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- PDB-6aa9: T166A mutant of D-Serine deaminase from Salmonella typhimurium -

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Basic information

Entry
Database: PDB / ID: 6aa9
TitleT166A mutant of D-Serine deaminase from Salmonella typhimurium
ComponentsD-serine dehydratase
KeywordsLYASE / Monomer / PLP bound / Salmonella typhimurium / deaminase
Function / homology
Function and homology information


D-serine ammonia-lyase / D-serine ammonia-lyase activity / D-serine catabolic process / hydro-lyase activity / pyridoxal phosphate binding
Similarity search - Function
D-serine ammonia-lyase / : / Serine/threonine dehydratase, pyridoxal-phosphate-binding site / Serine/threonine dehydratases pyridoxal-phosphate attachment site. / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme
Similarity search - Domain/homology
PHOSPHATE ION / D-serine dehydratase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsDeka, G. / Bharath, S.R. / Shavithri, H.S. / Murthy, M.R.N.
Funding support India, 1items
OrganizationGrant numberCountry
DBT 0425(Department of Biotechnology (DBT) India
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Structural studies on the decameric S. typhimurium arginine decarboxylase (ADC): Pyridoxal 5'-phosphate binding induces conformational changes
Authors: Deka, G. / Bharath, S.R. / Shavithri, H.S. / Murthy, M.R.N.
History
DepositionJul 17, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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-serine dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8033
Polymers48,6851
Non-polymers1182
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area16170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.310, 46.140, 99.280
Angle α, β, γ (deg.)90.00, 100.80, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-649-

HOH

21A-668-

HOH

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Components

#1: Protein D-serine dehydratase / D-serine deaminase / DSD


Mass: 48684.965 Da / Num. of mol.: 1 / Mutation: T166A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: dsdA, STM3802 / Plasmid: pET 21b / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: Q8ZL08, D-serine ammonia-lyase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.43 Å3/Da / Density % sol: 49.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 0.8 M lithium sulfate, 0.4 M ammonium sulfate, 100 mm trisodium citrate pH 6.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.7→53.2 Å / Num. obs: 13514 / % possible obs: 99.9 % / Redundancy: 3.6 % / Biso Wilson estimate: 15.8 Å2 / CC1/2: 0.897 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.109 / Net I/σ(I): 6.1
Reflection shellResolution: 2.7→2.83 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.191 / Mean I/σ(I) obs: 4.6 / Num. unique obs: 1791 / CC1/2: 0.904 / Rpim(I) all: 0.181 / Rrim(I) all: 0.259 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3R0Z

3r0z


Resolution: 2.7→53.2 Å / Cor.coef. Fo:Fc: 0.755 / Cor.coef. Fo:Fc free: 0.664 / SU B: 19.459 / SU ML: 0.423 / Cross valid method: THROUGHOUT / ESU R Free: 0.483 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.34854 673 5 %RANDOM
Rwork0.2891 ---
obs0.2922 12840 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.429 Å2
Baniso -1Baniso -2Baniso -3
1-2.27 Å2-0 Å2-0.12 Å2
2---2.4 Å20 Å2
3---0.16 Å2
Refinement stepCycle: 1 / Resolution: 2.7→53.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3095 0 6 156 3257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0193176
X-RAY DIFFRACTIONr_bond_other_d0.0010.022906
X-RAY DIFFRACTIONr_angle_refined_deg0.9121.9644317
X-RAY DIFFRACTIONr_angle_other_deg0.70636664
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7345418
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.45724.135133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.18915467
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2651515
X-RAY DIFFRACTIONr_chiral_restr0.0440.2475
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213704
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02733
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2971.9191669
X-RAY DIFFRACTIONr_mcbond_other0.2961.9181668
X-RAY DIFFRACTIONr_mcangle_it0.5522.8742082
X-RAY DIFFRACTIONr_mcangle_other0.5522.8752083
X-RAY DIFFRACTIONr_scbond_it0.161.8961507
X-RAY DIFFRACTIONr_scbond_other0.1591.8881503
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.3152.8392227
X-RAY DIFFRACTIONr_long_range_B_refined1.92815.3053674
X-RAY DIFFRACTIONr_long_range_B_other1.88215.2843648
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 50 -
Rwork0.239 931 -
obs--99.9 %

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