[English] 日本語
Yorodumi
- PDB-5dni: Crystal structure of Methanocaldococcus jannaschii Fumarate hydra... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5dni
TitleCrystal structure of Methanocaldococcus jannaschii Fumarate hydratase beta subunit
ComponentsPutative L(+)-tartrate dehydratase subunit beta
KeywordsLYASE / alpha beta barrel
Function / homology
Function and homology information


L(+)-tartrate dehydratase activity / L(+)-tartrate dehydratase
Similarity search - Function
fumarase / Fe-S hydro-lyase, tartrate dehydratase beta-type, catalytic domain / Fe-S hydro-lyase, tartrate dehydratase beta-type, catalytic domain / Fe-S hydro-lyase, tartrate dehydratase beta-type, catalytic domain superfamily / Fumarase C-terminus / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Putative L(+)-tartrate dehydratase subunit beta
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii DSM 2661 (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsJayaraman, V. / Kunala, J. / Balaram, H.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology India
CitationJournal: Biochemistry / Year: 2023
Title: Revisiting the Burden Borne by Fumarase: Enzymatic Hydration of an Olefin.
Authors: Bellur, A. / Das, S. / Jayaraman, V. / Behera, S. / Suryavanshi, A. / Balasubramanian, S. / Balaram, P. / Jindal, G. / Balaram, H.
History
DepositionSep 10, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative L(+)-tartrate dehydratase subunit beta
B: Putative L(+)-tartrate dehydratase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,73811
Polymers40,0422
Non-polymers6969
Water2,576143
1
A: Putative L(+)-tartrate dehydratase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4396
Polymers20,0211
Non-polymers4185
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint1 kcal/mol
Surface area7900 Å2
MethodPISA
2
B: Putative L(+)-tartrate dehydratase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2995
Polymers20,0211
Non-polymers2784
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint-3 kcal/mol
Surface area7950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.610, 85.610, 121.830
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Putative L(+)-tartrate dehydratase subunit beta / Putative fumarate hydratase subunit beta / L-TTD beta


Mass: 20021.168 Da / Num. of mol.: 2 / Fragment: UNP residues 1-179
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii DSM 2661 (archaea)
Strain: DSM 2661 / Gene: MjFHbeta, MJ0617 / Plasmid: pET-DUET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q58034, L(+)-tartrate dehydratase

-
Non-polymers , 5 types, 152 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 3.22 Å3/Da / Density % sol: 61.78 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 5.5 / Details: 0.1MBis-Tris, 25% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 22, 2013
RadiationMonochromator: OSMIC MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.3→60.92 Å / Num. all: 22550 / Num. obs: 22550 / % possible obs: 99.99 % / Redundancy: 4.85 %
Data reduction method: data reduction merge and scaling used SCALA (CCP4)
Rmerge(I) obs: 0.127 / Rrim(I) all: 0.143 / Net I/av σ(I): 4.5853 / Net I/σ(I): 7.0091 / Num. measured all: 109381
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) allNum. measured allNum. unique allDiffraction-ID% possible all
2.3-2.424.620.860.891516632821100
2.42-2.574.770.681.12148013104100
2.57-2.754.860.51.55141682916100
2.75-2.974.90.332.32133492727100
2.97-3.254.910.193.89122312490100
3.25-3.644.940.125.81112202271100
3.64-4.24.950.087.8798972000100
4.2-5.144.960.086.9284221699100
5.14-7.274.970.087.3965471317100
7.27-60.924.810.0412.77358074499.73

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata collection
SCALACCP4_3.3.22data scaling
PDB_EXTRACT3.15data extraction
PHASERphasing
SCALAdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ISB

2isb


Resolution: 2.3→28.022 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2307 1101 4.9 %
Rwork0.1807 --
obs0.183 22451 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→28.022 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2740 0 44 143 2927
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082827
X-RAY DIFFRACTIONf_angle_d1.1763816
X-RAY DIFFRACTIONf_dihedral_angle_d12.6031020
X-RAY DIFFRACTIONf_chiral_restr0.046437
X-RAY DIFFRACTIONf_plane_restr0.005480
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.40470.35741350.28442675X-RAY DIFFRACTION100
2.4047-2.53140.32211340.26762660X-RAY DIFFRACTION100
2.5314-2.68990.29191150.25012670X-RAY DIFFRACTION100
2.6899-2.89740.32151450.23072646X-RAY DIFFRACTION100
2.8974-3.18860.27721630.21112665X-RAY DIFFRACTION100
3.1886-3.64920.22021340.18112653X-RAY DIFFRACTION100
3.6492-4.59430.19641360.13922676X-RAY DIFFRACTION100
4.5943-28.02450.16821390.14292705X-RAY DIFFRACTION100

+
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