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- PDB-8qx7: Apo-C-Terminal Domain Homolog of the Orange Carotenoid Protein fr... -

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Basic information

Entry
Database: PDB / ID: 8qx7
TitleApo-C-Terminal Domain Homolog of the Orange Carotenoid Protein from Anabaena at a resolution of 1.95 Angstroms
ComponentsAll4940 protein
KeywordsPHOTOSYNTHESIS / Membrane / carotenoid / Orange carotenoid protein / Cyanobacteria
Function / homologyNuclear transport factor 2 (NTF2) domain / Nuclear transport factor 2 domain / NTF2-like domain superfamily / MALONIC ACID / All4940 protein
Function and homology information
Biological speciesCyanobacteriota (cyanobacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSklyar, J. / Wilson, A. / Kirilovsky, D. / Adir, N.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science Foundation1596/21 Israel
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Insights into energy quenching mechanisms and carotenoid uptake by orange carotenoid protein homologs: HCP4 and CTDH.
Authors: Sklyar, J. / Wilson, A. / Kirilovsky, D. / Adir, N.
History
DepositionOct 22, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: All4940 protein
B: All4940 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5254
Polymers32,3162
Non-polymers2082
Water2,000111
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-16 kcal/mol
Surface area12690 Å2
Unit cell
Length a, b, c (Å)111.929, 52.925, 48.595
Angle α, β, γ (deg.)90.00, 96.88, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein All4940 protein


Mass: 16158.193 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyanobacteriota (cyanobacteria) / Gene: all4940 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8YMJ3
#2: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.21 Å3/Da / Density % sol: 44.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 44% Tacsimate pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.95→47.78 Å / Num. obs: 20695 / % possible obs: 99.7 % / Redundancy: 6.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.049 / Rrim(I) all: 0.091 / Net I/σ(I): 12.8
Reflection shellResolution: 1.95→2 Å / Num. unique obs: 1410 / CC1/2: 0.843

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→47.78 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / Phase error: 26.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2421 1994 4.97 %
Rwork0.195 --
obs0.1974 20679 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→47.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1893 0 14 111 2018
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d0.953
X-RAY DIFFRACTIONf_dihedral_angle_d8.948258
X-RAY DIFFRACTIONf_chiral_restr0.065305
X-RAY DIFFRACTIONf_plane_restr0.007349
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-20.37021560.29072586X-RAY DIFFRACTION96
2-2.050.27751290.25822778X-RAY DIFFRACTION100
2.05-2.110.30111340.23972774X-RAY DIFFRACTION100
2.11-2.180.25331370.21952674X-RAY DIFFRACTION100
2.18-2.260.26911320.21142751X-RAY DIFFRACTION100
2.26-2.350.25641340.20652718X-RAY DIFFRACTION100
2.35-2.460.28191300.20232757X-RAY DIFFRACTION100
2.46-2.590.2131580.19912754X-RAY DIFFRACTION100
2.59-2.750.2471470.21672693X-RAY DIFFRACTION100
2.75-2.960.29061320.21272783X-RAY DIFFRACTION100
2.96-3.260.25931700.20682714X-RAY DIFFRACTION99
3.26-3.730.21781350.17852736X-RAY DIFFRACTION100
3.73-4.690.21641460.16172672X-RAY DIFFRACTION99
4.7-47.780.21721540.17832713X-RAY DIFFRACTION99

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