[English] 日本語
Yorodumi
- PDB-2ba2: Crystal structure of the DUF16 domain of MPN010 from Mycoplasma p... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ba2
TitleCrystal structure of the DUF16 domain of MPN010 from Mycoplasma pneumoniae
ComponentsHypothetical UPF0134 protein MPN010
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / DUF16 / MPN010 / hypothetical protein / coiled-coil / stutter / PSI / Protein Structure Initiative / Berkeley Structural Genomics Center / BSGC
Function / homologySingle alpha-helices involved in coiled-coils or other helix-helix interfaces - #40 / Domain of unknown function DUF16 / Protein of unknown function DUF16 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / UPF0134 protein MPN_010
Function and homology information
Biological speciesMycoplasma pneumoniae (Filterable agent of primary atypical pneumonia)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsShin, D.H. / Kim, J.-S. / Yokota, H. / Kim, R. / Kim, S.-H. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: Protein Sci. / Year: 2006
Title: Crystal structure of the DUF16 domain of MPN010 from Mycoplasma pneumoniae.
Authors: Shin, D.H. / Kim, J.-S. / Yokota, H. / Kim, R. / Kim, S.-H.
History
DepositionOct 13, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hypothetical UPF0134 protein MPN010
B: Hypothetical UPF0134 protein MPN010
C: Hypothetical UPF0134 protein MPN010


Theoretical massNumber of molelcules
Total (without water)29,3673
Polymers29,3673
Non-polymers00
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9870 Å2
ΔGint-77 kcal/mol
Surface area14600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.559, 38.874, 68.734
Angle α, β, γ (deg.)90.00, 99.21, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Hypothetical UPF0134 protein MPN010 / D12_orf131


Mass: 9789.110 Da / Num. of mol.: 3 / Fragment: DUF16 domain, residues 46-130
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasma pneumoniae (Filterable agent of primary atypical pneumonia)
Plasmid: pB3, pET21a derived / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3), pSJS1244 / References: UniProt: P75103
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 1.91 Å3/Da / Density % sol: 33.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M lithium Sulfate, 25% PEG3350, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.97938 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 11, 2005 / Details: Monochromator
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97938 Å / Relative weight: 1
ReflectionResolution: 1.8→42.01 Å / Num. all: 40349 / Num. obs: 32441 / % possible obs: 80.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 17.3 Å2
Reflection shellResolution: 1.8→1.83 Å / % possible all: 13

-
Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→19.55 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 215255.05 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.281 1651 10 %RANDOM
Rwork0.229 ---
all0.234 20869 --
obs0.229 16591 79.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 67.6333 Å2 / ksol: 0.405914 e/Å3
Displacement parametersBiso mean: 31.1 Å2
Baniso -1Baniso -2Baniso -3
1--5.82 Å20 Å25.04 Å2
2--5.82 Å20 Å2
3---0.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.8→19.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1970 0 0 190 2160
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg0.8
X-RAY DIFFRACTIONc_dihedral_angle_d15.3
X-RAY DIFFRACTIONc_improper_angle_d0.62
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.322 58 8 %
Rwork0.268 671 -
obs--21.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param

+
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