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- PDB-6htj: Crystal structure of the translation recovery factor Trf from Sul... -

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Basic information

Entry
Database: PDB / ID: 6htj
TitleCrystal structure of the translation recovery factor Trf from Sulfolobus solfataricus
ComponentsNucleic-acid-binding protein containing a Zn-ribbon
KeywordsTRANSLATION / translation initiation / ribosome / Sulfolobus solfataricus / translation recovery factor Trf
Function / homologyDomain of unknown function DUF35, rubredoxin-like zinc ribbon domain, N-terminal / Rubredoxin-like zinc ribbon domain (DUF35_N) / Nucleic acid-binding, OB-fold / Zn-ribbon domain-containing OB-fold protein / DUF35_N domain-containing protein
Function and homology information
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsWoehnert, J. / Pogoryelov, D. / Kaiser, M.
CitationJournal: Febs Open Bio / Year: 2019
Title: Crystal structure of the translation recovery factor Trf from Sulfolobus solfataricus.
Authors: Kaiser, M. / Wurm, J.P. / Martens, B. / Blasi, U. / Pogoryelov, D. / Wohnert, J.
History
DepositionOct 4, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 15, 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: Nucleic-acid-binding protein containing a Zn-ribbon
B: Nucleic-acid-binding protein containing a Zn-ribbon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4504
Polymers28,3192
Non-polymers1312
Water4,558253
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-9 kcal/mol
Surface area13210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.291, 58.493, 101.366
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 Nucleic-acid-binding protein containing a Zn-ribbon


Mass: 14159.465 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: SSOP1_2634, SULA_0310, SULB_0312, SULC_0310 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0E3M9E8, UniProt: Q97VU8*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.11 Å3/Da / Density % sol: 41.68 %
Crystal growTemperature: 277.5 K / Method: microdialysis / pH: 6.5
Details: 50 mM Bis Tris pH 6.5, 50 mM NaCl, 5 mM beta-mercapthoethanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00004 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 1.65→38.304 Å / Num. obs: 29528 / % possible obs: 99.82 % / Redundancy: 13.5 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.1447 / Rpim(I) all: 0.04051 / Rrim(I) all: 0.1504 / Net I/σ(I): 13.32
Reflection shellResolution: 1.65→1.709 Å / Redundancy: 12.1 % / Rmerge(I) obs: 1.238 / Num. unique obs: 2817 / Rpim(I) all: 0.3628 / Rrim(I) all: 1.292 / % possible all: 98.26

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
SHELXDEphasing
RESOLVEmodel building
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.65→38.304 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.06
RfactorNum. reflection% reflectionSelection details
Rfree0.2071 2767 4.98 %random selection
Rwork0.1915 ---
obs0.1923 29528 99.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 65.89 Å2 / Biso mean: 25.7392 Å2 / Biso min: 10.67 Å2
Refinement stepCycle: final / Resolution: 1.65→38.304 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1964 0 2 253 2219
Biso mean--13.77 33.17 -
Num. residues----237
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122008
X-RAY DIFFRACTIONf_angle_d1.1772688
X-RAY DIFFRACTIONf_chiral_restr0.081277
X-RAY DIFFRACTIONf_plane_restr0.005341
X-RAY DIFFRACTIONf_dihedral_angle_d22.965772
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6501-1.67850.33291300.2892577270796
1.6785-1.7090.28521370.269825502687100
1.709-1.74190.30061360.255726602796100
1.7419-1.77750.25521430.242226992842100
1.7775-1.81610.25531380.234226342772100
1.8161-1.85830.21911380.225725992737100
1.8583-1.90480.23461420.237526722814100
1.9048-1.95630.29471410.229926282769100
1.9563-2.01390.1891350.219326632798100
2.0139-2.07890.25161380.195726342772100
2.0789-2.15320.21291380.187126692807100
2.1532-2.23940.22291400.183726452785100
2.2394-2.34130.21221400.191426222762100
2.3413-2.46470.19811370.192526452782100
2.4647-2.61910.21361410.190526622803100
2.6191-2.82130.21131370.195226252762100
2.8213-3.10510.19521450.185426782823100
3.1051-3.55410.1891380.170826262764100
3.5541-4.47670.16941390.15526542793100
4.4767-38.31440.1691340.172526342768100

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