[English] 日本語
Yorodumi
- PDB-2orm: Crystal Structure of the 4-Oxalocrotonate Tautomerase Homologue D... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2orm
TitleCrystal Structure of the 4-Oxalocrotonate Tautomerase Homologue DmpI from Helicobacter pylori.
ComponentsProbable tautomerase HP0924
KeywordsISOMERASE / homohexamer / 4-OT / 4-Oxalocrotonate Tautomerase Homologue
Function / homology
Function and homology information


Isomerases; Intramolecular oxidoreductases; Interconverting keto- and enol-groups / : / isomerase activity
Similarity search - Function
4-oxalocrotonate tautomerase, Pseudomonas-type / 4-oxalocrotonate tautomerase / Tautomerase enzyme / Macrophage Migration Inhibitory Factor / Macrophage Migration Inhibitory Factor / Tautomerase/MIF superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable tautomerase HP_0924
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHackert, M.L. / Whitman, C.P. / Almrud, J.J. / Dasgupta, R. / Czerwinski, R.M. / Kern, A.D.
CitationJournal: Bioorg.Chem. / Year: 2010
Title: Kinetic and structural characterization of DmpI from Helicobacter pylori and Archaeoglobus fulgidus, two 4-oxalocrotonate tautomerase family members.
Authors: Almrud, J.J. / Dasgupta, R. / Czerwinski, R.M. / Kern, A.D. / Hackert, M.L. / Whitman, C.P.
History
DepositionFeb 3, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Aug 30, 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: Probable tautomerase HP0924
B: Probable tautomerase HP0924
C: Probable tautomerase HP0924
D: Probable tautomerase HP0924
E: Probable tautomerase HP0924
F: Probable tautomerase HP0924


Theoretical massNumber of molelcules
Total (without water)44,3366
Polymers44,3366
Non-polymers00
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12870 Å2
ΔGint-77 kcal/mol
Surface area16340 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)41.830, 50.770, 89.310
Angle α, β, γ (deg.)90.00, 99.13, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Probable tautomerase HP0924


Mass: 7389.381 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: J99 / Gene: dmpi (GI 7449587) / Plasmid: pET 24a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: O25581, Isomerases; Intramolecular oxidoreductases; Interconverting keto- and enol-groups
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.11 Å3/Da / Density % sol: 41.73 %
Crystal growTemperature: 277 K / pH: 7.5
Details: 2 uL of protein (20 mg/mL) in 20mM phosphate buffer (pH 7.4) were mixed with 2 uL of 0.2M CaCl2, 0.1M Hepes (pH 7.5), and 28% PEG 400. This combined volume was equilibrated at 4 degrees ...Details: 2 uL of protein (20 mg/mL) in 20mM phosphate buffer (pH 7.4) were mixed with 2 uL of 0.2M CaCl2, 0.1M Hepes (pH 7.5), and 28% PEG 400. This combined volume was equilibrated at 4 degrees Celcius against 50 uL of 0.2M CaCl2, 0.1M Hepes (pH 7.5), and 28% PEG 400 , VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 7.50

-
Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 10, 2000
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→24.5 Å / Num. obs: 20368 / % possible obs: 90 % / Observed criterion σ(I): 0 / Redundancy: 5.94 % / Biso Wilson estimate: 19.2 Å2 / Rsym value: 0.096 / Net I/σ(I): 13.5
Reflection shellResolution: 2.1→2.18 Å / Mean I/σ(I) obs: 4 / Rsym value: 0.476 / % possible all: 90

-
Processing

Software
NameClassification
HKL-2000data collection
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BJP

1bjp


Resolution: 2.1→24.5 Å / Isotropic thermal model: ANISOTROPIC / Cross valid method: RANDOM / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1044 -THROUGHOUT
Rwork0.217 ---
obs0.217 20368 92.1 %-
all-21823 --
Displacement parametersBiso mean: 31 Å2
Baniso -1Baniso -2Baniso -3
1-1.99 Å20 Å20.85 Å2
2---2.06 Å20 Å2
3---0.07 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.1→24.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2932 0 0 126 3058
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.1→2.2 Å / Rfactor Rfree error: 0.026
RfactorNum. reflection% reflection
Rfree0.289 120 -
Rwork0.257 --
obs--89 %

+
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