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- PDB-6s5l: Anabaena Apo-C-Terminal Domain Homolog Of The Orange Carotenoid P... -

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Basic information

Entry
Database: PDB / ID: 6s5l
TitleAnabaena Apo-C-Terminal Domain Homolog Of The Orange Carotenoid Protein In Native Conditions
ComponentsAll4940 protein
KeywordsPHOTOSYNTHESIS / OCP / orange carotenod protein / carotenoid transfer / CTDH / apoCTDH / CTT
Function / homologyNuclear transport factor 2 domain / Nuclear transport factor 2 (NTF2) domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / All4940 protein
Function and homology information
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsHarris, D. / Muzzopappa, F. / Kirilovsky, D. / Adir, N.
Funding support Israel, 2items
OrganizationGrant numberCountry
Israel Science Foundation843/16 Israel
United States - Israel Binational Science Foundation (BSF)2014395 Israel
CitationJournal: Biochim Biophys Acta Bioenerg / Year: 2020
Title: Structural dynamics in the C terminal domain homolog of orange carotenoid Protein reveals residues critical for carotenoid uptake.
Authors: Harris, D. / Muzzopappa, F. / Glaser, F. / Wilson, A. / Kirilovsky, D. / Adir, N.
History
DepositionJul 1, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Mar 30, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry
Revision 1.3Jan 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: All4940 protein
B: All4940 protein
C: All4940 protein
D: All4940 protein
E: All4940 protein
F: All4940 protein
G: All4940 protein
H: All4940 protein
I: All4940 protein
J: All4940 protein
K: All4940 protein
L: All4940 protein


Theoretical massNumber of molelcules
Total (without water)181,60912
Polymers181,60912
Non-polymers00
Water1,33374
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration, native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18750 Å2
ΔGint-120 kcal/mol
Surface area70220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.654, 112.276, 318.543
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
All4940 protein


Mass: 15134.114 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / Gene: all4940 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YMJ3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 3.23 Å3/Da / Density % sol: 61.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 1.26M NaH2PO4, 0.14M K2HPO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 5, 2018
RadiationMonochromator: C(110) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.9→47.99 Å / Num. obs: 53339 / % possible obs: 99.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.036 / Rrim(I) all: 0.071 / Net I/σ(I): 16.7
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 3.9 % / Num. unique obs: 7646 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FEJ

6fej


Resolution: 2.9→47.99 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.9 / SU B: 16.255 / SU ML: 0.292 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.948 / ESU R Free: 0.356
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2537 2692 5.1 %RANDOM
Rwork0.2094 ---
obs0.2116 50566 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 173.15 Å2 / Biso mean: 69.988 Å2 / Biso min: 22.43 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å20 Å2
2--0.35 Å2-0 Å2
3----0.87 Å2
Refinement stepCycle: final / Resolution: 2.9→47.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11355 0 0 74 11429
Biso mean---47.03 -
Num. residues----1502
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01911591
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210616
X-RAY DIFFRACTIONr_angle_refined_deg1.7121.94815810
X-RAY DIFFRACTIONr_angle_other_deg1.029324806
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.78651489
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.48427.073492
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.406151847
X-RAY DIFFRACTIONr_chiral_restr0.0950.21838
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02112983
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022049
LS refinement shellResolution: 2.9→2.975 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 224 -
Rwork0.333 3685 -
all-3909 -
obs--99.87 %

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