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- PDB-3hbn: Crystal structure PseG-UDP complex from Campylobacter jejuni -

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Basic information

Entry
Database: PDB / ID: 3hbn
TitleCrystal structure PseG-UDP complex from Campylobacter jejuni
ComponentsUDP-sugar hydrolase
KeywordsHYDROLASE / udp-sugar hydrolase / PseG
Function / homology
Function and homology information


UDP-2,4-diacetamido-2,4,6-trideoxy-beta-L-altropyranose hydrolase / hydrolase activity
Similarity search - Function
Rossmann fold - #11190 / UDP-2,4-diacetamido-2,4,6-trideoxy-beta-L-altropyranose hydrolase / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE / UDP-2,4-diacetamido-2,4,6-trideoxy-beta-L-altropyranose hydrolase
Similarity search - Component
Biological speciesCampylobacter jejuni subsp. jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsRangarajan, E.S. / Proteau, A. / Cygler, M. / Matte, A. / Sulea, T. / Schoenhofen, I.C.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structural and functional analysis of Campylobacter jejuni PseG: a udp-sugar hydrolase from the pseudaminic acid biosynthetic pathway.
Authors: Rangarajan, E.S. / Proteau, A. / Cui, Q. / Logan, S.M. / Potetinova, Z. / Whitfield, D. / Purisima, E.O. / Cygler, M. / Matte, A. / Sulea, T. / Schoenhofen, I.C.
History
DepositionMay 4, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UDP-sugar hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1965
Polymers32,5721
Non-polymers6244
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.442, 94.442, 43.566
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
DetailsMonomer

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Components

#1: Protein UDP-sugar hydrolase / Nucleotidase specific for PseC product / UDP-4-amino-4 / 6-dideoxy-beta-L-AltNAc


Mass: 32572.018 Da / Num. of mol.: 1 / Mutation: E155K
Source method: isolated from a genetically manipulated source
Details: C-term His tag (LEHHHHHH)
Source: (gene. exp.) Campylobacter jejuni subsp. jejuni (Campylobacter)
Strain: NCTC 11168 / Gene: PseG (Cj1312) / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q0P8U5
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.98 Å3/Da / Density % sol: 58.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Bis-Tris, 0.2M Ammonium sulfate, 23% (v/v) PEG monomethyl ether 550, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 29, 2006
RadiationMonochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.85→39.6 Å / Num. all: 32759 / Num. obs: 32741 / % possible obs: 98.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 6 % / Biso Wilson estimate: 30.4 Å2 / Rsym value: 0.056 / Net I/σ(I): 17
Reflection shellResolution: 1.85→1.92 Å / Mean I/σ(I) obs: 4.285 / Num. unique all: 2981 / % possible all: 91.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3HBM

3hbm


Resolution: 1.85→39.56 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.242 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.118 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20819 1631 5 %RANDOM
Rwork0.17707 ---
all0.194 32741 --
obs0.17866 31109 99.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.469 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å20 Å2
2--0.29 Å20 Å2
3----0.58 Å2
Refinement stepCycle: LAST / Resolution: 1.85→39.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2283 0 38 229 2550
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222389
X-RAY DIFFRACTIONr_angle_refined_deg1.251.9863222
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8115287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.63724.953107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.48915455
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.628157
X-RAY DIFFRACTIONr_chiral_restr0.0870.2357
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021741
X-RAY DIFFRACTIONr_mcbond_it0.7171.51419
X-RAY DIFFRACTIONr_mcangle_it1.37622297
X-RAY DIFFRACTIONr_scbond_it2.0683970
X-RAY DIFFRACTIONr_scangle_it3.4694.5923
LS refinement shellResolution: 1.852→1.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 102 -
Rwork0.213 2062 -
obs-2062 89.61 %

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