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- PDB-4xb5: Structure of orange carotenoid protein binding canthaxanthin -

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Basic information

Entry
Database: PDB / ID: 4xb5
TitleStructure of orange carotenoid protein binding canthaxanthin
ComponentsOrange carotenoid-binding protein
KeywordsCAROTENOID BINDING PROTEIN / carotenoid-binding / photoprotection
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 (NTF2) domain / Nuclear transport factor 2 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 (NTF2) domain / Nuclear transport factor 2 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
beta,beta-carotene-4,4'-dione / Orange carotenoid-binding protein
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKerfeld, C.A. / Sutter, M. / Leverenz, R.L.
CitationJournal: Science / Year: 2015
Title: PHOTOSYNTHESIS. A 12 angstrom carotenoid translocation in a photoswitch associated with cyanobacterial photoprotection.
Authors: Leverenz, R.L. / Sutter, M. / Wilson, A. / Gupta, S. / Thurotte, A. / Bourcier de Carbon, C. / Petzold, C.J. / Ralston, C. / Perreau, F. / Kirilovsky, D. / Kerfeld, C.A.
History
DepositionDec 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Data collection
Revision 1.2Sep 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 / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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)36,4023
Polymers35,7451
Non-polymers6572
Water4,252236
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.894, 82.894, 87.201
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: 35744.688 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: Escherichia coli (E. coli) / References: UniProt: P74102
#2: Chemical ChemComp-45D / beta,beta-carotene-4,4'-dione / Isomer of Canthaxanthin


Mass: 564.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C40H52O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 100 mM sodium acetate pH 4.5, 10% poly-ethylene glycol 20,000, 3% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→37.434 Å / Num. obs: 27757 / % possible obs: 99.94 % / Redundancy: 20.7 % / Rmerge(I) obs: 0.01658 / Net I/σ(I): 23.9
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.03 % / Rmerge(I) obs: 0.3633 / Mean I/σ(I) obs: 2.09 / % possible all: 99.38

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1690)refinement
SCALAdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Truncated form of 3MG1

3mg1


Resolution: 1.9→37.434 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2076 2008 7.24 %
Rwork0.1809 --
obs0.1828 27746 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→37.434 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2452 0 0 236 2688
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062510
X-RAY DIFFRACTIONf_angle_d0.9033418
X-RAY DIFFRACTIONf_dihedral_angle_d14.661926
X-RAY DIFFRACTIONf_chiral_restr0.035382
X-RAY DIFFRACTIONf_plane_restr0.006453
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94750.48581420.49231803X-RAY DIFFRACTION99
1.9475-2.00020.30351410.2871819X-RAY DIFFRACTION100
2.0002-2.05910.25651420.22481793X-RAY DIFFRACTION100
2.0591-2.12550.28731450.2221840X-RAY DIFFRACTION100
2.1255-2.20150.23471380.1991787X-RAY DIFFRACTION100
2.2015-2.28960.27471410.20951818X-RAY DIFFRACTION100
2.2896-2.39380.23581390.18691832X-RAY DIFFRACTION100
2.3938-2.520.22451420.18311830X-RAY DIFFRACTION100
2.52-2.67780.20381470.18671856X-RAY DIFFRACTION100
2.6778-2.88450.24361440.17771822X-RAY DIFFRACTION100
2.8845-3.17460.17061430.17471856X-RAY DIFFRACTION100
3.1746-3.63370.17951420.16091851X-RAY DIFFRACTION100
3.6337-4.57680.16471460.14031869X-RAY DIFFRACTION100
4.5768-37.4410.18971560.16681962X-RAY DIFFRACTION100

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