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- PDB-6t6k: Y201W mutant of the orange carotenoid protein from Synechocystis ... -

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Basic information

Entry
Database: PDB / ID: 6t6k
TitleY201W mutant of the orange carotenoid protein from Synechocystis at pH 6.5
ComponentsOrange carotenoid-binding protein
KeywordsPLANT PROTEIN / orange carotenoid protein / photoactive protein / mutant
Function / homology
Function and homology information


light absorption / phycobilisome / chloride ion binding / plasma membrane-derived thylakoid membrane / photoreceptor activity
Similarity search - Function
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 / NTF2-like domain superfamily
Similarity search - Domain/homology
beta,beta-caroten-4-one / GLYCINE / HISTIDINE / IMIDAZOLE / Orange carotenoid-binding protein
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsSluchanko, N.N. / Gushchin, I. / Botnarevskiy, V.S. / Slonimskiy, Y.B. / Remeeva, A. / Kovalev, K. / Stepanov, A.V. / Gordeliy, V. / Maksimov, E.G.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Foundation for Basic Research18-04-00691 Russian Federation
CitationJournal: Commun Biol / Year: 2021
Title: Role of hydrogen bond alternation and charge transfer states in photoactivation of the Orange Carotenoid Protein.
Authors: Yaroshevich, I.A. / Maksimov, E.G. / Sluchanko, N.N. / Zlenko, D.V. / Stepanov, A.V. / Slutskaya, E.A. / Slonimskiy, Y.B. / Botnarevskii, V.S. / Remeeva, A. / Gushchin, I. / Kovalev, K. / ...Authors: Yaroshevich, I.A. / Maksimov, E.G. / Sluchanko, N.N. / Zlenko, D.V. / Stepanov, A.V. / Slutskaya, E.A. / Slonimskiy, Y.B. / Botnarevskii, V.S. / Remeeva, A. / Gushchin, I. / Kovalev, K. / Gordeliy, V.I. / Shelaev, I.V. / Gostev, F.E. / Khakhulin, D. / Poddubnyy, V.V. / Gostev, T.S. / Cherepanov, D.A. / Polivka, T. / Kloz, M. / Friedrich, T. / Paschenko, V.Z. / Nadtochenko, V.A. / Rubin, A.B. / Kirpichnikov, M.P.
History
DepositionOct 18, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 29, 2021Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)37,70311
Polymers36,4551
Non-polymers1,24910
Water5,441302
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area580 Å2
ΔGint-5 kcal/mol
Surface area13800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.726, 82.726, 88.044
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Orange carotenoid-binding protein / OCP


Mass: 36454.523 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

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Non-polymers , 7 types, 312 molecules

#2: Chemical ChemComp-ECH / beta,beta-caroten-4-one / echinenone / Echinenone


Mass: 550.856 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H54O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GLY / GLYCINE / Glycine


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#6: Chemical ChemComp-HIS / HISTIDINE / Histidine


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10N3O2
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.39 Å3/Da / Density % sol: 48.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 0.1M DL-Glutamic acid monohydrate; 0.1M DL-Alanine; 0.1M Glycine; 0.1M DL-Lysine monohydrochloride; 0.1M DL-Serine; 0.1M Imidazole; MES monohydrate (acid), pH 6.5; 20% v/v Ethylene glycol; 10 % w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.37→44.02 Å / Num. obs: 73479 / % possible obs: 100 % / Redundancy: 20.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Net I/σ(I): 29.1 / Num. measured all: 1480976 / Scaling rejects: 14
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
1.37-1.3920.21.5327470436940.8162.3100
7.38-44.0214.30.04375835320.99381.597.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XB5

4xb5


Resolution: 1.37→37.54 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.974 / SU B: 2.263 / SU ML: 0.039 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.048 / ESU R Free: 0.047
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1668 3654 5 %RANDOM
Rwork0.1354 ---
obs0.1369 69781 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 205.74 Å2 / Biso mean: 29.765 Å2 / Biso min: 17.15 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20.35 Å20 Å2
2--0.7 Å2-0 Å2
3----2.26 Å2
Refinement stepCycle: final / Resolution: 1.37→37.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2343 0 50 305 2698
Biso mean--24.98 46.08 -
Num. residues----312
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132598
X-RAY DIFFRACTIONr_bond_other_d0.0070.0172459
X-RAY DIFFRACTIONr_angle_refined_deg1.3571.6483552
X-RAY DIFFRACTIONr_angle_other_deg1.5261.5745705
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7665336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.80321.486148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.33615418
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2651514
X-RAY DIFFRACTIONr_chiral_restr0.0780.2344
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022988
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02542
X-RAY DIFFRACTIONr_rigid_bond_restr16.46735057
LS refinement shellResolution: 1.37→1.406 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 263 -
Rwork0.21 5102 -
all-5365 -
obs--99.93 %
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)
10.00960.0050.00290.0325-0.00760.0278-0.00040.0006-0.0013-0.0035-0.001-0.00010.0006-0.0030.00140.00560.00090.00030.00490.00060.02584.1758-23.014715.2842
20.25130.13870.32320.13560.17650.41870.00480.0388-0.04480.00720.0335-0.018-0.01330.0472-0.03840.0148-0.001-0.00850.0143-0.01110.05164.8006-28.432110.8465
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 401
2X-RAY DIFFRACTION2A402 - 410

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