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- PDB-7yvr: Crystal Structure of L-Threonine Aldolase from Neptunomonas marina -

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Basic information

Entry
Database: PDB / ID: 7yvr
TitleCrystal Structure of L-Threonine Aldolase from Neptunomonas marina
ComponentsL-threonine aldolase
KeywordsLYASE / Alpha and beta proteins PLP-dependent transferases Aldehyde-lyases
Function / homology
Function and homology information


low-specificity L-threonine aldolase / threonine catabolic process / L-allo-threonine aldolase activity
Similarity search - Function
Low specificity L-threonine aldolase, bacteria / Aromatic amino acid beta-eliminating lyase/threonine aldolase / Beta-eliminating lyase / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
L-threonine aldolase
Similarity search - Component
Biological speciesNeptunomonas marina (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHe, Y.Z. / Wang, J. / Yan, W.P. / Zhang, Y. / Feng, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Acs Catalysis / Year: 2023
Title: Discovery and Engineering of the L-Threonine Aldolase from Neptunomonas marine for the Efficient Synthesis of beta-Hydroxy-alpha-amino Acids via C-C Formation
Authors: He, Y. / Li, S. / Wang, J. / Yang, X. / Zhu, J. / Zhang, Q. / Cui, L. / Tan, Z. / Yan, W. / Zhang, Y. / Tang, L. / Da, L.T. / Feng, Y.
History
DepositionAug 19, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-threonine aldolase
B: L-threonine aldolase
C: L-threonine aldolase
D: L-threonine aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,7987
Polymers157,5214
Non-polymers2763
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14950 Å2
ΔGint-73 kcal/mol
Surface area44130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)264.430, 59.859, 95.112
Angle α, β, γ (deg.)90.000, 106.087, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein
L-threonine aldolase


Mass: 39380.320 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neptunomonas marina (bacteria) / Gene: EOE65_08265 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A437Q8X1, low-specificity L-threonine aldolase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.31 Å3/Da / Density % sol: 46.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 21%(v/v) MPD, 0.02M Calcium chloride dihydrate, and 0.1M Sodium acetate at pH4.65

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.798→19.82 Å / Num. obs: 35454 / % possible obs: 98.97 % / Redundancy: 4.5 % / Biso Wilson estimate: 35.44 Å2 / CC1/2: 0.984 / Rsym value: 0.139 / Net I/σ(I): 7.65
Reflection shellResolution: 2.798→2.898 Å / Num. unique obs: 15522 / CC1/2: 0.819 / Rsym value: 0.412

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VYE

5vye


Resolution: 2.8→19.82 Å / SU ML: 0.3628 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.413
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2404 2010 5.67 %
Rwork0.2012 33419 -
obs0.2034 35429 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.14 Å2
Refinement stepCycle: LAST / Resolution: 2.8→19.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10332 0 18 169 10519
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001310539
X-RAY DIFFRACTIONf_angle_d0.401514317
X-RAY DIFFRACTIONf_chiral_restr0.03711638
X-RAY DIFFRACTIONf_plane_restr0.00321872
X-RAY DIFFRACTIONf_dihedral_angle_d11.63933728
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.870.35941490.28562357X-RAY DIFFRACTION98.82
2.87-2.950.34211300.26282372X-RAY DIFFRACTION99.64
2.95-3.030.29851500.2492376X-RAY DIFFRACTION99.68
3.03-3.130.30371450.25332351X-RAY DIFFRACTION99.13
3.13-3.240.28821270.24652339X-RAY DIFFRACTION98.21
3.24-3.370.29671560.22432365X-RAY DIFFRACTION99.41
3.37-3.520.25231320.20852428X-RAY DIFFRACTION99.84
3.52-3.710.21741500.18912367X-RAY DIFFRACTION99.92
3.71-3.940.21351410.17912390X-RAY DIFFRACTION99.8
3.94-4.240.21921400.172411X-RAY DIFFRACTION99.77
4.24-4.660.18291530.17122383X-RAY DIFFRACTION99.3
4.66-5.320.22751420.1852384X-RAY DIFFRACTION98.56
5.32-6.660.22611500.20992430X-RAY DIFFRACTION99.58
6.66-19.820.18341450.15882466X-RAY DIFFRACTION98.6
Refinement TLS params.Method: refined / Origin x: -41.3251780009 Å / Origin y: -15.4886638247 Å / Origin z: 21.3114672772 Å
111213212223313233
T0.245747425607 Å20.00492913111002 Å2-0.022214129386 Å2-0.17023125691 Å20.00311298036665 Å2--0.24107736763 Å2
L0.406071573937 °2-0.0106181120746 °20.123229635615 °2-0.163651183758 °2-0.0370168361524 °2--0.402269839616 °2
S0.0131235450143 Å °-0.0333545633379 Å °-0.00580500998068 Å °0.0206335530284 Å °-0.0328041626025 Å °-0.0207882856183 Å °0.00617671854009 Å °0.0461775987853 Å °0.0196604929025 Å °
Refinement TLS groupSelection details: all

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