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- PDB-5fcy: Structure of Anabaena (Nostoc) sp. PCC 7120 Red Carotenoid Protei... -

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Basic information

Entry
Database: PDB / ID: 5fcy
TitleStructure of Anabaena (Nostoc) sp. PCC 7120 Red Carotenoid Protein binding a mixture of carotenoids
ComponentsRed carotenoid protein (RCP)
KeywordsCARTENOID BINDING PROTEIN / carotenoid / photoprotection / cyanobacteria
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-CAROTENE / All1123 protein
Similarity search - Component
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.508 Å
AuthorsSutter, M. / Leverrenz, R.L. / Kerfeld, C.A.
CitationJournal: Mol Plant / Year: 2016
Title: Structure, Diversity, and Evolution of a New Family of Soluble Carotenoid-Binding Proteins in Cyanobacteria.
Authors: Melnicki, M.R. / Leverenz, R.L. / Sutter, M. / Lopez-Igual, R. / Wilson, A. / Pawlowski, E.G. / Perreau, F. / Kirilovsky, D. / Kerfeld, C.A.
History
DepositionDec 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
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

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Assembly

Deposited unit
A: Red carotenoid protein (RCP)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7202
Polymers19,1841
Non-polymers5371
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-10 kcal/mol
Surface area7040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.373, 58.373, 42.251
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Red carotenoid protein (RCP)


Mass: 19183.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (strain PCC 7120 / UTEX 2576) (bacteria)
Strain: PCC 7120 / UTEX 2576 / Gene: all1123 / Production host: Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: Q8YXT8
#2: Chemical ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H56
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.26 Å3/Da / Density % sol: 45.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 100 mM HEPES pH 7.5, 10% 2-propanol, 25% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.00003 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.508→32.419 Å / Num. obs: 5403 / % possible obs: 98 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.031 / Net I/σ(I): 34.7
Reflection shellResolution: 2.51→2.64 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.156 / Mean I/σ(I) obs: 5.1 / % possible all: 83.7

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Processing

Software
NameVersionClassification
PHENIX(1.10_2152: ???)refinement
XDSdata reduction
SCALAdata scaling
AutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XB4

4xb4


Resolution: 2.508→32.419 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 2.02 / Phase error: 30.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2921 540 10.01 %Random selection
Rwork0.2318 ---
obs0.2378 5393 97.58 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.508→32.419 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1101 0 40 23 1164
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031165
X-RAY DIFFRACTIONf_angle_d0.7191574
X-RAY DIFFRACTIONf_dihedral_angle_d14.586695
X-RAY DIFFRACTIONf_chiral_restr0.033165
X-RAY DIFFRACTIONf_plane_restr0.004209
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5084-2.76070.34771260.3051135X-RAY DIFFRACTION90
2.7607-3.15990.38631360.28991225X-RAY DIFFRACTION100
3.1599-3.980.32381390.23281253X-RAY DIFFRACTION100
3.98-32.42170.22931390.19661240X-RAY DIFFRACTION100

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