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- PDB-3x44: Crystal structure of O-ureido-L-serine-bound K43A mutant of O-ure... -

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Basic information

Entry
Database: PDB / ID: 3x44
TitleCrystal structure of O-ureido-L-serine-bound K43A mutant of O-ureido-L-serine synthase
ComponentsO-ureido-L-serine synthase
KeywordsTRANSFERASE / D-cycloserine / type II PLP enzyme / synthase
Function / homology
Function and homology information


O-ureido-L-serine synthase / cysteine synthase / cysteine synthase activity / cysteine biosynthetic process from serine / antibiotic biosynthetic process
Similarity search - Function
Cysteine synthase CysK / Cysteine synthase / Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site / Cysteine synthase/cystathionine beta-synthase P-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
Chem-PUS / O-ureido-L-serine synthase
Similarity search - Component
Biological speciesStreptomyces lavendulae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMatoba, Y. / Uda, N. / Oda, K. / Sugiyama, M.
CitationJournal: Febs J. / Year: 2015
Title: The structural and mutational analyses of O-ureido-L-serine synthase necessary for D-cycloserine biosynthesis.
Authors: Uda, N. / Matoba, Y. / Oda, K. / Kumagai, T. / Sugiyama, M.
History
DepositionMar 13, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2015Group: Database references
Revision 1.2Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _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
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: O-ureido-L-serine synthase
B: O-ureido-L-serine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0694
Polymers71,2852
Non-polymers7852
Water8,431468
1
A: O-ureido-L-serine synthase
B: O-ureido-L-serine synthase
hetero molecules

A: O-ureido-L-serine synthase
B: O-ureido-L-serine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,1388
Polymers142,5694
Non-polymers1,5694
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area14190 Å2
ΔGint-89 kcal/mol
Surface area40480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.350, 80.260, 74.670
Angle α, β, γ (deg.)90.00, 117.96, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-521-

HOH

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Components

#1: Protein O-ureido-L-serine synthase / Cysteine synthase homolog DscD / O-acetylserine sulfhydrylase


Mass: 35642.301 Da / Num. of mol.: 2 / Mutation: K43A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lavendulae (bacteria) / Strain: ATCC11924 / Gene: dcsD / Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: D2Z027, O-ureido-L-serine synthase, cysteine synthase
#2: Chemical ChemComp-PUS / (E)-O-(carbamoylamino)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-serine


Mass: 392.259 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H17N4O9P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 468 / 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: 2.1 Å3/Da / Density % sol: 41.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.1
Details: Tris-HCl, polyethylene glycol 8,000, sodium acetate, pH 8.1, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 22, 2013
RadiationMonochromator: Fixed exit double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→100 Å / Num. all: 44755 / Num. obs: 44755 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 7.8 Å2 / Rmerge(I) obs: 0.112 / Net I/σ(I): 12.5
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 2.2 / Num. unique all: 3820 / % possible all: 82.4

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Processing

Software
NameVersionClassification
BSSdata collection
MOLREPphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→29.87 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 4848590.07 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.26 2193 5.1 %RANDOM
Rwork0.212 ---
obs0.212 43207 92.6 %-
all-43207 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.301 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 24.2 Å2
Baniso -1Baniso -2Baniso -3
1-21.08 Å20 Å2-8.48 Å2
2---14.96 Å20 Å2
3----6.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.9→29.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4787 0 52 468 5307
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.64
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.641.5
X-RAY DIFFRACTIONc_mcangle_it2.152
X-RAY DIFFRACTIONc_scbond_it2.312
X-RAY DIFFRACTIONc_scangle_it2.932.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.314 327 5.4 %
Rwork0.26 5676 -
obs--77.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep-3.paramtophcsdx-3.pro
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3PUS.paramPUS.top

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