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Basic information

Entry
Database: PDB / ID: 5tv0
Titlecrystal structure and light induced structural changes in orange carotenoid protein bound with 3 'OH echinenone
ComponentsOrange carotenoid-binding protein
KeywordsCarotenoid binding protein / Photoprotection / photoreceptor / Dynamic crystallography
Function / homology
Function and homology information


light absorption / phycobilisome / chloride ion binding / plasma membrane-derived thylakoid membrane / photoreceptor activity
Similarity search - Function
orange carotenoid protein, domain 2 / Orange carotenoid-binding protein, N-terminal domain / Orange carotenoid-binding protein, N-terminal / Orange carotenoid-binding protein, N-terminal domain superfamily / Orange carotenoid protein, N-terminal / Orange carotenoid protein (OCP) N-terminal domain profile. / Nuclear transport factor 2 domain / Nuclear transport factor 2 (NTF2) domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily ...orange carotenoid protein, domain 2 / Orange carotenoid-binding protein, N-terminal domain / Orange carotenoid-binding protein, N-terminal / Orange carotenoid-binding protein, N-terminal domain superfamily / Orange carotenoid protein, N-terminal / Orange carotenoid protein (OCP) N-terminal domain profile. / Nuclear transport factor 2 domain / Nuclear transport factor 2 (NTF2) domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
(3'R)-3'-hydroxy-beta,beta-caroten-4-one / Orange carotenoid-binding protein
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.648 Å
AuthorsYang, X. / Bandara, S. / Ren, Z.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)R01EY024363 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Photoactivation mechanism of a carotenoid-based photoreceptor.
Authors: Bandara, S. / Ren, Z. / Lu, L. / Zeng, X. / Shin, H. / Zhao, K.H. / Yang, X.
History
DepositionNov 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2017Group: 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.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jun 21, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Sep 20, 2017Group: Author supporting evidence / 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 / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Orange carotenoid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1723
Polymers35,5131
Non-polymers6592
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-21 kcal/mol
Surface area13750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.720, 82.720, 88.083
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Orange carotenoid-binding protein / OCP


Mass: 35513.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / Gene: slr1963 / Production host: Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P74102
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-EQ3 / (3'R)-3'-hydroxy-beta,beta-caroten-4-one / 3'-Hydroxyechinenone / 3'-OH-Echinenone / 3'-Hydroxyechinenone


Mass: 566.856 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H54O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.61 Å3/Da / Density % sol: 52.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 100 mM sodium acetate (pH 4.5), 16% PEG 8000, 2% glycerol.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 41139 / % possible obs: 96.9 % / Redundancy: 3.5 % / Net I/σ(I): 25.06
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 2 % / Num. measured obs: 1933 / Rpim(I) all: 0.039 / % possible all: 92.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.9phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MG1

3mg1


Resolution: 1.648→41.36 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1994 2075 5.04 %
Rwork0.1752 --
obs0.1764 41133 96.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.648→41.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2342 0 48 199 2589
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062468
X-RAY DIFFRACTIONf_angle_d0.823365
X-RAY DIFFRACTIONf_dihedral_angle_d12.8921482
X-RAY DIFFRACTIONf_chiral_restr0.052376
X-RAY DIFFRACTIONf_plane_restr0.006436
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6481-1.68640.31031110.26132432X-RAY DIFFRACTION91
1.6864-1.72860.26281430.22842539X-RAY DIFFRACTION96
1.7286-1.77530.21231500.21042620X-RAY DIFFRACTION99
1.7753-1.82760.24971300.20182637X-RAY DIFFRACTION99
1.8276-1.88650.21151770.18682609X-RAY DIFFRACTION99
1.8865-1.9540.20121560.17272593X-RAY DIFFRACTION98
1.954-2.03220.18721220.16352632X-RAY DIFFRACTION99
2.0322-2.12470.19431210.1652676X-RAY DIFFRACTION98
2.1247-2.23670.19271510.16962624X-RAY DIFFRACTION98
2.2367-2.37680.18931590.17662588X-RAY DIFFRACTION98
2.3768-2.56030.19021420.17922623X-RAY DIFFRACTION98
2.5603-2.81790.24551240.18252622X-RAY DIFFRACTION97
2.8179-3.22550.21051230.1842628X-RAY DIFFRACTION96
3.2255-4.06330.17541260.16352622X-RAY DIFFRACTION95
4.0633-41.3730.18351400.16062613X-RAY DIFFRACTION91
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)
10.41980.0437-0.04720.28170.00950.4006-0.0886-0.0195-0.0945-0.0540.03280.02540.022-0.15090.0280.2311-0.029-0.00630.2705-0.00160.2242-18.1626-16.1305-13.5594
21.163-0.0998-0.35880.70070.14351.1135-0.10890.0147-0.0825-0.09970.05440.07190.0827-0.2260.04230.1607-0.0135-0.02680.16590.01220.1584-17.9016-15.321-13.9668
31.0139-0.5518-1.12621.09680.93782.0234-0.0706-0.13620.0535-0.02540.0792-0.0174-0.1031-0.04160.00150.14360.0014-0.02440.2572-0.03780.1826-20.674-11.4998-12.5896
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 501:699 )A501 - 699
2X-RAY DIFFRACTION2( CHAIN A AND RESID 2:312 )A2 - 312
3X-RAY DIFFRACTION3( CHAIN A AND RESID 402:402 )A402

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