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- PDB-6hje: Trypanosoma cruzi proline racemase in complex with inhibitor NG-P27 -

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Basic information

Entry
Database: PDB / ID: 6hje
TitleTrypanosoma cruzi proline racemase in complex with inhibitor NG-P27
ComponentsProline racemase A
KeywordsISOMERASE / Proline Racemase / Drug Design / Michael Reaction
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
Chem-7N0 / PHOSPHATE ION / Proline racemase A
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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_leaving_atom_flag
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)91,9725
Polymers91,5922
Non-polymers3793
Water7,008389
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-21 kcal/mol
Surface area27520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.233, 90.640, 85.394
Angle α, β, γ (deg.)90.00, 126.04, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-761-

HOH

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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 (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4DA80, proline racemase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-7N0 / 2-[(1~{S})-2-oxidanylidenecyclopentyl]ethanoic acid


Mass: 142.152 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 389 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.17 %
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

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.00637 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00637 Å / Relative weight: 1
ReflectionResolution: 2→45.3 Å / Num. obs: 54731 / % possible obs: 98.8 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 7.8
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.758 / Mean I/σ(I) obs: 1.7 / % possible all: 98

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Processing

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

1w61


Resolution: 2→45 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.357 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.158 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1049 2 %RANDOM
Rwork0.177 ---
obs0.178 52236 96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 49.07 Å2
Baniso -1Baniso -2Baniso -3
1-4.41 Å20 Å21.61 Å2
2---2.41 Å20 Å2
3----1.54 Å2
Refinement stepCycle: LAST / Resolution: 2→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5423 0 25 403 5851
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195600
X-RAY DIFFRACTIONr_bond_other_d0.0010.025364
X-RAY DIFFRACTIONr_angle_refined_deg1.461.9717612
X-RAY DIFFRACTIONr_angle_other_deg0.75312361
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2865725
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.39824.5240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.98615921
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8481531
X-RAY DIFFRACTIONr_chiral_restr0.0790.2866
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216414
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021237
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: 2→2.03 Å / Total num. of bins used: 40
RfactorNum. reflection% reflection
Rfree0.331 22 -
Rwork0.254 993 -
obs--50.32 %

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