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- PDB-6r76: Crystal structure of trans-3-Hydroxy-L-proline dehydratase from T... -

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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 / catalytic activity / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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 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


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

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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

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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

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