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- PDB-2po3: Crystal Structure Analysis of DesI in the presence of its TDP-sug... -

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Basic information

Entry
Database: PDB / ID: 2po3
TitleCrystal Structure Analysis of DesI in the presence of its TDP-sugar product
Components4-dehydrase
KeywordsTRANSFERASE / external aldimine / PLP / aminotransferase / TDP-sugar
Function / homology
Function and homology information


antibiotic biosynthetic process / catalytic activity
Similarity search - Function
dTDP-4-dehydro-6-deoxyglucose aminotransferase / DegT/DnrJ/EryC1/StrS aminotransferase / DegT/DnrJ/EryC1/StrS aminotransferase family / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase ...dTDP-4-dehydro-6-deoxyglucose aminotransferase / DegT/DnrJ/EryC1/StrS aminotransferase / DegT/DnrJ/EryC1/StrS aminotransferase family / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-T4K / 4-dehydrase
Similarity search - Component
Biological speciesStreptomyces venezuelae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBurgie, E.S. / Holden, H.M.
CitationJournal: Biochemistry / Year: 2007
Title: Molecular Architecture of DesI: A Key Enzyme in the Biosynthesis of Desosamine
Authors: Burgie, E.S. / Holden, H.M.
History
DepositionApr 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 4-dehydrase
B: 4-dehydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,5134
Polymers90,9602
Non-polymers1,5532
Water10,683593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.5, 66.8, 242.0
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121
DetailsThe asymmetric unit contains one homodimer comprising subunits A and B

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Components

#1: Protein 4-dehydrase


Mass: 45480.098 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces venezuelae (bacteria) / Gene: desI / Plasmid: pET31b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): HMS 174 DE3 / References: UniProt: Q9ZGH0
#2: Chemical ChemComp-T4K / (2R,3R,4S,5S,6R)-3,4-DIHYDROXY-5-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)IMINO]-6-METHYLTETRAHYDRO-2H-PYRAN-2-YL [(2R,3S,5R)-3-HYDROXY-5-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)TETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN DIPHOSPHATE


Mass: 776.471 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H35N4O19P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 593 / 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: 2.64 Å3/Da / Density % sol: 53.45 %
Crystal growTemperature: 293 K / Method: sitting drop (batch) / pH: 8
Details: 7 mg/ml DesI, 75 mM NaCl, 150 mM LiCl, 14%PEG 8000, 10 mM dTDP-4-amino-4,6-dideoxy-alpha,D-glucose, 5 mM HEPES, 50 mM HEPPS, pH 8.0, Sitting drop (batch), temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Feb 19, 2007 / Details: Montel
RadiationMonochromator: Nickel filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.08→50 Å / Num. all: 59056 / Num. obs: 56057 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 16
Reflection shellResolution: 2.08→2.18 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.4 / Num. unique all: 7630 / Rsym value: 0.35 / % possible all: 73.4

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Processing

Software
NameClassification
PROTEUM PLUSdata collection
PHASERphasing
TNTrefinement
SAINTdata reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2OGA

2oga


Resolution: 2.1→44.84 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.248 5599 -random
Rwork0.18 ---
all0.184 57438 --
obs0.184 55830 97.2 %-
Refinement stepCycle: LAST / Resolution: 2.1→44.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5942 0 100 593 6635
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.27
X-RAY DIFFRACTIONt_bond_d0.011
X-RAY DIFFRACTIONt_trig_c_planes0.008
X-RAY DIFFRACTIONt_gen_planes0.008

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