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- PDB-6j7c: Crystal structure of proline racemase-like protein from Thermococ... -

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Basic information

Entry
Database: PDB / ID: 6j7c
TitleCrystal structure of proline racemase-like protein from Thermococcus litoralis in complex with proline
ComponentsProline racemase
KeywordsISOMERASE / Proline racemase / Hydroxyproline 2-epimerase / Hyperthermophilic archaea
Function / homologyProline racemase family / Proline racemase / Diaminopimelate Epimerase; Chain A, domain 1 / Diaminopimelate Epimerase; Chain A, domain 1 / Roll / Alpha Beta / PROLINE / Proline racemase
Function and homology information
Biological speciesThermococcus litoralis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsWatanabe, Y. / Watanabe, S. / Itoh, Y. / Watanabe, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science16K07297 Japan
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2019
Title: Crystal structure of substrate-bound bifunctional proline racemase/hydroxyproline epimerase from a hyperthermophilic archaeon.
Authors: Watanabe, Y. / Watanabe, S. / Itoh, Y. / Watanabe, Y.
History
DepositionJan 17, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 13, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 2023Group: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3172
Polymers38,2021
Non-polymers1151
Water52229
1
A: Proline racemase
hetero molecules

A: Proline racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,6344
Polymers76,4032
Non-polymers2302
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area3900 Å2
ΔGint-24 kcal/mol
Surface area23450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.379, 125.379, 140.633
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Proline racemase /


Mass: 38201.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus litoralis (strain ATCC 51850 / DSM 5473 / JCM 8560 / NS-C) (archaea)
Strain: ATCC 51850 / DSM 5473 / JCM 8560 / NS-C / Gene: OCC_00372 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: H3ZMH5
#2: Chemical ChemComp-PRO / PROLINE / Proline


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 4.35 Å3/Da / Density % sol: 71.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M HEPES pH 7.0, 30% (v/v) Jeffamine ED-2001 pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 18535 / % possible obs: 100 % / Redundancy: 20.1 % / Biso Wilson estimate: 58.24 Å2 / Rpim(I) all: 0.041 / Rrim(I) all: 0.185 / Rsym value: 0.18 / Net I/σ(I): 25.4
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 19.7 % / Mean I/σ(I) obs: 2 / Num. unique obs: 889 / CC1/2: 0.734 / Rpim(I) all: 0.446 / Rrim(I) all: 1.993 / Rsym value: 1.941 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1W61

1w61


Resolution: 2.7→46.793 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.93
RfactorNum. reflection% reflection
Rfree0.2958 1820 9.83 %
Rwork0.2454 --
obs0.2505 18509 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 98.65 Å2 / Biso mean: 58.1317 Å2 / Biso min: 30.76 Å2
Refinement stepCycle: final / Resolution: 2.7→46.793 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2562 0 8 29 2599
Biso mean--58.84 47.57 -
Num. residues----331
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092621
X-RAY DIFFRACTIONf_angle_d1.0363554
X-RAY DIFFRACTIONf_chiral_restr0.06409
X-RAY DIFFRACTIONf_plane_restr0.006455
X-RAY DIFFRACTIONf_dihedral_angle_d9.1671559
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.7004-2.77340.4911260.402112661392
2.7734-2.8550.42991340.382212471381
2.855-2.94710.41391350.355312461381
2.9471-3.05240.43221420.354212561398
3.0524-3.17460.38851380.314612541392
3.1746-3.3190.36511500.289812611411
3.319-3.4940.29321190.267512921411
3.494-3.71280.31561490.239312541403
3.7128-3.99930.29931600.230412621422
3.9993-4.40150.23631380.206812881426
4.4015-5.03780.25351370.183613041441
5.0378-6.34460.23831430.209313251468
6.3446-46.80020.24261490.220814341583

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