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- PDB-6ov6: CRYSTALLOGRAPHIC STRUCTURE OF THE C24 PROTEIN FROM THE ANTARCTIC ... -

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Basic information

Entry
Database: PDB / ID: 6ov6
TitleCRYSTALLOGRAPHIC STRUCTURE OF THE C24 PROTEIN FROM THE ANTARCTIC MICROORGANISM BIZIONIA ARGENTINENSIS
ComponentsC24 PROTEIN
KeywordsUNKNOWN FUNCTION / FIBER / VIRAL ORIGIN
Function / homologymetal ion binding / : / Tail fiber protein
Function and homology information
Biological speciesBizionia argentinensis JUB59 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.82 Å
AuthorsKlinke, S. / Rinaldi, J. / Guimaraes, B.G. / Pellizza, L. / Aran, M.
CitationJournal: J.Struct.Biol. / Year: 2020
Title: Structure of the putative long tail fiber receptor-binding tip of a novel temperate bacteriophage from the Antarctic bacterium Bizionia argentinensis JUB59.
Authors: Pellizza, L. / Lopez, J.L. / Vazquez, S. / Sycz, G. / Guimaraes, B.G. / Rinaldi, J. / Goldbaum, F.A. / Aran, M. / Mac Cormack, W.P. / Klinke, S.
History
DepositionMay 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 7, 2020Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: C24 PROTEIN
B: C24 PROTEIN
C: C24 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,2444
Polymers89,1893
Non-polymers551
Water10,809600
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28710 Å2
ΔGint-164 kcal/mol
Surface area31650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.130, 65.250, 239.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein C24 PROTEIN


Mass: 29729.789 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bizionia argentinensis JUB59 (bacteria)
Gene: BZARG_797 / Plasmid: PDEST-527 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: G2EBB4
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 600 / 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: 2.77 Å3/Da / Density % sol: 55.53 % / Description: Rhomboidal-shaped crystals
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 12% PEG 8000, 0.1 M SODIUM CITRATE, 0.1 M AMMONIUM SULFATE
PH range: 7.5

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSOLEIL PROXIMA 110.98011
SYNCHROTRONSOLEIL PROXIMA 121.89202
Detector
TypeIDDetectorDateDetails
DECTRIS PILATUS 6M1PIXELNov 17, 2012KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS
DECTRIS PILATUS 6M2PIXELNov 21, 2012KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1CHANNEL CUT CRYOGENICALLY COOLED MONOCHROMATOR CRYSTALSINGLE WAVELENGTHMx-ray1
2CHANNEL CUT CRYOGENICALLY COOLED MONOCHROMATOR CRYSTALSINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.980111
21.892021
ReflectionResolution: 1.82→50 Å / Num. obs: 87380 / % possible obs: 97.2 % / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 33.28 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 17.3
Reflection shellResolution: 1.82→1.93 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.593 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 6246 / Rsym value: 0.593 / % possible all: 95.6

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
SHELXphasing
BUSTER2.10.0refinement
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.82→44.12 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.937 / SU R Cruickshank DPI: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.23 4365 5 %RANDOM
Rwork0.198 ---
obs0.199 87375 97.3 %-
Displacement parametersBiso mean: 38.1 Å2
Baniso -1Baniso -2Baniso -3
1-3.7417 Å20 Å20 Å2
2---5.9411 Å20 Å2
3---2.1994 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: LAST / Resolution: 1.82→44.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5532 0 1 600 6133
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015634HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.17647HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1880SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes132HARMONIC2
X-RAY DIFFRACTIONt_gen_planes841HARMONIC5
X-RAY DIFFRACTIONt_it5634HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.84
X-RAY DIFFRACTIONt_other_torsion14.91
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion755SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6953SEMIHARMONIC4
LS refinement shellResolution: 1.82→1.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2439 313 5.01 %
Rwork0.2292 5933 -
all0.2299 6246 -
obs--97.34 %

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