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- PDB-7ol1: The X-ray structure of L-threonine dehydrogenase from the common ... -

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Basic information

Entry
Database: PDB / ID: 7ol1
TitleThe X-ray structure of L-threonine dehydrogenase from the common hospital pathogen Clostridium difficile.
ComponentsL-threonine 3-dehydrogenase
KeywordsOXIDOREDUCTASE / Dehydrogenase / apoenzyme.
Function / homologyL-threonine 3-dehydrogenase / L-threonine 3-dehydrogenase activity / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding domain superfamily / L-threonine 3-dehydrogenase
Function and homology information
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsGuo, J. / Cooper, J.B.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2021
Title: The X-ray structure of L-threonine dehydrogenase from the common hospital pathogen Clostridium difficile.
Authors: Adjogatse, E. / Bennett, J. / Guo, J. / Erskine, P.T. / Wood, S.P. / Wren, B.W. / Cooper, J.B.
History
DepositionMay 18, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / diffrn_source / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-threonine 3-dehydrogenase
B: L-threonine 3-dehydrogenase


Theoretical massNumber of molelcules
Total (without water)76,4172
Polymers76,4172
Non-polymers00
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Likely to be dimeric based on gel-filtration and crystallographic studies of related short-chain TDHs and PISA analysis of buried surface area and contacts (Krissinel, E. & Henrick, K. ...Evidence: Likely to be dimeric based on gel-filtration and crystallographic studies of related short-chain TDHs and PISA analysis of buried surface area and contacts (Krissinel, E. & Henrick, K. (2007). J. Molec. Biol. 372, 774-797).
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-14 kcal/mol
Surface area24590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.870, 180.870, 88.350
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein L-threonine 3-dehydrogenase / / L-threonine dehydrogenase / UDP-glucose 4-epimerase / Uncharacterized epimerase/dehydratase SAV0553


Mass: 38208.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The N-terminal sequence MGHHHHHHHHHHSSGHIEGRH originates from the expression tag.
Source: (gene. exp.) Clostridioides difficile (bacteria)
Gene: cdgr_08060, NCTC13307_02322, SAMEA1402406_00083, SAMEA3375037_00176
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A346VYB9, L-threonine 3-dehydrogenase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 5.8 Å3/Da / Density % sol: 78.9 % / Description: Multifaceted.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 5 microlitres of enzyme at a concentration of 5 mg/ml and 5 microlitres of 0.2 M lithium sulphate, 0.1 M Tris-HCl pH 8.5, 30 % v/v PEG 4000 (Molecular Dimensions Limited Structure Screen I, condition 35).
Temp details: Ambient temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.56→63.28 Å / Num. obs: 53475 / % possible obs: 99.5 % / Redundancy: 9.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.04 / Rrim(I) all: 0.125 / Rsym value: 0.118 / Net I/av σ(I): 4.2 / Net I/σ(I): 12.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym value% possible all
2.56-2.78.31.7780.477580.5260.6461.8971.77899.4
2.7-2.8691.1680.773220.4071.2391.16899.6
2.86-3.069.40.7121.169090.2420.7530.71299.8
3.06-3.38.50.3342.364050.1210.3560.33499.2
3.3-3.6210.10.1784.259260.0580.1870.17899.6
3.62-4.0510.30.099753830.0320.1040.09999.6
4.05-4.679.70.0689.547710.0230.0720.06899.5
4.67-5.729.50.0618.840310.0210.0650.06199.2
5.72-8.110.20.0666.831710.0210.0690.06699.8
8.1-63.1979.50.0627.917990.0210.0650.06299.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.22data scaling
MOLREPphasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5lc1

5lc1


Resolution: 2.6→63.28 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.939 / SU B: 10.429 / SU ML: 0.198 / SU R Cruickshank DPI: 0.234 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.234 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2389 2500 5 %RANDOM
Rwork0.2004 ---
obs0.2024 47443 97.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 205.04 Å2 / Biso mean: 75.367 Å2 / Biso min: 27.12 Å2
Baniso -1Baniso -2Baniso -3
1--2.95 Å2-1.47 Å2-0 Å2
2---2.95 Å20 Å2
3---9.56 Å2
Refinement stepCycle: final / Resolution: 2.6→63.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5030 0 0 112 5142
Biso mean---66.63 -
Num. residues----638
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0135134
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174875
X-RAY DIFFRACTIONr_angle_refined_deg1.791.6436938
X-RAY DIFFRACTIONr_angle_other_deg1.2971.58311296
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6375636
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.91123.629248
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.79715928
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0261522
X-RAY DIFFRACTIONr_chiral_restr0.0790.2682
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025746
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021107
LS refinement shellResolution: 2.6→2.668 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 156 -
Rwork0.367 2989 -
all-3145 -
obs--83.2 %

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