[English] 日本語
Yorodumi
- PDB-7akp: Crystal structure of E. coli RNA helicase HrpA-D305A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7akp
TitleCrystal structure of E. coli RNA helicase HrpA-D305A
ComponentsATP-dependent RNA helicase HrpA
KeywordsRNA BINDING PROTEIN / RNA helicase / NTPase / bacterial helicase / DExH-box
Function / homology
Function and homology information


nucleic acid binding / RNA helicase activity / RNA helicase / ATP hydrolysis activity / ATP binding
Similarity search - Function
RNA helicase HrpA / RNA helicase HrpA, C-terminal / Domain of unknown function (DUF3418) / : / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase associated domain (HA2), winged-helix / Helicase-associated domain / Helicase associated domain (HA2) Add an annotation ...RNA helicase HrpA / RNA helicase HrpA, C-terminal / Domain of unknown function (DUF3418) / : / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase associated domain (HA2), winged-helix / Helicase-associated domain / Helicase associated domain (HA2) Add an annotation / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ATP-dependent RNA helicase HrpA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsGrass, L.M. / Wollenhaupt, J. / Barthel, T. / Loll, B. / Wahl, M.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Large-scale ratcheting in a bacterial DEAH/RHA-type RNA helicase that modulates antibiotics susceptibility.
Authors: Grass, L.M. / Wollenhaupt, J. / Barthel, T. / Parfentev, I. / Urlaub, H. / Loll, B. / Klauck, E. / Antelmann, H. / Wahl, M.C.
History
DepositionOct 1, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Aug 4, 2021Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 31, 2024Group: 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: ATP-dependent RNA helicase HrpA


Theoretical massNumber of molelcules
Total (without water)89,7861
Polymers89,7861
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area35670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.894, 114.902, 94.614
Angle α, β, γ (deg.)90.000, 101.937, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein ATP-dependent RNA helicase HrpA / ATP-dependent RNA helicase HrpB / ATP-dependent helicase / ATP-dependent helicase HrpA / Putative ...ATP-dependent RNA helicase HrpB / ATP-dependent helicase / ATP-dependent helicase HrpA / Putative ATP-dependent helicase


Mass: 89785.781 Da / Num. of mol.: 1 / Mutation: D305A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: hrpA, hrpB_2, ACU57_01855, AUQ13_00250, BANRA_00811, BANRA_04135, BMA87_16915, BUE81_10335, BvCms2454_02596, BvCmsHHP001_04653, C5N07_19950, C9Z39_02430, CA593_20890, CI694_27345, CIG45_23500, ...Gene: hrpA, hrpB_2, ACU57_01855, AUQ13_00250, BANRA_00811, BANRA_04135, BMA87_16915, BUE81_10335, BvCms2454_02596, BvCmsHHP001_04653, C5N07_19950, C9Z39_02430, CA593_20890, CI694_27345, CIG45_23500, D0X26_25730, D3821_04265, D9G69_18360, D9J52_23225, DBQ99_13815, DJ503_20330, DL326_20175, DT034_20065, E2119_23590, E4K55_22820, E4K60_22175, E4K61_19375, EA213_21160, EC3234A_28c00370, EC3426_02431, EEP23_09730, EI021_18420, EI028_21745, EI041_18575, ELT20_16685, EPT01_12920, EYD11_11805, FV293_21585, GHR40_16525, GKF86_19260, GKF89_18325, GP689_04140, GQM17_20230, NCTC12650_02980, NCTC9062_00712, PGD_01858, RK56_010590, SAMEA3472080_03366, SAMEA3752559_04937, SK85_01607
Production host: Escherichia coli (E. coli) / References: UniProt: A0A024L2B5, RNA helicase

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.95 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 7 % PEG 3350, 0.05 M HEPES, pH 7, 0.1 M potassium chloride, 0.01 M magnesium chloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.59→48.81 Å / Num. obs: 25697 / % possible obs: 99.1 % / Redundancy: 6.9 % / CC1/2: 0.987 / Net I/σ(I): 7.27
Reflection shellResolution: 2.59→2.75 Å / Num. unique obs: 4048 / CC1/2: 0.333

-
Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PHENIX1.19.1_4122refinement
XDSdata reduction
PHASERphasing
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZWX

6zwx


Resolution: 2.59→48.81 Å / Cross valid method: FREE R-VALUE / σ(F): 165.93 / Phase error: 39.6277
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2392 1292 5.03 %
Rwork0.2109 24404 -
obs0.2195 25696 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.52 Å2
Refinement stepCycle: LAST / Resolution: 2.59→48.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5800 0 0 0 5800
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00345902
X-RAY DIFFRACTIONf_angle_d0.61497969
X-RAY DIFFRACTIONf_chiral_restr0.0414893
X-RAY DIFFRACTIONf_plane_restr0.00491039
X-RAY DIFFRACTIONf_dihedral_angle_d14.23842286
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.70.32431390.3122653X-RAY DIFFRACTION91.29
2.7-2.820.32431410.29452672X-RAY DIFFRACTION94.32
2.82-2.970.32031420.29232704X-RAY DIFFRACTION94.41
2.97-3.160.2831420.27092700X-RAY DIFFRACTION94.6
3.16-3.40.28841440.25962723X-RAY DIFFRACTION94.71
3.4-3.740.27431420.22912698X-RAY DIFFRACTION94.83
3.74-4.280.2171440.19732744X-RAY DIFFRACTION94.85
4.28-5.40.19761440.16972734X-RAY DIFFRACTION94.86
5.4-48.810.22291470.18582783X-RAY DIFFRACTION94.92
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.01388603891010.0124437356990.00403071651370.01941368984990.006534718262310.002988255637040.0001567021763-0.00476989197259-0.005464187836880.00697724914171-0.00249062891237-0.02715330734120.02236979240280.006046686391210.0108875471290.4062399206660.0203778684897-0.05154819809460.122051409978-0.03355658884190.476591075391-5.26064733425-0.19128085054860.2334173183
20.0107573761203-0.005742174771260.005147674034610.00715752487922-0.0006880890627140.003214611367140.00971313025967-0.00111528882230.000157943771814-0.00508974580783-0.005265511839320.004503721250340.03834772422680.005040202330530.01650939466320.4340111269770.0358385036999-0.08428269515060.138280576040.005873768097920.516491753105-9.2992339517412.579890604531.9327739574
30.01427347299090.00014152082189-0.001032049580340.0195045889055-0.005502751721090.0178925201831-0.01203627765620.003429935772480.0310616612437-0.00577947035637-0.000191922894817-0.0125094837049-0.00311130054550.00376684243211-0.03397871265730.3626043248960.0257874313873-0.1313518378190.1343134301060.01120749951650.4974057868985.61077787126-11.795864109513.5175889785
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 7 through 229 )7 - 2291 - 220
22chain 'A' and (resid 230 through 471 )230 - 471221 - 448
33chain 'A' and (resid 472 through 751 )472 - 751449 - 723

+
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://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