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- PDB-3hfo: Crystal Structure of an Hfq protein from Synechocystis sp. -

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Basic information

Entry
Database: PDB / ID: 3hfo
TitleCrystal Structure of an Hfq protein from Synechocystis sp.
ComponentsSsr3341 protein
KeywordsRNA BINDING PROTEIN / HFQ / SM / RNA-BINDING PROTEIN / SRNA / TRANSLATIONAL REGULATION
Function / homologySH3 type barrels. - #100 / LSM domain superfamily / SH3 type barrels. / Roll / Mainly Beta / Ssr3341 protein
Function and homology information
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å
AuthorsBoggild, A. / Overgaard, M. / Valentin-Hansen, P. / Brodersen, D.E.
CitationJournal: Febs J. / Year: 2009
Title: Cyanobacteria contain a structural homologue of the Hfq protein with altered RNA-binding properties.
Authors: Boggild, A. / Overgaard, M. / Valentin-Hansen, P. / Brodersen, D.E.
History
DepositionMay 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 16, 2011Group: Atomic model
Revision 1.3Mar 21, 2012Group: Database references
Revision 1.4Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Sep 6, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ssr3341 protein
B: Ssr3341 protein
C: Ssr3341 protein


Theoretical massNumber of molelcules
Total (without water)23,5203
Polymers23,5203
Non-polymers00
Water4,900272
1
A: Ssr3341 protein
B: Ssr3341 protein
C: Ssr3341 protein

A: Ssr3341 protein
B: Ssr3341 protein
C: Ssr3341 protein


Theoretical massNumber of molelcules
Total (without water)47,0406
Polymers47,0406
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area8200 Å2
ΔGint-58 kcal/mol
Surface area19720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.470, 86.160, 103.180
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11B-89-

HOH

21B-95-

HOH

31B-252-

HOH

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Components

#1: Protein Ssr3341 protein


Mass: 7839.961 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: codons optimised for E. coli expression / Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC6803 / Gene: ssr3341 / Plasmid: pTYP11 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: P74112
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 1.92 Å3/Da / Density % sol: 36.09 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 60% Tacsimate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.9 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 19, 2008
RadiationMonochromator: Double crystal monochromator, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.21→26.2 Å / Num. obs: 52709 / % possible obs: 96.5 % / Redundancy: 4.8 % / Biso Wilson estimate: 16.864 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 24.23
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.21-1.250.9021.411448318079.2
1.25-1.280.8011.916912375696.5
1.28-1.320.6642.518324371197.2
1.32-1.360.5812.817555355897.4
1.36-1.40.4353.617421351697.8
1.4-1.450.3444.716745338097.8
1.45-1.510.2496.416350329898.3
1.51-1.570.1977.915711317598.3
1.57-1.640.15310.115132304298.5
1.64-1.720.11213.314405290798.7
1.72-1.810.07918.313893279398.8
1.81-1.920.05326.513171265099
1.92-2.050.0434.312350250199.4
2.05-2.220.0345.111436230898.9
2.22-2.430.02651.710516212898.7
2.43-2.720.02554.49649196098.7
2.72-3.140.0265.78368169497.8
3.14-3.840.01677.77109143797.2
3.84-5.430.01481.65477112595.9
5.430.01577.2273359087.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 51.73
Highest resolutionLowest resolution
Rotation2.5 Å26.2 Å
Translation2.5 Å26.2 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.3phasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1HK9

1hk9


Resolution: 1.3→26.199 Å / Occupancy max: 1 / Occupancy min: 0.16 / FOM work R set: 0.891 / SU ML: 0.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2 1652 3.78 %
Rwork0.152 --
obs0.154 43747 98.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.911 Å2 / ksol: 0.389 e/Å3
Displacement parametersBiso max: 64.74 Å2 / Biso mean: 17.734 Å2 / Biso min: 5.63 Å2
Baniso -1Baniso -2Baniso -3
1--0.009 Å20 Å2-0 Å2
2--1.237 Å2-0 Å2
3----1.229 Å2
Refinement stepCycle: LAST / Resolution: 1.3→26.199 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1531 0 0 272 1803
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0171667
X-RAY DIFFRACTIONf_angle_d1.7982294
X-RAY DIFFRACTIONf_chiral_restr0.113284
X-RAY DIFFRACTIONf_plane_restr0.008297
X-RAY DIFFRACTIONf_dihedral_angle_d15.115663
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3-1.3380.2531290.1893480360997
1.338-1.3810.2351320.1713441357398
1.381-1.4310.2291510.1593461361298
1.431-1.4880.2251310.1423491362298
1.488-1.5560.2231370.1323473361098
1.556-1.6380.1911460.1223508365499
1.638-1.740.1691370.1193498363599
1.74-1.8750.1791380.1153547368599
1.875-2.0630.1811430.1263518366199
2.063-2.3620.1551330.1273570370399
2.362-2.9750.2051370.1543563370099
2.975-26.2040.21380.1713545368395

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