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- PDB-7jp2: Crystal structure of TP0037 from Treponema pallidum, a D-lactate ... -

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Basic information

Entry
Database: PDB / ID: 7jp2
TitleCrystal structure of TP0037 from Treponema pallidum, a D-lactate dehydrogenase
ComponentsD-lactate dehydrogenase
KeywordsOXIDOREDUCTASE / D-lactate dehydrogenase / spirochete / acetogenesis
Function / homology
Function and homology information


D-lactate dehydrogenase / D-lactate dehydrogenase activity / NAD binding
Similarity search - Function
D-isomer specific 2-hydroxyacid dehydrogenases signature 2. / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
D-lactate dehydrogenase
Similarity search - Component
Biological speciesTreponema pallidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsBrautigam, C.A. / Deka, R.K. / Norgard, M.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Mbio / Year: 2020
Title: Biophysical and Biochemical Characterization of TP0037, a d-Lactate Dehydrogenase, Supports an Acetogenic Energy Conservation Pathway in Treponema pallidum.
Authors: Deka, R.K. / Liu, W.Z. / Norgard, M.V. / Brautigam, C.A.
History
DepositionAug 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 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: D-lactate dehydrogenase
B: D-lactate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,08910
Polymers74,6452
Non-polymers4438
Water11,584643
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, Also, sedimentation velocity analytical ultracentrifugation was performed.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7120 Å2
ΔGint-38 kcal/mol
Surface area27050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.660, 94.687, 101.455
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein D-lactate dehydrogenase / / D-LDH / D-specific 2-hydroxyacid dehydrogenase


Mass: 37322.742 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Treponema pallidum (bacteria) / Gene: ldhD, TP_0037 / Production host: Escherichia coli (E. coli) / References: UniProt: O83080, D-lactate dehydrogenase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 643 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.34 Å3/Da / Density % sol: 47.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 200 mM sodium-potassium phosphate, 100 mM Bis-Tris propane pH 7.5, 20% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97914 Å
DetectorType: DECTRIS PILATUS3 X 1M / Detector: PIXEL / Date: Oct 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 1.38→50 Å / Num. obs: 143109 / % possible obs: 99.5 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.025 / Rrim(I) all: 0.054 / Χ2: 0.469 / Net I/σ(I): 6.8 / Num. measured all: 618853
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.38-1.44.30.29670710.9230.1570.3370.43798.8
1.4-1.434.40.25870750.9410.1360.2920.4599.7
1.43-1.464.30.22771270.9440.120.2570.45799.7
1.46-1.494.30.270720.9610.1060.2270.4499.7
1.49-1.524.20.16970890.9710.0910.1920.4499.6
1.52-1.5540.15370670.9690.0850.1760.44999.2
1.55-1.594.30.13371190.9820.0710.1520.43299.7
1.59-1.644.50.12171180.9870.0630.1370.42799.6
1.64-1.684.40.10671400.9890.0560.120.42999.8
1.68-1.744.40.09570860.9910.050.1070.4399.6
1.74-1.84.30.0871350.9920.0430.0920.43499.7
1.8-1.8740.06870660.9940.0380.0780.42298.7
1.87-1.964.50.0671670.9960.0310.0670.44999.6
1.96-2.064.50.0571600.9970.0260.0570.44299.8
2.06-2.194.40.04471720.9970.0230.050.45399.8
2.19-2.364.10.03971490.9970.0220.0450.45998.9
2.36-2.64.60.03672150.9980.0190.0410.46599.6
2.6-2.974.50.03572590.9980.0190.040.54899.9
2.97-3.754.20.03172640.9980.0170.0360.63499
3.75-504.30.02975580.9980.0160.0330.67599.1

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XDW

1xdw


Resolution: 1.38→38.082 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 12.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.158 7172 5.01 %
Rwork0.1358 135844 -
obs0.1369 143016 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 57.42 Å2 / Biso mean: 14.866 Å2 / Biso min: 3.31 Å2
Refinement stepCycle: final / Resolution: 1.38→38.082 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5186 0 62 643 5891
Biso mean--28.17 22.83 -
Num. residues----662
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055540
X-RAY DIFFRACTIONf_angle_d0.9017531
X-RAY DIFFRACTIONf_dihedral_angle_d13.5812077
X-RAY DIFFRACTIONf_chiral_restr0.07842
X-RAY DIFFRACTIONf_plane_restr0.006982
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.3804-1.39610.17132090.1286441197
1.3961-1.41250.18362210.12254502100
1.4125-1.42970.15012570.12034470100
1.4297-1.44780.15222250.11354503100
1.4478-1.46690.16142250.11644502100
1.4669-1.4870.16222340.11874501100
1.487-1.50820.16552660.1084447699
1.5082-1.53080.1452390.10454474100
1.5308-1.55470.13662620.1024446099
1.5547-1.58020.14652150.10124543100
1.5802-1.60740.1522410.10324479100
1.6074-1.63660.15162210.10584535100
1.6366-1.66810.14452420.10864496100
1.6681-1.70220.14272480.10754497100
1.7022-1.73920.13472380.11034500100
1.7392-1.77960.14792430.11494556100
1.7796-1.82410.14962590.11624482100
1.8241-1.87350.14622130.1208446598
1.8735-1.92860.15262150.1234573100
1.9286-1.99080.14612470.12344521100
1.9908-2.0620.14992470.12994524100
2.062-2.14450.14722420.1294543100
2.1445-2.24210.16112210.134566100
2.2421-2.36030.14732210.1295452599
2.3603-2.50820.15252260.13364571100
2.5082-2.70180.15592400.14554598100
2.7018-2.97360.17012510.16124583100
2.9736-3.40360.1782360.1634459999
3.4036-4.28730.152630.15614628100
4.2873-38.0820.18763050.1744476199

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