[English] 日本語
Yorodumi
- PDB-1nh9: Crystal Structure of a DNA Binding Protein Mja10b from the hypert... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1nh9
TitleCrystal Structure of a DNA Binding Protein Mja10b from the hyperthermophile Methanococcus jannaschii
ComponentsDNA-binding protein Alba
KeywordsDNA BINDING PROTEIN / Mja10b
Function / homology
Function and homology information


chromosome / double-stranded DNA binding / RNA binding / cytoplasm
Similarity search - Function
DNA/RNA-binding protein Alba / Alba-like domain / DNA/RNA-binding protein Alba-like / Alba / Alba-like domain superfamily / Translation Initiation Factor IF3 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA/RNA-binding protein Alba
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWang, G. / Bartlam, M. / Guo, R. / Yang, H. / Xue, H. / Liu, Y. / Huang, L. / Rao, Z.
CitationJournal: Protein Sci. / Year: 2003
Title: Crystal structure of a DNA binding protein from the hyperthermophilic euryarchaeon Methanococcus jannaschii
Authors: Wang, G. / Guo, R. / Bartlam, M. / Yang, H. / Xue, H. / Liu, Y. / Huang, L. / Rao, Z.
History
DepositionDec 19, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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: DNA-binding protein Alba


Theoretical massNumber of molelcules
Total (without water)9,6911
Polymers9,6911
Non-polymers00
Water43224
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.506, 51.506, 125.307
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsThe biological assembly is a monomer in the asymmetric unit

-
Components

#1: Protein DNA-binding protein Alba / Mja10b


Mass: 9690.525 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q57665
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.73 Å3/Da / Density % sol: 54.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.25
Details: Tris-HCl, MPD, pH 8.25, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: Wang, G.G., (2002) Acta Cryst., D58, 1240.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
240 %MPD1reservoir
30.1 MTris-HCl1reservoirpH8.25

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9868 Å
DetectorType: SBC-2 / Detector: CCD / Date: Apr 15, 2002 / Details: mirrors
RadiationMonochromator: sagitally focused Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9868 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 7093 / Num. obs: 7093 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 13.2 % / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 21.4
Reflection shellResolution: 2→2.07 Å / Redundancy: 13.6 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 4.2 / Num. unique all: 692 / % possible all: 99.1
Reflection
*PLUS
Num. obs: 6946 / % possible obs: 96.6 % / Redundancy: 13.1 % / Num. measured all: 91002 / Rmerge(I) obs: 0.049
Reflection shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.06 Å / % possible obs: 99.1 % / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 6.2

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1h0x
Resolution: 2→20 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.264 678 10 %random
Rwork0.209 ---
obs-6217 94.2 %-
Displacement parametersBiso mean: 40.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.818 Å2-1.751 Å20 Å2
2---0.818 Å20 Å2
3---1.635 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms619 0 0 24 643
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_improper_angle_d0.78
LS refinement shellResolution: 2→2.06 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.288 121 10.7 %
Rwork0.263 761 -
obs-1298 81.1 %
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.405
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78

+
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