[English] 日本語
Yorodumi
- PDB-6hjf: Trypanosoma cruzi proline racemase in complex with inhibitor BrOxoPA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6hjf
TitleTrypanosoma cruzi proline racemase in complex with inhibitor BrOxoPA
ComponentsProline racemase A
KeywordsISOMERASE / PROLINE RACEMASE / DRUG DESIGN / MICHAEL REACTION / SUICIDE SUBSTRATE
Function / homology
Function and homology information


proline racemase activity / proline racemase / 4-hydroxyproline epimerase activity / extracellular region / membrane / cytoplasm
Similarity search - Function
Proline racemase family / Proline racemase / Diaminopimelate Epimerase; Chain A, domain 1 / Diaminopimelate Epimerase; Chain A, domain 1 / Roll / Alpha Beta
Similarity search - Domain/homology
LAEVULINIC ACID / Proline racemase A
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSaul, F. / Haouz, A. / Uriac, P. / Blondel, A. / Minoprio, P.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-14-CE16-0001-01 France
CitationJournal: PLoS Negl Trop Dis / Year: 2018
Title: Designed mono- and di-covalent inhibitors trap modeled functional motions for Trypanosoma cruzi proline racemase in crystallography.
Authors: Amaral, P.A. / Autheman, D. / de Melo, G.D. / Gouault, N. / Cupif, J.F. / Goyard, S. / Dutra, P. / Coatnoan, N. / Cosson, A. / Monet, D. / Saul, F. / Haouz, A. / Uriac, P. / Blondel, A. / Minoprio, P.
History
DepositionSep 3, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Proline racemase A
B: Proline racemase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,8254
Polymers91,5922
Non-polymers2322
Water9,512528
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-13 kcal/mol
Surface area26490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.666, 90.841, 85.919
Angle α, β, γ (deg.)90.00, 126.29, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Proline racemase A / TcPA45-A / TcPRACA / rTcPA45


Mass: 45796.246 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / Gene: PA45-A, Tc00.1047053506795.80 / Plasmid: PET28B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4DA80, proline racemase
#2: Chemical ChemComp-SHF / LAEVULINIC ACID / LEVULINIC ACID


Mass: 116.115 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 528 / 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: 2.23 Å3/Da / Density % sol: 44.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2M POTASSIUM PHOSPHATE DIBASIC 21% (W/V) PEG-3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9184 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 23, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.7→42.7 Å / Num. obs: 86740 / % possible obs: 98.5 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 12
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.675 / Mean I/σ(I) obs: 1.7 / % possible all: 95.8

-
Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMAC5.7.0029refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1W61

1w61


Resolution: 1.7→41.39 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.377 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.093 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.203 1741 2 %RANDOM
Rwork0.171 ---
obs0.172 84997 98.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 35.37 Å2
Baniso -1Baniso -2Baniso -3
1-2.69 Å20 Å21.36 Å2
2---2.06 Å20 Å2
3----0.78 Å2
Refinement stepCycle: LAST / Resolution: 1.7→41.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5388 0 16 540 5944
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195546
X-RAY DIFFRACTIONr_bond_other_d0.0010.025301
X-RAY DIFFRACTIONr_angle_refined_deg1.4011.9687538
X-RAY DIFFRACTIONr_angle_other_deg0.753312208
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3945719
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.92324.538238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.78715906
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.3431530
X-RAY DIFFRACTIONr_chiral_restr0.0820.2858
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216370
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021228
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.72 Å / Total num. of bins used: 40
RfactorNum. reflection% reflection
Rfree0.425 68 -
Rwork0.328 3050 -
obs--94.17 %

+
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