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- PDB-7dib: Crystal structure of D-threonine aldolase from Filomicrobium marinum -

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Basic information

Entry
Database: PDB / ID: 7dib
TitleCrystal structure of D-threonine aldolase from Filomicrobium marinum
ComponentsD-threonine aldolase
KeywordsBIOSYNTHETIC PROTEIN / aldolase / PLP-dependent enzyme
Function / homology
Function and homology information


D-threonine aldolase / D-threonine aldolase activity
Similarity search - Function
D-serine dehydratase-like domain / D-serine dehydratase-like domain superfamily / Putative serine dehydratase domain / Putative serine dehydratase domain / Alanine racemase, N-terminal / Alanine racemase, N-terminal domain / PLP-binding barrel
Similarity search - Domain/homology
D-threonine aldolase
Similarity search - Component
Biological speciesCandidatus Filomicrobium marinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsSeo, H. / Kim, K.-J.
CitationJournal: Acs Catalysis / Year: 2021
Title: Cbeta-Selective Aldol Addition of d-Threonine Aldolase by Spatial Constraint of Aldehyde Binding.
Authors: Park, S.-H. / Seo, H. / Seok, J. / Kim, H. / Kwon, K.K. / Yeom, S.-J. / Lee, S.-G. / Kim, K.-J.
History
DepositionNov 18, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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-threonine aldolase
B: D-threonine aldolase


Theoretical massNumber of molelcules
Total (without water)84,9902
Polymers84,9902
Non-polymers00
Water1,15364
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration, dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4630 Å2
ΔGint-14 kcal/mol
Surface area26140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.965, 178.051, 65.458
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein D-threonine aldolase


Mass: 42495.023 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The sequence "MGSSHHHHHHSSGLVPRGSH" are derived from pET28a vector.
Source: (gene. exp.) Candidatus Filomicrobium marinum (bacteria)
Gene: YBN1229_v1_3680 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0D6JKM4, D-threonine aldolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.43 Å3/Da / Density % sol: 49.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: PEG 400, Sodium acetate tribasic, Cadmium chloride hydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 17, 2018
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 41469 / % possible obs: 96.1 % / Redundancy: 4 % / CC1/2: 0.982 / Rmerge(I) obs: 0.082 / Net I/σ(I): 19.3
Reflection shellResolution: 2.2→2.24 Å / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 1981 / CC1/2: 0.585

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4v15

4v15


Resolution: 2.2→31.3 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.907 / SU B: 7.593 / SU ML: 0.183 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.276 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2543 1988 4.8 %RANDOM
Rwork0.2114 ---
obs0.2134 39459 95.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 125.36 Å2 / Biso mean: 31.372 Å2 / Biso min: 12.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å2-0 Å2-0 Å2
2---0.82 Å20 Å2
3---0.59 Å2
Refinement stepCycle: final / Resolution: 2.2→31.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5560 0 0 64 5624
Biso mean---24.23 -
Num. residues----740
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0135672
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175313
X-RAY DIFFRACTIONr_angle_refined_deg1.5671.6357707
X-RAY DIFFRACTIONr_angle_other_deg1.2481.57712259
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6045737
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.2421.208298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.84915886
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8751551
X-RAY DIFFRACTIONr_chiral_restr0.0650.2739
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026517
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021186
LS refinement shellResolution: 2.2→2.253 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.334 148 -
Rwork0.3 2680 -
obs--89.75 %

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