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- PDB-6r77: Crystal structure of trans-3-Hydroxy-L-proline dehydratase in com... -

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Basic information

Entry
Database: PDB / ID: 6r77
TitleCrystal structure of trans-3-Hydroxy-L-proline dehydratase in complex with substrate - closed conformation
ComponentsProline racemase
KeywordsLYASE / trans-3-Hydroxy-L-proline dehydratase / hydro-lyase / hydroxyproline metabolism
Function / homologyProline racemase family / Proline racemase / Diaminopimelate Epimerase; Chain A, domain 1 / Diaminopimelate Epimerase; Chain A, domain 1 / Roll / Alpha Beta / 3-HYDROXYPROLINE / Proline racemase
Function and homology information
Biological speciesThermococcus litoralis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.1Jan 24, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)83,6144
Polymers83,3512
Non-polymers2622
Water7,152397
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5700 Å2
ΔGint-39 kcal/mol
Surface area25810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.415, 106.547, 149.456
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 0 / Auth seq-ID: 1 - 348 / Label seq-ID: 21 - 368

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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 (archaea) / Gene: OCC_00387 / Production host: Escherichia coli (E. coli) / References: UniProt: H3ZMH8
#2: Chemical ChemComp-HY3 / 3-HYDROXYPROLINE / (2S,3S)-3-hydroxypyrrolidine-2-carboxylic acid / Hydroxyproline


Type: L-peptide linking / Mass: 131.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 397 / Source method: isolated from a natural source / Formula: H2O

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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: 2.69 Å3/Da / Density % sol: 54.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Na HEPES 0.1 M, PEG 400, 2.0 Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→86.8 Å / Num. obs: 59449 / % possible obs: 95.7 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.0774 / Net I/σ(I): 5.2
Reflection shellResolution: 2→2.1 Å / Rmerge(I) obs: 0.29 / Num. unique obs: 5864

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1W61

1w61


Resolution: 2→45.07 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.95 / SU B: 6.12 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.143 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21252 2935 5 %RANDOM
Rwork0.18818 ---
obs0.18937 56179 95.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.299 Å2
Baniso -1Baniso -2Baniso -3
1-4.49 Å20 Å20 Å2
2---0.69 Å20 Å2
3----3.8 Å2
Refinement stepCycle: LAST / Resolution: 2→45.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5536 0 18 397 5951
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0135684
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175386
X-RAY DIFFRACTIONr_angle_refined_deg1.441.6517680
X-RAY DIFFRACTIONr_angle_other_deg1.3011.57912514
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5085694
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.28422.553282
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.172151010
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4751530
X-RAY DIFFRACTIONr_chiral_restr0.0640.2742
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026272
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021178
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_it1.9932.9332782
X-RAY DIFFRACTIONr_mcbond_other1.9922.9332781
X-RAY DIFFRACTIONr_mcangle_it2.9094.3923474
X-RAY DIFFRACTIONr_mcangle_other2.9094.3923475
X-RAY DIFFRACTIONr_scbond_it3.1373.3792902
X-RAY DIFFRACTIONr_scbond_other3.1363.382901
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0144.8964207
X-RAY DIFFRACTIONr_long_range_B_refined6.7134.8856154
X-RAY DIFFRACTIONr_long_range_B_other6.64134.546070
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 11437 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 244 -
Rwork0.279 4130 -
obs--96.68 %

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