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- PDB-5tuw: Crystal structure of Orange Carotenoid Protein with partial loss ... -

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Basic information

Entry
Database: PDB / ID: 5tuw
TitleCrystal structure of Orange Carotenoid Protein with partial loss of 3'OH Echinenone chromophore
ComponentsOrange carotenoid-binding protein
KeywordsCarotenoid binding protein / Photoreceptor / Photoprotection / 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 (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
(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: 2.302 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
B: Orange carotenoid-binding protein
C: Orange carotenoid-binding protein
D: Orange carotenoid-binding protein
E: Orange carotenoid-binding protein
F: Orange carotenoid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,85016
Polymers213,0816
Non-polymers3,77010
Water4,738263
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21650 Å2
ΔGint-82 kcal/mol
Surface area73380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.947, 82.914, 87.438
Angle α, β, γ (deg.)89.79, 89.91, 60.04
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Orange carotenoid-binding protein / OCP


Mass: 35513.477 Da / Num. of mol.: 6
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


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


Mass: 566.856 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C40H54O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.45 Å3/Da / Density % sol: 49.69 %
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-D / Wavelength: 1.0781 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 85419 / % possible obs: 96 % / Redundancy: 1.9 % / Net I/σ(I): 10.5
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 1.9 % / Num. measured obs: 3806 / Rpim(I) all: 0.102 / % possible all: 89

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Processing

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

3mg1


Resolution: 2.302→41.49 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.51
RfactorNum. reflection% reflection
Rfree0.2386 1918 2.25 %
Rwork0.1846 --
obs0.1859 85190 95.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.302→41.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14083 0 276 263 14622
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00914745
X-RAY DIFFRACTIONf_angle_d1.01220094
X-RAY DIFFRACTIONf_dihedral_angle_d13.7298872
X-RAY DIFFRACTIONf_chiral_restr0.0562251
X-RAY DIFFRACTIONf_plane_restr0.0072598
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3023-2.35990.33481230.29585219X-RAY DIFFRACTION83
2.3599-2.42370.27881360.2735593X-RAY DIFFRACTION92
2.4237-2.4950.34131470.2785889X-RAY DIFFRACTION94
2.495-2.57550.32331490.25675957X-RAY DIFFRACTION95
2.5755-2.66760.34721430.24636021X-RAY DIFFRACTION96
2.6676-2.77440.36051340.2436019X-RAY DIFFRACTION97
2.7744-2.90060.23241200.22386121X-RAY DIFFRACTION98
2.9006-3.05350.2571530.21296153X-RAY DIFFRACTION98
3.0535-3.24470.34051290.20126112X-RAY DIFFRACTION98
3.2447-3.49510.24271570.18176121X-RAY DIFFRACTION98
3.4951-3.84660.2381190.15996103X-RAY DIFFRACTION98
3.8466-4.40270.21371480.14786045X-RAY DIFFRACTION97
4.4027-5.54490.15721280.14855950X-RAY DIFFRACTION95
5.5449-41.49630.18871320.15155969X-RAY DIFFRACTION96
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)
12.2305-0.2958-1.07171.37960.47622.7338-0.27950.1501-0.1784-0.2430.10040.36760.2604-0.68920.16310.3493-0.0949-0.04810.44760.0340.4315-17.7307-15.571-13.9418
22.07010.7891.29561.83220.85263.06550.01860.04810.3774-0.2651-0.1808-0.0075-0.67620.1410.1610.4445-0.00580.05290.32060.01560.3899-3.798723.121915.1576
32.37450.53311.39041.25170.56363.0853-0.1943-0.11920.12160.20160.06940.3241-0.2458-0.67370.14010.35150.03910.05770.42280.02840.4134-17.644415.17642.8031
41.3628-0.11990.09382.3395-1.39953.2182-0.03270.3457-0.17250.0024-0.1486-0.3210.41840.54470.16840.31550.04230.00240.4192-0.06120.399122.802-8.119444.3634
52.0761-0.4303-1.3381.76690.90263.17730.0347-0.0717-0.34680.3326-0.2109-0.0060.67440.09540.16320.4548-0.0369-0.07090.31460.03450.3806-3.7508-23.553113.6353
61.3190.1896-0.06172.4661-1.40572.7797-0.0478-0.34680.19230.0408-0.1209-0.3151-0.49720.52820.16770.3542-0.09020.01390.437-0.06910.427922.86658.063271.9313
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'D' and resid 3 through 311)
2X-RAY DIFFRACTION2(chain 'A' and resid 3 through 311)
3X-RAY DIFFRACTION3(chain 'B' and resid 3 through 311)
4X-RAY DIFFRACTION4(chain 'E' and resid 3 through 311)
5X-RAY DIFFRACTION5(chain 'C' and resid 3 through 311)
6X-RAY DIFFRACTION6(chain 'F' and resid 3 through 311)

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