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- PDB-3hbm: Crystal Structure of PseG from Campylobacter jejuni -

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Basic information

Entry
Database: PDB / ID: 3hbm
TitleCrystal Structure of PseG from Campylobacter jejuni
ComponentsUDP-sugar hydrolase
KeywordsHYDROLASE / udp-sugar hydrolase / PseG
Function / homologyRossmann fold - #11190 / UDP-2,4-diacetamido-2,4,6-trideoxy-beta-L-altropyranose hydrolase / UDP-2,4-diacetamido-2,4,6-trideoxy-beta-L-altropyranose hydrolase / Glycogen Phosphorylase B; / hydrolase activity / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / UDP-2,4-diacetamido-2,4,6-trideoxy-beta-L-altropyranose hydrolase
Function and homology information
Biological speciesCampylobacter jejuni subsp. jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 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 1.3Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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)32,6682
Polymers32,5721
Non-polymers961
Water4,972276
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.647, 93.647, 42.702
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 Histag (LEHHHHHH)
Source: (gene. exp.) Campylobacter jejuni subsp. jejuni (Campylobacter)
Strain: NCTC 11168 / Gene: Cj1312 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q0P8U5
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.87 Å3/Da / Density % sol: 57.21 %
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: X12B / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 28, 2006
RadiationMonochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.8→33.11 Å / Num. obs: 34208 / % possible obs: 98.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 7.4 % / Biso Wilson estimate: 31.4 Å2 / Rsym value: 0.073 / Net I/σ(I): 22.6
Reflection shellResolution: 1.8→1.87 Å / Redundancy: 2 % / Mean I/σ(I) obs: 8.4 / Num. unique all: 3377 / Rsym value: 0.114 / % possible all: 97.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXDEphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.8→33.11 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.929 / SU B: 2.485 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.122 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23458 1718 5 %RANDOM
Rwork0.19618 ---
all0.212 34203 --
obs0.1981 32485 98.84 %-
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: 24.736 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20 Å20 Å2
2--0.49 Å20 Å2
3----0.97 Å2
Refinement stepCycle: LAST / Resolution: 1.8→33.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2272 0 5 276 2553
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222321
X-RAY DIFFRACTIONr_angle_refined_deg1.2611.9733125
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9635279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.95625.143105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.17315446
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.201156
X-RAY DIFFRACTIONr_chiral_restr0.0920.2349
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021696
X-RAY DIFFRACTIONr_mcbond_it0.7591.51401
X-RAY DIFFRACTIONr_mcangle_it1.42422263
X-RAY DIFFRACTIONr_scbond_it2.4163920
X-RAY DIFFRACTIONr_scangle_it3.5974.5862
LS refinement shellResolution: 1.801→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 124 -
Rwork0.22 2356 -
obs-2356 97.37 %

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