[English] 日本語
Yorodumi
- PDB-5mao: HERA HELICASE RNA BINDING DOMAIN with TNCS in P212121 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5mao
TitleHERA HELICASE RNA BINDING DOMAIN with TNCS in P212121
ComponentsHeat resistant RNA dependent ATPase
KeywordsRNA BINDING PROTEIN / HYDROLASE / RNA HELICASE / RNA RECOGNITION MOTIF / ATP-BINDING / HELICASE / NUCLEOTIDE-BINDING
Function / homology
Function and homology information


nucleic acid binding / RNA helicase activity / hydrolase activity / ATP binding / metal ion binding / cytosol
Similarity search - Function
Alpha-Beta Plaits - #1800 / : / 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 ...Alpha-Beta Plaits - #1800 / : / 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 / Alpha-Beta Plaits / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Heat resistant RNA dependent ATPase
Similarity search - Component
Biological speciesThermus thermophilus HB27 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsRudolph, M.G. / Klostermeier, D.
CitationJournal: To be published
Title: Crystal Structure of HERA CTD
Authors: Rudolph, M.G. / Klostermeier, D.
History
DepositionNov 3, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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: Heat resistant RNA dependent ATPase
B: Heat resistant RNA dependent ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2993
Polymers15,2032
Non-polymers961
Water2,054114
1
A: Heat resistant RNA dependent ATPase


Theoretical massNumber of molelcules
Total (without water)7,6021
Polymers7,6021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Heat resistant RNA dependent ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6982
Polymers7,6021
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.510, 48.270, 64.970
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Heat resistant RNA dependent ATPase


Mass: 7601.699 Da / Num. of mol.: 2 / Fragment: RESIDUES 421-491
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB27 (bacteria) / Gene: TT_C1895 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q72GF3
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 1.99 Å3/Da / Density % sol: 38.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: unknown

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.35→38.75 Å / Num. obs: 26573 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 4.87 % / Biso Wilson estimate: 15.6 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.124 / Rrim(I) all: 0.139 / Χ2: 0.977 / Net I/σ(I): 6.67 / Num. measured all: 129298
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
1.35-1.391.690.860.286196
1.39-1.421.4251.050.434196.9
1.42-1.461.311.180.462196.9
1.46-1.511.0681.50.64196.1
1.51-1.560.8372.110.777196.4
1.56-1.610.6982.440.844196.1
1.61-1.670.5912.790.879195.8
1.67-1.740.4813.620.898196.9
1.74-1.820.3395.670.949198.1
1.82-1.910.2916.660.964197.8
1.91-2.010.19990.982198.4
2.01-2.130.14910.060.985198.6
2.13-2.280.13211.030.987195.7
2.28-2.460.10112.540.992198.7
2.46-2.70.08813.750.994198.8
2.7-3.020.07515.540.994198.8
3.02-3.490.06217.690.996197.6
3.49-4.270.05720.140.997197.4
4.27-6.040.04619.570.997198.4
6.04-38.750.04519.590.997197

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.11_2558refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3i31

3i31


Resolution: 1.35→38.747 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.66
RfactorNum. reflection% reflectionSelection details
Rfree0.2488 1287 4.86 %random
Rwork0.2379 ---
obs0.2385 26504 97.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 69.66 Å2 / Biso mean: 22.1259 Å2 / Biso min: 10.35 Å2
Refinement stepCycle: final / Resolution: 1.35→38.747 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1070 0 5 114 1189
Biso mean--18.96 28.58 -
Num. residues----142
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051098
X-RAY DIFFRACTIONf_angle_d0.8021484
X-RAY DIFFRACTIONf_chiral_restr0.076160
X-RAY DIFFRACTIONf_plane_restr0.006197
X-RAY DIFFRACTIONf_dihedral_angle_d29.632424
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3501-1.40410.38731510.3692726287796
1.4041-1.4680.43981620.37912734289697
1.468-1.54540.37431500.37012737288796
1.5454-1.64230.39111340.35772720285496
1.6423-1.76910.35581330.33792769290296
1.7691-1.94710.27831530.23392800295398
1.9471-2.22880.24541130.20752864297798
2.2288-2.80790.19851420.21352868301098
2.8079-38.76250.18971490.18912999314898
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)
12.23991.65193.03221.28982.56157.00910.0178-0.03540.00910.12560.0304-0.09540.09650.0531-0.02920.1140.03250.01220.1112-0.00270.185213.119526.763236.841
27.5111-2.6282-3.13223.9243-2.56967.40940.10180.2348-0.1743-0.1649-0.10390.17930.1602-0.2562-0.00960.1132-0.0217-0.03840.1013-0.02090.1660.246419.110925.0808
34.36910.4529-1.04014.25670.92856.50420.03670.0166-0.22480.06010.0054-0.04570.2287-0.0113-0.01970.09380.021-0.0260.06630.00980.14147.529420.084932.0948
42.23862.2059-3.43013.7834-4.93549.11-0.0165-0.0482-0.12540.1811-0.0283-0.0473-0.0758-0.00830.02780.11880.0099-0.0130.120.00530.17256.3749-2.647119.422
57.7397-2.74894.04894.4359-0.41135.217-0.0177-0.03320.2613-0.0962-0.0465-0.2903-0.17960.1330.07820.1063-0.0240.04150.0975-0.00280.157819.39315.45298.4947
65.51980.30211.01694.7281-2.08665.1054-0.0647-0.08970.08050.14350.14880.0201-0.22730.009-0.08210.1230.00930.01530.0877-0.01460.124111.52683.82414.5933
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 421 through 441 )A421 - 441
2X-RAY DIFFRACTION2chain 'A' and (resid 442 through 456 )A442 - 456
3X-RAY DIFFRACTION3chain 'A' and (resid 457 through 491 )A457 - 491
4X-RAY DIFFRACTION4chain 'B' and (resid 421 through 441 )B421 - 441
5X-RAY DIFFRACTION5chain 'B' and (resid 442 through 457 )B442 - 457
6X-RAY DIFFRACTION6chain 'B' and (resid 458 through 491 )B458 - 491

+
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://pdbjlc1.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