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- PDB-3x43: Crystal structure of O-ureido-L-serine synthase -

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Basic information

Entry
Database: PDB / ID: 3x43
TitleCrystal structure 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
PYRIDOXAL-5'-PHOSPHATE / O-ureido-L-serine synthase
Similarity search - Component
Biological speciesStreptomyces lavendulae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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_conn / 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_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 8, 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: O-ureido-L-serine synthase
B: O-ureido-L-serine synthase
C: O-ureido-L-serine synthase
D: O-ureido-L-serine synthase
E: O-ureido-L-serine synthase
F: O-ureido-L-serine synthase
G: O-ureido-L-serine synthase
H: O-ureido-L-serine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)287,58016
Polymers285,6038
Non-polymers1,9778
Water14,574809
1
A: O-ureido-L-serine synthase
B: O-ureido-L-serine synthase
C: O-ureido-L-serine synthase
D: O-ureido-L-serine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,7908
Polymers142,8024
Non-polymers9894
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16380 Å2
ΔGint-93 kcal/mol
Surface area42220 Å2
MethodPISA
2
E: O-ureido-L-serine synthase
F: O-ureido-L-serine synthase
G: O-ureido-L-serine synthase
H: O-ureido-L-serine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,7908
Polymers142,8024
Non-polymers9894
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16330 Å2
ΔGint-93 kcal/mol
Surface area42300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.480, 154.130, 118.520
Angle α, β, γ (deg.)90.00, 90.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 35700.402 Da / Num. of mol.: 8
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-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 809 / 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: 2.32 Å3/Da / Density % sol: 46.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Tris-HCl, polyethylene glycol 8,000, KH2PO4, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Dec 7, 2010
RadiationMonochromator: Rotated-inclined double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→100 Å / Num. all: 122927 / Num. obs: 122927 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 25.3 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.1
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 2.8 / Num. unique all: 17914 / % possible all: 100

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Processing

Software
NameVersionClassification
BSSdata collection
MOLREPphasing
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Q3D

2q3d


Resolution: 2.25→29.83 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3018007.28 / 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
Rfree0.264 6178 5 %RANDOM
Rwork0.209 ---
obs0.209 122865 99.7 %-
all-122865 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.3809 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 51.4 Å2
Baniso -1Baniso -2Baniso -3
1-6.12 Å20 Å219.34 Å2
2---0.32 Å20 Å2
3----5.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.25→29.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19095 0 120 809 20024
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_d26.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.63
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.881.5
X-RAY DIFFRACTIONc_mcangle_it2.952
X-RAY DIFFRACTIONc_scbond_it2.542
X-RAY DIFFRACTIONc_scangle_it3.512.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.25→2.39 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.343 1048 5.1 %
Rwork0.331 19331 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep-3.paramtophcsdx-3.pro
X-RAY DIFFRACTION2water_rep.paramwater.top

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