[English] 日本語
Yorodumi
- PDB-3nbf: Q28E mutant of hera helicase N-terminal domain bound to 8-oxo-ADP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3nbf
TitleQ28E mutant of hera helicase N-terminal domain bound to 8-oxo-ADP
ComponentsHeat resistant RNA dependent ATPase
KeywordsHYDROLASE / rna helicase / ribosome biogenesis / atp hydrolysis / base specificity / thermostability
Function / homology
Function and homology information


nucleic acid binding / RNA helicase activity / hydrolase activity / ATP binding / metal ion binding / cytosol
Similarity search - Function
: / RNA helicase Hera, dimerization domain / DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain ...: / RNA helicase Hera, dimerization domain / DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-8OD / Chem-8OP / Heat resistant RNA dependent ATPase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRudolph, M.G. / Klostermeier, D.
CitationJournal: Biol.Chem. / Year: 2011
Title: Changing nucleotide specificity of the DEAD-box helicase Hera abrogates communication between the Q-motif and the P-loop.
Authors: Strohmeier, J. / Hertel, I. / Diederichsen, U. / Rudolph, M.G. / Klostermeier, D.
History
DepositionJun 3, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Heat resistant RNA dependent ATPase
B: Heat resistant RNA dependent ATPase
C: Heat resistant RNA dependent ATPase
D: Heat resistant RNA dependent ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,12513
Polymers89,3764
Non-polymers3,7499
Water4,774265
1
A: Heat resistant RNA dependent ATPase
B: Heat resistant RNA dependent ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4616
Polymers44,6882
Non-polymers1,7734
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-8 kcal/mol
Surface area17510 Å2
MethodPISA
2
C: Heat resistant RNA dependent ATPase
D: Heat resistant RNA dependent ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6647
Polymers44,6882
Non-polymers1,9765
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-16 kcal/mol
Surface area17010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.648, 60.676, 74.085
Angle α, β, γ (deg.)68.90, 77.29, 72.64
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Heat resistant RNA dependent ATPase


Mass: 22343.938 Da / Num. of mol.: 4 / Fragment: n-terminal domain / Mutation: Q28E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q72GF3
#2: Chemical
ChemComp-8OD / [(2R,3S,4R,5R)-5-(6-azanyl-8-oxo-7H-purin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl phosphono hydrogen phosphate


Mass: 443.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O11P2
#3: Chemical ChemComp-8OP / [(2R,3S,4R,5R)-5-(6-azanyl-8-oxo-7H-purin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl dihydrogen phosphate


Mass: 363.221 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H14N5O8P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.69 Å3/Da / Density % sol: 54.35 %
Crystal growTemperature: 310 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 15% PEG 3350, 0.2M sodium citrate, 0.1M HEPES/NaOH pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 310K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 31, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→46.5 Å / Num. obs: 70329 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 30.5 Å2 / Rsym value: 0.041 / Net I/σ(I): 7.6
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 1.2 / Num. unique all: 2091 / Rsym value: 0.592 / % possible all: 94.6

-
Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.6_289)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GXS

2gxs


Resolution: 1.9→41.512 Å / SU ML: 0.27 / σ(F): 0.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2218 3231 4.98 %random
Rwork0.1841 ---
obs0.1861 64866 88.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.934 Å2 / ksol: 0.308 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.7702 Å2-0.9355 Å24.6631 Å2
2---4.516 Å25.7191 Å2
3---0.7458 Å2
Refinement stepCycle: LAST / Resolution: 1.9→41.512 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6232 0 240 265 6737
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076619
X-RAY DIFFRACTIONf_angle_d1.0929048
X-RAY DIFFRACTIONf_dihedral_angle_d17.1032458
X-RAY DIFFRACTIONf_chiral_restr0.071083
X-RAY DIFFRACTIONf_plane_restr0.0061128
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-1.92840.3391140.3254237779
1.9284-1.95850.32611130.3075221972
1.9585-1.99060.35821150.2862228276
1.9906-2.02490.36931270.2922229875
2.0249-2.06180.28871320.2672231578
2.0618-2.10140.34451340.2564246881
2.1014-2.14430.29971190.23255884
2.1443-2.19090.27271340.2212259685
2.1909-2.24190.25681340.2032266087
2.2419-2.2980.25511480.2017264889
2.298-2.36010.24141250.1935276490
2.3601-2.42950.26291400.1988276491
2.4295-2.50790.25811380.1991278592
2.5079-2.59760.28031400.1956282293
2.5976-2.70150.26681610.2012288395
2.7015-2.82450.25891530.2039286895
2.8245-2.97330.22431670.2144289995
2.9733-3.15960.25741400.2107287995
3.1596-3.40340.23781540.1883290695
3.4034-3.74570.21741640.1644289996
3.7457-4.28720.16351650.1329291396
4.2872-5.39960.12811610.121288695
5.3996-41.52160.18791530.1527294697
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)
11.02470.03280.12191.61420.0820.87480.0239-0.00790.03920.132-0.04350.2398-0.0564-0.16150.02660.12380.01270.00040.231-0.0120.2285-42.2026.1468-16.9869
21.21260.4683-0.08990.2691-0.36590.0818-0.2144-0.3091-0.0517-0.07970.163-0.17590.08110.01470.04030.12960.0742-0.00050.2452-0.0310.1951-8.3424-8.7851-21.4902
31.18210.45470.1572.1488-1.30591.7919-0.0080.1082-0.0659-0.0633-0.0079-0.1124-0.32340.1153-0.00020.2997-0.04180.02910.19-0.04030.1696-34.6787-27.013-41.7483
40.77630.2847-0.40351.1232-0.76111.5278-0.06020.0781-0.0093-0.0861-0.00660.01340.67310.00610.06170.5487-0.051-0.02650.22820.02860.1895-30.63686.9764-56.8436
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

+
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