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- PDB-3r0x: Crystal structure of Selenomethionine incorporated apo D-serine d... -

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Basic information

Entry
Database: PDB / ID: 3r0x
TitleCrystal structure of Selenomethionine incorporated apo D-serine deaminase from Salmonella tyhimurium
ComponentsD-serine dehydratase
KeywordsLYASE / Foldtype 2 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 / isoleucine biosynthetic process / 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 / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate 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 / SYNCHROTRON / MAD / Resolution: 1.93 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

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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)49,71810
Polymers49,0971
Non-polymers6229
Water6,972387
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.460, 188.390, 46.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 49096.504 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 / Sulfate


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


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 387 / 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: 2.52 Å3/Da / Density % sol: 51.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 0.1M Trisodium citrate pH 6.1, 0.4M Ammonium sulphatem, 0.8M Lithium sulphate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONESRF BM1410.97848, 0.97872, 1.01876, 0.97083
ROTATING ANODEBRUKER AXS MICROSTAR21.5418
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDOct 28, 2009
MAR scanner 345 mm plate2IMAGE PLATENov 6, 2009
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-IDMonochromator
1MADMx-ray1
2SINGLE WAVELENGTHMx-ray1OSMIC MIRROR
Radiation wavelength
IDWavelength (Å)Relative weight
10.978481
20.978721
31.018761
40.970831
51.54181
ReflectionResolution: 1.93→48.4 Å / Num. obs: 36067 / % possible obs: 93.7 % / Redundancy: 9.1 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 28.2
Reflection shellResolution: 1.9→2 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.174 / Mean I/σ(I) obs: 12 / Num. unique all: 4560 / % possible all: 82.5

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
Auto-Rickshawphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.93→36.17 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.921 / SU B: 2.656 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.20986 1822 5.1 %RANDOM
Rwork0.18063 ---
obs0.18212 34192 94.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.799 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.93→36.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3291 0 36 387 3714
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223435
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9151.9644657
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.85451
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.54124.392148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.63815543
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1551517
X-RAY DIFFRACTIONr_chiral_restr0.0610.2513
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212621
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_it0.2941.52188
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.56523477
X-RAY DIFFRACTIONr_scbond_it0.8331247
X-RAY DIFFRACTIONr_scangle_it1.3324.51175
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.935→1.985 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 113 -
Rwork0.21 2293 -
obs--87.65 %

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