[English] 日本語
Yorodumi
- PDB-5szd: Crystal structure of Aquifex aeolicus Hfq at 1.5A -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more