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- PDB-6mcj: Structure of Helical Carotenoid Protein 2 from Fremyella diplosiphon -

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Basic information

Entry
Database: PDB / ID: 6mcj
TitleStructure of Helical Carotenoid Protein 2 from Fremyella diplosiphon
ComponentsOrange carotenoid-binding protein
KeywordsPROTEIN BINDING / PHOTOPROTECTION / CAROTENOID BINDING PROTEIN
Function / homology
Function and homology information


light absorption / : / phycobilisome / chloride ion binding
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. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
beta,beta-carotene-4,4'-dione / IODIDE ION / Putative orange carotenoid-binding protein
Similarity search - Component
Biological speciesTolypothrix sp. PCC 7601 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.712 Å
AuthorsSutter, M. / Dominguez-Martin, M.A.
CitationJournal: Biochim Biophys Acta Bioenerg / Year: 2019
Title: Structural and spectroscopic characterization of HCP2.
Authors: Dominguez-Martin, M.A. / Polivka, T. / Sutter, M. / Ferlez, B. / Lechno-Yossef, S. / Montgomery, B.L. / Kerfeld, C.A.
History
DepositionAug 31, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ISSN ..._citation.country / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Orange carotenoid-binding protein
B: Orange carotenoid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,40913
Polymers37,0252
Non-polymers2,38311
Water3,027168
1
A: Orange carotenoid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8237
Polymers18,5131
Non-polymers1,3116
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Orange carotenoid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5856
Polymers18,5131
Non-polymers1,0725
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.162, 71.635, 56.341
Angle α, β, γ (deg.)90.00, 92.32, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Orange carotenoid-binding protein


Mass: 18512.666 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tolypothrix sp. PCC 7601 (bacteria) / Gene: FDUTEX481_01662 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D6L0Q7
#2: Chemical ChemComp-45D / beta,beta-carotene-4,4'-dione / Isomer of Canthaxanthin / Canthaxanthin


Mass: 564.840 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H52O2
#3: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: I
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 1.91 Å3/Da / Density % sol: 35.77 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Ammonium Iodide, 23 % PEG 3.350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.71→44.263 Å / Num. obs: 59576 / % possible obs: 98.8 % / Redundancy: 3.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.034 / Rrim(I) all: 0.05 / Net I/σ(I): 15.7
Reflection shellResolution: 1.71→1.8 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 13974 / CC1/2: 0.893 / Rpim(I) all: 0.245 / Rrim(I) all: 0.368 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M98

1m98
PDB Unreleased entry


Resolution: 1.712→44.263 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20
RfactorNum. reflection% reflection
Rfree0.1988 3751 6.74 %
Rwork0.1667 --
obs0.1689 55663 93.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.712→44.263 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2300 0 108 168 2576
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052449
X-RAY DIFFRACTIONf_angle_d0.6783326
X-RAY DIFFRACTIONf_dihedral_angle_d14.6361485
X-RAY DIFFRACTIONf_chiral_restr0.037348
X-RAY DIFFRACTIONf_plane_restr0.004454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7115-1.73320.3471190.28331739X-RAY DIFFRACTION84
1.7332-1.7560.2781570.24991966X-RAY DIFFRACTION96
1.756-1.78010.29051220.24491957X-RAY DIFFRACTION96
1.7801-1.80550.25241600.22091871X-RAY DIFFRACTION95
1.8055-1.83240.22731330.20762026X-RAY DIFFRACTION96
1.8324-1.86110.25261550.19531987X-RAY DIFFRACTION96
1.8611-1.89160.21291380.19081897X-RAY DIFFRACTION95
1.8916-1.92420.27211520.18961919X-RAY DIFFRACTION94
1.9242-1.95920.21971370.17931952X-RAY DIFFRACTION94
1.9592-1.99690.22521200.17211939X-RAY DIFFRACTION95
1.9969-2.03760.25831500.17661977X-RAY DIFFRACTION97
2.0376-2.08190.18351480.17331975X-RAY DIFFRACTION96
2.0819-2.13040.22121440.16521935X-RAY DIFFRACTION97
2.1304-2.18360.20161360.16552046X-RAY DIFFRACTION97
2.1836-2.24270.21951500.1711941X-RAY DIFFRACTION95
2.2427-2.30870.20431200.16091900X-RAY DIFFRACTION94
2.3087-2.38320.22161330.16011957X-RAY DIFFRACTION95
2.3832-2.46840.20321350.1571951X-RAY DIFFRACTION94
2.4684-2.56720.17771490.16361877X-RAY DIFFRACTION93
2.5672-2.6840.18831440.16051946X-RAY DIFFRACTION95
2.684-2.82550.19071370.16921940X-RAY DIFFRACTION95
2.8255-3.00250.19821360.17461868X-RAY DIFFRACTION93
3.0025-3.23420.19151380.16141925X-RAY DIFFRACTION92
3.2342-3.55960.17051420.16551815X-RAY DIFFRACTION89
3.5596-4.07430.15461320.14561810X-RAY DIFFRACTION90
4.0743-5.1320.16781240.13371941X-RAY DIFFRACTION93
5.132-44.27730.21171400.17131855X-RAY DIFFRACTION91

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