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- PDB-2yht: Crystal structure of Hfq riboregulator from E. coli (P1 space group) -

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Basic information

Entry
Database: PDB / ID: 2yht
TitleCrystal structure of Hfq riboregulator from E. coli (P1 space group)
ComponentsPROTEIN HFQ
KeywordsCHAPERONE / RNA CHAPERONE
Function / homology
Function and homology information


sRNA-mediated post-transcriptional gene silencing / positive regulation of translation, ncRNA-mediated / regulation of translation, ncRNA-mediated / RNA folding chaperone / bent DNA binding / regulation of RNA stability / regulation of DNA-templated transcription / DNA binding / RNA binding / cytosol
Similarity search - Function
RNA-binding protein Hfq / Hfq protein / SH3 type barrels. - #100 / : / Sm domain profile. / LSM domain superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
RNA-binding protein Hfq
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsBasquin, J. / Sauter, C.
Citation
Journal: Cryst.Growth Des. / Year: 2011
Title: Exploiting Protein Engineering and Crystal Polymorphism for Successful X-Ray Structure Determination
Authors: Bonnefond, L. / Schellenberger, P. / Basquin, J. / Demangeat, G. / Ritzenthaler, C. / Chenevert, R. / Balg, C. / Frugier, M. / Rudinger-Thirion, J. / Giege, R. / Lorber, B. / Sauter, C.
#1: Journal: Nucleic Acids Res. / Year: 2003
Title: Sm-Like Proteins in Eubacteria: The Crystal Structure of the Hfq Protein from Escherichia Coli.
Authors: Sauter, C. / Basquin, J. / Suck, D.
History
DepositionMay 6, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 30-STRANDED BARREL THIS IS REPRESENTED BY A 31-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "GA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 30-STRANDED BARREL THIS IS REPRESENTED BY A 31-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN HFQ
B: PROTEIN HFQ
C: PROTEIN HFQ
D: PROTEIN HFQ
E: PROTEIN HFQ
F: PROTEIN HFQ
G: PROTEIN HFQ
H: PROTEIN HFQ
I: PROTEIN HFQ
J: PROTEIN HFQ
K: PROTEIN HFQ
L: PROTEIN HFQ


Theoretical massNumber of molelcules
Total (without water)99,09112
Polymers99,09112
Non-polymers00
Water0
1
A: PROTEIN HFQ
B: PROTEIN HFQ
C: PROTEIN HFQ
D: PROTEIN HFQ
E: PROTEIN HFQ
F: PROTEIN HFQ


Theoretical massNumber of molelcules
Total (without water)49,5456
Polymers49,5456
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8730 Å2
ΔGint-75.1 kcal/mol
Surface area17010 Å2
MethodPISA
2
G: PROTEIN HFQ
H: PROTEIN HFQ
I: PROTEIN HFQ
J: PROTEIN HFQ
K: PROTEIN HFQ
L: PROTEIN HFQ


Theoretical massNumber of molelcules
Total (without water)49,5456
Polymers49,5456
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8770 Å2
ΔGint-76.2 kcal/mol
Surface area17010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.200, 61.200, 53.100
Angle α, β, γ (deg.)82.60, 87.30, 60.00
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81
91
101
111
121
12
22
32
42
52
62
72
82
92
102
112
13
23
33
43
53
63
73
83
93
103

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 7:24 OR RESSEQ 32:38 OR RESSEQ 44:68)
211CHAIN B AND (RESSEQ 7:24 OR RESSEQ 32:38 OR RESSEQ 44:68)
311CHAIN C AND (RESSEQ 7:24 OR RESSEQ 32:38 OR RESSEQ 44:68)
411CHAIN D AND (RESSEQ 7:24 OR RESSEQ 32:38 OR RESSEQ 44:68)
511CHAIN E AND (RESSEQ 7:24 OR RESSEQ 32:38 OR RESSEQ 44:68)
611CHAIN F AND (RESSEQ 7:24 OR RESSEQ 32:38 OR RESSEQ 44:68)
711CHAIN G AND (RESSEQ 7:24 OR RESSEQ 32:38 OR RESSEQ 44:68)
811CHAIN H AND (RESSEQ 7:24 OR RESSEQ 32:38 OR RESSEQ 44:68)
911CHAIN I AND (RESSEQ 7:24 OR RESSEQ 32:38 OR RESSEQ 44:68)
1011CHAIN J AND (RESSEQ 7:24 OR RESSEQ 32:38 OR RESSEQ 44:68)
1111CHAIN K AND (RESSEQ 7:24 OR RESSEQ 32:38 OR RESSEQ 44:68)
1211CHAIN L AND (RESSEQ 7:24 OR RESSEQ 32:38 OR RESSEQ 44:68)
112CHAIN A AND (RESSEQ 38:44)
212CHAIN B AND (RESSEQ 38:44)
312CHAIN C AND (RESSEQ 38:44)
412CHAIN D AND (RESSEQ 38:44)
512CHAIN E AND (RESSEQ 38:44)
612CHAIN G AND (RESSEQ 38:44)
712CHAIN H AND (RESSEQ 38:44)
812CHAIN I AND (RESSEQ 38:44)
912CHAIN J AND (RESSEQ 38:44)
1012CHAIN K AND (RESSEQ 38:44)
1112CHAIN L AND (RESSEQ 38:44)
113CHAIN A AND (RESSEQ 24:32)
213CHAIN B AND (RESSEQ 24:32)
313CHAIN C AND (RESSEQ 24:32)
413CHAIN D AND (RESSEQ 24:32)
513CHAIN E AND (RESSEQ 24:32)
613CHAIN G AND (RESSEQ 24:32)
713CHAIN H AND (RESSEQ 24:32)
813CHAIN I AND (RESSEQ 24:32)
913CHAIN J AND (RESSEQ 24:32)
1013CHAIN F AND (RESSEQ 24:32)

