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- PDB-5szd: Crystal structure of Aquifex aeolicus Hfq at 1.5A -

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Basic information

Entry
Database: PDB / ID: 5szd
TitleCrystal structure of Aquifex aeolicus Hfq at 1.5A
ComponentsRNA-binding protein Hfq
KeywordsRNA BINDING PROTEIN / Hfq / Aquifex / RNA-binding
Function / homology
Function and homology information


regulation of translation, ncRNA-mediated / regulation of RNA stability / regulation of DNA-templated transcription / 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
GUANIDINE / DI(HYDROXYETHYL)ETHER / RNA-binding protein Hfq
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.494 Å
AuthorsStanek, K. / Patterson, J. / Randolph, P.S. / Mura, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1350957 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2017
Title: Crystal structure and RNA-binding properties of an Hfq homolog from the deep-branching Aquificae: conservation of the lateral RNA-binding mode.
Authors: Stanek, K.A. / Patterson-West, J. / Randolph, P.S. / Mura, C.
History
DepositionAug 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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: RNA-binding protein Hfq
B: RNA-binding protein Hfq
C: RNA-binding protein Hfq
D: RNA-binding protein Hfq
E: RNA-binding protein Hfq
F: RNA-binding protein Hfq
G: RNA-binding protein Hfq
H: RNA-binding protein Hfq
I: RNA-binding protein Hfq
J: RNA-binding protein Hfq
K: RNA-binding protein Hfq
L: RNA-binding protein Hfq
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,07556
Polymers113,97512
Non-polymers4,10044
Water7,440413
1
A: RNA-binding protein Hfq
B: RNA-binding protein Hfq
C: RNA-binding protein Hfq
D: RNA-binding protein Hfq
E: RNA-binding protein Hfq
F: RNA-binding protein Hfq
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,79625
Polymers56,9886
Non-polymers1,80819
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16020 Å2
ΔGint-114 kcal/mol
Surface area20010 Å2
2
G: RNA-binding protein Hfq
H: RNA-binding protein Hfq
I: RNA-binding protein Hfq
J: RNA-binding protein Hfq
K: RNA-binding protein Hfq
L: RNA-binding protein Hfq
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,27931
Polymers56,9886
Non-polymers2,29225
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19570 Å2
ΔGint-176 kcal/mol
Surface area18900 Å2
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area40610 Å2
ΔGint-334 kcal/mol
Surface area33890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.460, 66.060, 66.100
Angle α, β, γ (deg.)60.05, 83.94, 77.17
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
RNA-binding protein Hfq


Mass: 9497.957 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria)
Strain: VF5 / Gene: hfq, aq_108, aq_108B / Production host: Escherichia coli (E. coli) / References: UniProt: O66512

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Non-polymers , 6 types, 457 molecules

#2: Chemical
ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical
ChemComp-GAI / GUANIDINE


Mass: 59.070 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CH5N3
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 413 / 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: 2.05 Å3/Da / Density % sol: 40.12 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: sodium cacodylate, PEG 8000, MPD, 0.1 M hexamminecobalt(III) chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.49→57.27 Å / Num. obs: 138120 / % possible obs: 93.7 % / Redundancy: 2.2 % / Net I/σ(I): 14

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Processing

Software
NameVersionClassification
PHENIX(1.10-2155_1309: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U1S

1u1s


Resolution: 1.494→46.351 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 15.99
RfactorNum. reflection% reflection
Rfree0.1696 10625 7.69 %
Rwork0.1323 --
obs0.1351 138105 93.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.494→46.351 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7006 0 267 413 7686
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058068
X-RAY DIFFRACTIONf_angle_d0.74510904
X-RAY DIFFRACTIONf_dihedral_angle_d15.0543169
X-RAY DIFFRACTIONf_chiral_restr0.0761246
X-RAY DIFFRACTIONf_plane_restr0.0041340
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.494-1.5110.2532510.18033290X-RAY DIFFRACTION72
1.511-1.52880.20123510.15034200X-RAY DIFFRACTION93
1.5288-1.54740.19463810.13644266X-RAY DIFFRACTION94
1.5474-1.5670.19423250.13164221X-RAY DIFFRACTION94
1.567-1.58760.2033480.13884314X-RAY DIFFRACTION94
1.5876-1.60940.21173560.14624233X-RAY DIFFRACTION94
1.6094-1.63240.20073510.13524264X-RAY DIFFRACTION95
1.6324-1.65670.19863310.1294307X-RAY DIFFRACTION94
1.6567-1.68260.17533880.12124237X-RAY DIFFRACTION94
1.6826-1.71020.18573750.12064224X-RAY DIFFRACTION95
1.7102-1.73970.15693310.11474333X-RAY DIFFRACTION94
1.7397-1.77130.18083510.11634249X-RAY DIFFRACTION95
1.7713-1.80540.15793600.11174288X-RAY DIFFRACTION95
1.8054-1.84230.17383520.11174354X-RAY DIFFRACTION95
1.8423-1.88230.15583540.10864278X-RAY DIFFRACTION95
1.8823-1.92610.14673630.10974276X-RAY DIFFRACTION95
1.9261-1.97430.17173820.11044260X-RAY DIFFRACTION95
1.9743-2.02760.15183770.11874281X-RAY DIFFRACTION95
2.0276-2.08730.16973310.11894345X-RAY DIFFRACTION95
2.0873-2.15470.1563530.11834320X-RAY DIFFRACTION95
2.1547-2.23170.14583810.11414261X-RAY DIFFRACTION95
2.2317-2.3210.16343400.12184301X-RAY DIFFRACTION95
2.321-2.42670.16613480.12814353X-RAY DIFFRACTION95
2.4267-2.55460.17423640.14394309X-RAY DIFFRACTION95
2.5546-2.71460.19673890.15214229X-RAY DIFFRACTION95
2.7146-2.92420.19813600.15464301X-RAY DIFFRACTION95
2.9242-3.21840.16413410.14374305X-RAY DIFFRACTION95
3.2184-3.6840.16333670.1364342X-RAY DIFFRACTION95
3.684-4.64070.13383750.12164302X-RAY DIFFRACTION96
4.6407-46.37340.18493490.16534237X-RAY DIFFRACTION93

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