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- PDB-3r0z: Crystal structure of apo D-serine deaminase from Salmonella typhi... -

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Basic information

Entry
Database: PDB / ID: 3r0z
TitleCrystal structure of apo D-serine deaminase from Salmonella typhimurium
ComponentsD-serine dehydratase
KeywordsLYASE / Foldtype 2 family of PLP-dependent enzymes / alpha / beta elimination of D-serine
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. / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
D-serine dehydratase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBharath, S.R. / Shveta, B. / Savithri, H.S. / Murthy, M.R.N.
CitationJournal: Febs J. / Year: 2011
Title: Crystal structures of open and closed forms of D-serine deaminase from Salmonella typhimurium - implications on substrate specificity and catalysis
Authors: Bharath, S.R. / Bisht, S. / Savithri, H.S. / Murthy, M.R.N.
History
DepositionMar 9, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)48,8996
Polymers48,4871
Non-polymers4125
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.020, 46.790, 100.040
Angle α, β, γ (deg.)90.00, 93.75, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 48486.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: dsdA, STM3802 / Plasmid: pET21b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Rosetta / References: UniProt: Q8ZL08, D-serine ammonia-lyase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.41 Å3/Da / Density % sol: 48.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.1
Details: 0.1M Trisodium citrate pH 6.1, 0.4M Ammonium sulphate, 0.8M Ammonium sulphate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 11, 2009 / Details: Mirror
RadiationMonochromator: OSMIC MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→49.9 Å / Num. obs: 17806 / % possible obs: 97.1 % / Redundancy: 4.1 % / Biso Wilson estimate: 37.4 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 6
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 2.3 / Num. unique all: 2301 / % possible all: 87.8

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→45.85 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.881 / SU B: 9.895 / SU ML: 0.232 / Cross valid method: THROUGHOUT / ESU R Free: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27226 910 5.1 %RANDOM
Rwork0.2117 ---
obs0.21496 16864 96.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.113 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.4→45.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3220 0 23 140 3383
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223318
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4371.9634498
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.295434
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.7424.234137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.07715515
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4561515
X-RAY DIFFRACTIONr_chiral_restr0.10.2500
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212517
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.661.52136
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.16223375
X-RAY DIFFRACTIONr_scbond_it1.86131182
X-RAY DIFFRACTIONr_scangle_it2.8154.51121
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 68 -
Rwork0.262 1071 -
obs--87.08 %

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