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- PDB-6fej: Anabaena Apo-C-Terminal Domain Homolog Protein -

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Basic information

Entry
Database: PDB / ID: 6fej
TitleAnabaena Apo-C-Terminal Domain Homolog Protein
ComponentsAll4940 protein
KeywordsPHOTOSYNTHESIS / carotene cyanobacteria photoprotection urea
Function / homology
Function and homology information


Nuclear transport factor 2 (NTF2) domain / Nuclear transport factor 2 domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
UREA / All4940 protein
Similarity search - Component
Biological speciesNostoc sp. PCC 7120 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsHarris, D. / Wilson, A. / Muzzopappa, F. / Kirilovsky, D. / Adir, N.
Funding support Israel, 1items
OrganizationGrant numberCountry
ISF 843/16 Israel
CitationJournal: Commun Biol / Year: 2018
Title: Structural rearrangements in the C-terminal domain homolog of Orange Carotenoid Protein are crucial for carotenoid transfer.
Authors: Harris, D. / Wilson, A. / Muzzopappa, F. / Sluchanko, N.N. / Friedrich, T. / Maksimov, E.G. / Kirilovsky, D. / Adir, N.
History
DepositionJan 2, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Category: citation / citation_author
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
Revision 1.2Jan 17, 2024Group: 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7665
Polymers26,5862
Non-polymers1803
Water27015
1
A: All4940 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4133
Polymers13,2931
Non-polymers1202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: All4940 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3532
Polymers13,2931
Non-polymers601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: All4940 protein
hetero molecules

B: All4940 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7665
Polymers26,5862
Non-polymers1803
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_445x-y-1,-y-1,-z1
Buried area2800 Å2
ΔGint-16 kcal/mol
Surface area11440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.080, 81.080, 162.943
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein All4940 protein


Mass: 13292.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. PCC 7120 (bacteria) / Gene: all4940 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YMJ3
#2: Chemical ChemComp-URE / UREA


Mass: 60.055 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH4N2O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
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: 2.91 Å3/Da / Density % sol: 57.7 % / Description: elongated hexagonal rod
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 4.2 / Details: 0.1M citric acid 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Aug 21, 2017
RadiationMonochromator: C(110) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.75→70.22 Å / Num. obs: 8819 / % possible obs: 99.8 % / Redundancy: 5.6 % / CC1/2: 0.935 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.032 / Net I/σ(I): 11.7
Reflection shellResolution: 2.75→2.848 Å / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 5 / Num. unique obs: 1247 / CC1/2: 0.898 / Rpim(I) all: 0.142 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
SCALAdata scaling
PDB_EXTRACT3.24data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UI2

5ui2


Resolution: 2.75→70.22 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.898 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.408
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2921 959 10.9 %RANDOM
Rwork0.2409 ---
obs0.2465 7807 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 119.62 Å2 / Biso mean: 67.309 Å2 / Biso min: 22.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20.02 Å20 Å2
2--0.05 Å2-0 Å2
3----0.16 Å2
Refinement stepCycle: final / Resolution: 2.75→70.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1828 0 12 15 1855
Biso mean--78.36 45.17 -
Num. residues----242
LS refinement shellResolution: 2.75→2.821 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 57 -
Rwork0.279 562 -
all-619 -
obs--100 %
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)
15.5033-1.2670.90824.01920.17175.587-0.10180.56650.3266-0.3824-0.02750.2823-0.4438-0.2050.12920.09870.0187-0.03720.20820.05450.0586-5.441-32.585-10.614
26.12390.1043-1.1314.379-2.15395.4941-0.3613-0.77370.32360.38520.0793-0.1994-0.42840.40950.28210.09330.0452-0.05230.2544-0.07390.06073.441-31.75611.252
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 138
2X-RAY DIFFRACTION2B16 - 133

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