[English] 日本語
Yorodumi
- PDB-6r76: Crystal structure of trans-3-Hydroxy-L-proline dehydratase from T... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6r76
TitleCrystal structure of trans-3-Hydroxy-L-proline dehydratase from Thermococcus litoralis - open conformation
Components(Proline racemase) x 2
KeywordsLYASE / Hydro-lyase / hydroxyproline dehydratase
Function / homologyProline racemase family / Proline racemase / Diaminopimelate Epimerase; Chain A, domain 1 / Diaminopimelate Epimerase; Chain A, domain 1 / Roll / Alpha Beta / Proline racemase
Function and homology information
Biological speciesThermococcus litoralis DSM 5473 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsFerraris, D.M. / Miggiano, R. / Rizzi, M.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2019
Title: Structure of Thermococcus litoralis trans-3-hydroxy-l-proline dehydratase in the free and substrate-complexed form.
Authors: Ferraris, D.M. / Miggiano, R. / Watanabe, S. / Rizzi, M.
History
DepositionMar 28, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2024Group: 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: Proline racemase
B: Proline racemase
C: Proline racemase
D: Proline racemase


Theoretical massNumber of molelcules
Total (without water)166,8634
Polymers166,8634
Non-polymers00
Water28816
1
A: Proline racemase
B: Proline racemase


Theoretical massNumber of molelcules
Total (without water)83,4312
Polymers83,4312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-35 kcal/mol
Surface area27190 Å2
MethodPISA
2
C: Proline racemase
D: Proline racemase


Theoretical massNumber of molelcules
Total (without water)83,4312
Polymers83,4312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint-35 kcal/mol
Surface area27230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.923, 46.090, 143.512
Angle α, β, γ (deg.)90.00, 110.48, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Proline racemase /


Mass: 41675.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The construct carries an N-term 6xHis-tag and a TEV cleavage site
Source: (gene. exp.) Thermococcus litoralis DSM 5473 (archaea)
Gene: OCC_00387 / Variant: ATCC 51850 / DSM 5473 / JCM 8560 / NS-C / Production host: Escherichia coli (E. coli) / References: UniProt: H3ZMH8
#2: Protein Proline racemase /


Mass: 41755.641 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The construct carries an N-term 6xHis-tag and a TEV cleavage site
Source: (gene. exp.) Thermococcus litoralis DSM 5473 (archaea)
Gene: OCC_00387 / Variant: ATCC 51850 / DSM 5473 / JCM 8560 / NS-C / Production host: Escherichia coli (E. coli) / References: UniProt: H3ZMH8
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.16 Å3/Da / Density % sol: 43.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Magnesium formate, 15% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.979163 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979163 Å / Relative weight: 1
ReflectionResolution: 2.4→44.8 Å / Num. obs: 53298 / % possible obs: 99.3 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 7.6
Reflection shellResolution: 2.4→2.5 Å / Rmerge(I) obs: 0.41 / Num. unique obs: 5281

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1W61

1w61


Resolution: 2.4→44.8 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.92
RfactorNum. reflection% reflection
Rfree0.2645 2676 5.03 %
Rwork0.2049 --
obs0.208 53233 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→44.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10895 0 0 16 10911
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111147
X-RAY DIFFRACTIONf_angle_d1.38615059
X-RAY DIFFRACTIONf_dihedral_angle_d9.3526662
X-RAY DIFFRACTIONf_chiral_restr0.071642
X-RAY DIFFRACTIONf_plane_restr0.0081924
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.44370.40471310.3132655X-RAY DIFFRACTION100
2.4437-2.49070.31541320.29662641X-RAY DIFFRACTION100
2.4907-2.54150.34031300.27772646X-RAY DIFFRACTION100
2.5415-2.59680.34021190.26722653X-RAY DIFFRACTION99
2.5968-2.65720.32161320.26062651X-RAY DIFFRACTION99
2.6572-2.72360.27911210.25082643X-RAY DIFFRACTION99
2.7236-2.79720.29911410.24942614X-RAY DIFFRACTION100
2.7972-2.87950.36741320.25952695X-RAY DIFFRACTION99
2.8795-2.97250.33121550.24762607X-RAY DIFFRACTION100
2.9725-3.07870.30041540.23532671X-RAY DIFFRACTION100
3.0787-3.20190.31251440.2282641X-RAY DIFFRACTION100
3.2019-3.34760.3221560.22282653X-RAY DIFFRACTION100
3.3476-3.52410.2511580.20462620X-RAY DIFFRACTION99
3.5241-3.74480.26261370.19592654X-RAY DIFFRACTION100
3.7448-4.03380.2471400.18092674X-RAY DIFFRACTION100
4.0338-4.43950.20681540.15542692X-RAY DIFFRACTION100
4.4395-5.08130.20531740.14612655X-RAY DIFFRACTION99
5.0813-6.39970.21631210.17972716X-RAY DIFFRACTION99
6.3997-48.99540.23241450.17972776X-RAY DIFFRACTION97

+
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