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- PDB-6c7p: Crystal structure of D477G ACO/RPE65 chimera, monoclinic crystal form -

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Basic information

Entry
Database: PDB / ID: 6c7p
TitleCrystal structure of D477G ACO/RPE65 chimera, monoclinic crystal form
ComponentsApocarotenoid-15,15'-oxygenase
KeywordsOXIDOREDUCTASE / non-heme iron / chimera / 7-bladed propeller / dominant mutation
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: 2.6 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 23, 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 ...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
B: Apocarotenoid-15,15'-oxygenase
A: Apocarotenoid-15,15'-oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,9144
Polymers108,8032
Non-polymers1122
Water95553
1
B: Apocarotenoid-15,15'-oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4572
Polymers54,4011
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Apocarotenoid-15,15'-oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4572
Polymers54,4011
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)191.431, 56.170, 136.912
Angle α, β, γ (deg.)90.00, 133.82, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: THR / End label comp-ID: THR / Refine code: _ / Auth seq-ID: 11 - 490 / Label seq-ID: 11 - 490

Dom-IDAuth asym-IDLabel asym-ID
1BA
2AB

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Components

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


Mass: 54401.344 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.44 Å3/Da / Density % sol: 49.6 %
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-1 / Wavelength: 0.918401 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918401 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 31744 / % possible obs: 96.7 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 11.6
Reflection shellResolution: 2.6→2.76 Å / Redundancy: 3 % / Rmerge(I) obs: 0.998 / Mean I/σ(I) obs: 0.93 / Num. unique obs: 5023 / % possible all: 96

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6C7K

6c7k


Resolution: 2.6→41.76 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.937 / SU B: 19.865 / SU ML: 0.36 / Cross valid method: THROUGHOUT / ESU R Free: 0.347 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25981 1588 5 %RANDOM
Rwork0.21993 ---
obs0.22194 30156 97.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 77.163 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å2-0 Å2-1.28 Å2
2--7.6 Å20 Å2
3----1.92 Å2
Refinement stepCycle: 1 / Resolution: 2.6→41.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7491 0 2 53 7546
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0197711
X-RAY DIFFRACTIONr_bond_other_d0.0010.026963
X-RAY DIFFRACTIONr_angle_refined_deg1.1071.95210494
X-RAY DIFFRACTIONr_angle_other_deg0.831316178
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8725944
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.72623.808365
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.16151195
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.3841544
X-RAY DIFFRACTIONr_chiral_restr0.0690.21116
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218646
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021618
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_it2.4687.8143794
X-RAY DIFFRACTIONr_mcbond_other2.4687.8143793
X-RAY DIFFRACTIONr_mcangle_it4.15511.7144732
X-RAY DIFFRACTIONr_mcangle_other4.15411.7144733
X-RAY DIFFRACTIONr_scbond_it2.0757.9923917
X-RAY DIFFRACTIONr_scbond_other2.0757.9923917
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.56511.9035762
X-RAY DIFFRACTIONr_long_range_B_refined6.08287.7137830
X-RAY DIFFRACTIONr_long_range_B_other6.07687.7227826
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 29704 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1B
2A
LS refinement shellResolution: 2.603→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.448 110 -
Rwork0.469 2090 -
obs--92.17 %

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