[English] 日本語
Yorodumi
- PDB-1pm4: Crystal structure of Yersinia pseudotuberculosis-derived mitogen (YPM) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1pm4
TitleCrystal structure of Yersinia pseudotuberculosis-derived mitogen (YPM)
ComponentsYPM
KeywordsTOXIN / Jelly roll fold
Function / homologyMitogen Ypm / Mitogen, Yersinia pseudotuberculosis / Mitogen Ypm superfamily / Yersinia pseudo-tuberculosis mitogen / Jelly Rolls / Sandwich / Mainly Beta / -derived mitogen
Function and homology information
Biological speciesYersinia pseudotuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.755 Å
AuthorsDonadini, R. / Liew, C.W. / Kwan, A.H. / Mackay, J.P. / Fields, B.A.
CitationJournal: Structure / Year: 2004
Title: Crystal and Solution Structures of a Superantigen from Yersinia pseudotuberculosis Reveal a Jelly-Roll Fold.
Authors: Donadini, R. / Liew, C.W. / Kwan, A.H. / Mackay, J.P. / Fields, B.A.
History
DepositionJun 9, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S). The trimerization may be biologically relevant but has not yet been established experimentally. The protein is a monomer in solution.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: YPM
B: YPM
C: YPM


Theoretical massNumber of molelcules
Total (without water)39,6713
Polymers39,6713
Non-polymers00
Water6,107339
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)138.651, 78.652, 32.901
Angle α, β, γ (deg.)90.00, 91.97, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein YPM


Mass: 13223.785 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pseudotuberculosis (bacteria) / Gene: ypma / Plasmid: pMAL-p2x / Production host: Escherichia coli (E. coli) / Strain (production host): Novablue / References: UniProt: Q57221
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: Ammonium sulfate, PEG 200, sodium citrate, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 293 K / pH: 7.2 / Method: vapor diffusion, sitting drop / Details: Donadini, R., (2003) Acta Cryst., D59, 1330.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.95-2.10 Mammonium sulfate1reservoir
24-5 %(v/v)PEG2001reservoir
30.1 Msodium citrate1reservoirpH5.8-7.6
475 mg/mlprotein1drop
50.1 Msodium citrate1droppH7.2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 1.071 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 12, 2002
RadiationMonochromator: 2-crystal monochromator, Si111, 1m long Rh coated bent cylindrical mirror for horizontal and vertical focussing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.071 Å / Relative weight: 1
ReflectionResolution: 1.75→40 Å / Num. all: 253851 / Num. obs: 253092 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 39.1
Reflection shellResolution: 1.755→1.8 Å / Rmerge(I) obs: 0.515 / Mean I/σ(I) obs: 3.2 / % possible all: 99.1
Reflection
*PLUS
Num. obs: 35166 / Num. measured all: 253092
Reflection shell
*PLUS
Highest resolution: 1.75 Å / % possible obs: 99.1 %

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.755→34.71 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.441 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.125 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22926 1749 5 %RANDOM
Rwork0.18201 ---
all0.18438 35113 --
obs0.18438 33364 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.498 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20 Å2-0.9 Å2
2--0.07 Å20 Å2
3----0.91 Å2
Refinement stepCycle: LAST / Resolution: 1.755→34.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2748 0 0 339 3087
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0212799
X-RAY DIFFRACTIONr_bond_other_d0.0020.022450
X-RAY DIFFRACTIONr_angle_refined_deg1.8971.9513796
X-RAY DIFFRACTIONr_angle_other_deg0.93235759
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8365348
X-RAY DIFFRACTIONr_chiral_restr0.120.2428
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023104
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02504
X-RAY DIFFRACTIONr_nbd_refined0.2270.2544
X-RAY DIFFRACTIONr_nbd_other0.2630.22966
X-RAY DIFFRACTIONr_nbtor_other0.0880.21765
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2242
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1260.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3080.274
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1260.222
X-RAY DIFFRACTIONr_mcbond_it1.3981.51732
X-RAY DIFFRACTIONr_mcangle_it2.39322803
X-RAY DIFFRACTIONr_scbond_it2.83331067
X-RAY DIFFRACTIONr_scangle_it4.24.5993
LS refinement shellResolution: 1.755→1.8 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.256 124
Rwork0.222 2350
Refinement
*PLUS
Highest resolution: 1.75 Å / Lowest resolution: 40 Å / Rfactor Rfree: 0.229 / Rfactor Rwork: 0.182
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.021
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.9
LS refinement shell
*PLUS
Highest resolution: 1.75 Å / Lowest resolution: 1.8 Å

+
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