.95221148
X-RAY DIFFRACTIONr_angle_other_deg3.742332541
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.54351910
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.00223.875738
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.368152404
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8911588
X-RAY DIFFRACTIONr_chiral_restr0.0910.22246
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02117478
X-RAY DIFFRACTIONr_gen_planes_other0.0080.023258
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_it4.3335.8897652
X-RAY DIFFRACTIONr_mcbond_other4.335.8887651
X-RAY DIFFRACTIONr_mcangle_it6.28.8439558
X-RAY DIFFRACTIONr_mcangle_other6.2018.8449559
X-RAY DIFFRACTIONr_scbond_it5.0566.3437878
X-RAY DIFFRACTIONr_scbond_other5.0566.3437878
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.5559.31711590
X-RAY DIFFRACTIONr_long_range_B_refined9.61867.38816252
X-RAY DIFFRACTIONr_long_range_B_other9.61667.37216233
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 / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A301380.05
12B301380.05
21A297140.06
22C297140.06
31A296820.06
32D296820.06
41B300100.05
42C300100.05
51B300240.05
52D300240.05
61C303840.04
62D303840.04
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 401 -
Rwork0.339 7281 -
obs--98.65 %

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