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- PDB-7yqa: Crystal structure of D-threonine aldolase from Chlamydomonas rein... -

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Basic information

Entry
Database: PDB / ID: 7yqa
TitleCrystal structure of D-threonine aldolase from Chlamydomonas reinhardtii
ComponentsD-threonine aldolase
KeywordsLYASE / aldolase / plp-dependent enzyme / D-amino acid metabolism
Function / homology
Function and homology information


lyase activity / metal ion binding
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 speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsHirato, Y. / Goto, M. / Mizobuchi, T. / Muramatsu, H. / Tanigawa, M. / Nishimura, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2023
Title: Structure of pyridoxal 5'-phosphate-bound D-threonine aldolase from Chlamydomonas reinhardtii.
Authors: Hirato, Y. / Goto, M. / Mizobuchi, T. / Muramatsu, H. / Tanigawa, M. / Nishimura, K.
History
DepositionAug 5, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 15, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)181,4988
Polymers181,4014
Non-polymers974
Water12,358686
1
A: D-threonine aldolase
B: D-threonine aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,7494
Polymers90,7002
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6640 Å2
ΔGint-20 kcal/mol
Surface area26550 Å2
MethodPISA
2
C: D-threonine aldolase
D: D-threonine aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,7494
Polymers90,7002
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6750 Å2
ΔGint-21 kcal/mol
Surface area26640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.792, 74.096, 89.939
Angle α, β, γ (deg.)77.070, 69.340, 71.930
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
D-threonine aldolase


Mass: 45350.133 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Plasmid: pET41b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1C9ZZ39, D-threonine aldolase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 686 / 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: 2.1 Å3/Da / Density % sol: 41.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 1540, 2-methyl-2,4-pentanediol, Magnesium nitrate

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→83.46 Å / Num. obs: 111548 / % possible obs: 88.6 % / Redundancy: 1.6 % / Rpim(I) all: 0.044 / Rrim(I) all: 0.062 / Rsym value: 0.044 / Net I/av σ(I): 11.8 / Net I/σ(I): 9.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.85-1.951.60.1425.426299168310.1420.2010.142391.3
1.95-2.071.60.1067.324805157630.1060.1490.1064.290.8
2.07-2.211.60.0789.323504148030.0780.1110.0785.990.4
2.21-2.391.60.06610.621991136970.0660.0930.0667.289.8
2.39-2.621.60.05712.120187124120.0570.0810.0578.488.9
2.62-2.931.60.04713.718452112000.0470.0660.04710.888
2.93-3.381.70.03815.61625496930.0380.0540.0381586.9
3.38-4.141.70.03217.81371380180.0320.0450.03219.885
4.14-5.851.70.0318.21054660520.030.0420.0320.883.1
5.85-42.2811.80.02423554930790.0240.0340.02420.577.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
SCALA3.3.22data scaling
PDB_EXTRACT3.27data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4V15

4v15


Resolution: 1.85→83.46 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.909 / WRfactor Rfree: 0.2565 / WRfactor Rwork: 0.2215 / FOM work R set: 0.845 / SU B: 3.494 / SU ML: 0.109 / SU R Cruickshank DPI: 0.2002 / SU Rfree: 0.1672 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.2 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.249 5566 5 %RANDOM
Rwork0.2171 ---
obs0.2187 105911 88.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.67 Å2 / Biso mean: 25.556 Å2 / Biso min: 9.3 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.85→83.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11654 0 4 686 12344
Biso mean--21.14 29.68 -
Num. residues----1584
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01911966
X-RAY DIFFRACTIONr_angle_refined_deg1.3841.96716284
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.24651605
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.4223.443517
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.484151796
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.24615113
X-RAY DIFFRACTIONr_chiral_restr0.0840.21815
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219279
LS refinement shellResolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 427 -
Rwork0.238 8059 -
all-8486 -
obs--91.41 %

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