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
PROTEIN HFQ / HF-1 / HOST FACTOR-I PROTEIN / HF-I


Mass: 8257.572 Da / Num. of mol.: 12 / Fragment: SM-LIKE FOLD, RESIDUES 1-72
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: P0A6X3

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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: 1.8 Å3/Da / Density % sol: 30 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.4
Details: CRYSTALS WERE OBTAINED BY VAPOR DIFFUSION IN 2UL SITTING DROPS. THE RESERVOIR CONTAINED 30% PEG 3350, 0.1 M NA-CITRATE PH 5.4. CRYSTALLIZATIONS WERE CARRIED OUT AT 20 DEGREES CELSIUS.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.9→62 Å / Num. obs: 14455 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 28.19 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12
Reflection shellResolution: 2.9→3 Å / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 6.5 / % possible all: 82.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Y90

2y90


Resolution: 2.9→30.566 Å / SU ML: 0.29 / σ(F): 0.05 / Phase error: 23.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2285 700 5 %
Rwork0.1809 --
obs0.1833 14073 96.05 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 19.061 Å2 / ksol: 0.369 e/Å3
Displacement parametersBiso mean: 26.6 Å2
Baniso -1Baniso -2Baniso -3
1--9.9152 Å2-0.978 Å20.3209 Å2
2---9.2556 Å20.9528 Å2
3---18.9369 Å2
Refinement stepCycle: LAST / Resolution: 2.9→30.566 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6048 0 0 0 6048
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096156
X-RAY DIFFRACTIONf_angle_d1.1548352
X-RAY DIFFRACTIONf_dihedral_angle_d14.742340
X-RAY DIFFRACTIONf_chiral_restr0.0691008
X-RAY DIFFRACTIONf_plane_restr0.0051056
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A396X-RAY DIFFRACTIONPOSITIONAL
12B396X-RAY DIFFRACTIONPOSITIONAL0.044
13C396X-RAY DIFFRACTIONPOSITIONAL0.047
14D396X-RAY DIFFRACTIONPOSITIONAL0.045
15E396X-RAY DIFFRACTIONPOSITIONAL0.053
16F396X-RAY DIFFRACTIONPOSITIONAL0.044
17G396X-RAY DIFFRACTIONPOSITIONAL0.046
18H396X-RAY DIFFRACTIONPOSITIONAL0.039
19I396X-RAY DIFFRACTIONPOSITIONAL0.041
110J396X-RAY DIFFRACTIONPOSITIONAL0.045
111K396X-RAY DIFFRACTIONPOSITIONAL0.047
112L396X-RAY DIFFRACTIONPOSITIONAL0.047
21A60X-RAY DIFFRACTIONPOSITIONAL
22B60X-RAY DIFFRACTIONPOSITIONAL0.035
23C60X-RAY DIFFRACTIONPOSITIONAL0.034
24D60X-RAY DIFFRACTIONPOSITIONAL0.034
25E60X-RAY DIFFRACTIONPOSITIONAL0.046
26G60X-RAY DIFFRACTIONPOSITIONAL0.047
27H60X-RAY DIFFRACTIONPOSITIONAL0.03
28I60X-RAY DIFFRACTIONPOSITIONAL0.034
29J60X-RAY DIFFRACTIONPOSITIONAL0.041
210K60X-RAY DIFFRACTIONPOSITIONAL0.048
211L60X-RAY DIFFRACTIONPOSITIONAL0.042
31A72X-RAY DIFFRACTIONPOSITIONAL
32B72X-RAY DIFFRACTIONPOSITIONAL0.036
33C72X-RAY DIFFRACTIONPOSITIONAL0.043
34D72X-RAY DIFFRACTIONPOSITIONAL0.046
35E72X-RAY DIFFRACTIONPOSITIONAL0.06
36G72X-RAY DIFFRACTIONPOSITIONAL0.05
37H72X-RAY DIFFRACTIONPOSITIONAL0.041
38I72X-RAY DIFFRACTIONPOSITIONAL0.053
39J72X-RAY DIFFRACTIONPOSITIONAL0.048
310F72X-RAY DIFFRACTIONPOSITIONAL0.048
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9001-3.12380.26521160.21572531X-RAY DIFFRACTION90
3.1238-3.43780.2291500.17392728X-RAY DIFFRACTION98
3.4378-3.93440.24071580.1842669X-RAY DIFFRACTION97
3.9344-4.95350.18951330.15782681X-RAY DIFFRACTION96
4.9535-30.56720.24581430.19222764X-RAY DIFFRACTION99

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