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- PDB-3dr4: GDP-perosamine synthase K186A mutant from Caulobacter crescentus ... -

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Basic information

Entry
Database: PDB / ID: 3dr4
TitleGDP-perosamine synthase K186A mutant from Caulobacter crescentus with bound sugar ligand
ComponentsPutative perosamine synthetase
KeywordsTRANSFERASE / Perosamine / deoxysugar / pyridoxal phosphate / aspartate aminotransferase / o-antigen
Function / homology
Function and homology information


GDP-perosamine synthase / GDP-4-dehydro-6-deoxy-D-mannose-4-aminotransferase activity / O antigen biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
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 ...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-G4M / GDP-perosamine synthase / GDP-perosamine synthase
Similarity search - Component
Biological speciesCaulobacter crescentus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsHolden, H.M. / Cook, P.D. / Carney, A.E.
CitationJournal: Biochemistry / Year: 2008
Title: Accommodation of GDP-linked sugars in the active site of GDP-perosamine synthase
Authors: Cook, P.D. / Carney, A.E. / Holden, H.M.
History
DepositionJul 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 28, 2021Group: Database references / Derived calculations ...Database references / Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / refine ...entity_src_gen / refine / struct_ref_seq_dif / struct_site
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _refine.ls_percent_reflns_obs ..._entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _refine.ls_percent_reflns_obs / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 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: Putative perosamine synthetase
B: Putative perosamine synthetase
C: Putative perosamine synthetase
D: Putative perosamine synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,32610
Polymers171,9244
Non-polymers3,4026
Water22,6811259
1
A: Putative perosamine synthetase
B: Putative perosamine synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,7256
Polymers85,9622
Non-polymers1,7634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8550 Å2
ΔGint-49.5 kcal/mol
Surface area24550 Å2
MethodPISA
2
C: Putative perosamine synthetase
D: Putative perosamine synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,6014
Polymers85,9622
Non-polymers1,6392
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8170 Å2
ΔGint-54.4 kcal/mol
Surface area25010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.099, 151.921, 105.747
Angle α, β, γ (deg.)90.00, 102.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Putative perosamine synthetase


Mass: 42980.969 Da / Num. of mol.: 4 / Mutation: K186A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter crescentus (bacteria) / Strain: CB15 / Gene: per / Plasmid: pET28T / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174 / References: UniProt: O85354, UniProt: Q9A9H3*PLUS
#2: Chemical
ChemComp-G4M / [(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S,5S,6R)-3,4-dihydroxy-5-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]-6-methyltetrahydro-2H-pyran-2-yl dihydrogen diphosphate


Mass: 819.499 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H36N7O19P3
#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.: 1259 / 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: 2.29 Å3/Da / Density % sol: 46.26 %
Crystal growTemperature: 298 K / Method: batch / pH: 6.5
Details: 50 mM MES, 10% PEG 8000, 1 mM PLP, 1mM glutamate, pH 6.5, batch, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97 Å
DetectorType: SBC-3 / Detector: CCD / Date: Feb 8, 2008
RadiationMonochromator: Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 202983 / Num. obs: 186452 / % possible obs: 91.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rsym value: 0.041 / Net I/σ(I): 11.5
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 7.6 / Num. unique all: 16930 / Rsym value: 0.214 / % possible all: 83.8

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Processing

Software
NameClassification
EPMRphasing
TNTrefinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3bn1

3bn1


Resolution: 1.6→26.2 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.238 18930 -random
Rwork0.166 ---
all0.169 202880 --
obs-186447 91.1 %-
Refinement stepCycle: LAST / Resolution: 1.6→26.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11299 0 220 1259 12778
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.01
X-RAY DIFFRACTIONt_bond_d0.013
X-RAY DIFFRACTIONt_dihedral_angle_d16.4

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