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- PDB-1sb8: Crystal structure of Pseudomonas aeruginosa UDP-N-acetylglucosami... -

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Basic information

Entry
Database: PDB / ID: 1sb8
TitleCrystal structure of Pseudomonas aeruginosa UDP-N-acetylglucosamine 4-epimerase complexed with UDP-N-acetylgalactosamine
ComponentswbpP
KeywordsISOMERASE / WbpP / epimerase / 4-epimerase / UDP-GalNAc / UDP-GlcNAc / SDR / GalE / NAD / SYK / pseudomonas aeruginosa / UDP / N-acetylglucosamine / N-acetylgalactosamine / UDP-Glc
Function / homology
Function and homology information


UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE / : / WbpP
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsIshiyama, N. / Creuzenet, C. / Lam, J.S. / Berghuis, A.M.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Crystal Structure of WbpP, a Genuine UDP-N-acetylglucosamine 4-Epimerase from Pseudomonas aeruginosa: SUBSTRATE SPECIFICITY IN UDP-HEXOSE 4-EPIMERASES.
Authors: Ishiyama, N. / Creuzenet, C. / Lam, J.S. / Berghuis, A.M.
History
DepositionFeb 10, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: wbpP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3513
Polymers39,0801
Non-polymers1,2712
Water3,279182
1
A: wbpP
hetero molecules

A: wbpP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,7026
Polymers78,1602
Non-polymers2,5424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area7000 Å2
ΔGint-43 kcal/mol
Surface area25180 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)60.438, 95.877, 139.638
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly is a homodimer generated from the monomer in the asymmetric unit by the operation: x, -y, -z+1

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Components

#1: Protein wbpP


Mass: 39080.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: wbpP / Plasmid: pET23 derivative / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)pLysS
References: GenBank: 20560072, UniProt: Q8KN66*PLUS, UDP-N-acetylglucosamine 4-epimerase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-UD2 / URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE / (2R,3R,4R,5R,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate


Mass: 607.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27N3O17P2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.63 Å3/Da / Density % sol: 52.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: PEG 600, phosphate-citrate buffer, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.98
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 6, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.1→41.25 Å / Num. all: 24082 / Num. obs: 23213 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 11.9 Å2 / Rsym value: 0.083 / Net I/σ(I): 8.7
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 2271 / Rsym value: 0.328 / % possible all: 89.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: partially refined model of PDB entry 1SB9
Resolution: 2.1→41.25 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 145620.51 / Data cutoff high rms absF: 145620.51 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.228 2334 10.1 %RANDOM
Rwork0.19 ---
obs0.19 23213 96.3 %-
all-24082 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.1887 Å2 / ksol: 0.392563 e/Å3
Displacement parametersBiso mean: 22.3 Å2
Baniso -1Baniso -2Baniso -3
1-12.28 Å20 Å20 Å2
2---4.02 Å20 Å2
3----8.26 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 2.1→41.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2662 0 83 182 2927
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_mcbond_it1.211.5
X-RAY DIFFRACTIONc_mcangle_it1.832
X-RAY DIFFRACTIONc_scbond_it1.992
X-RAY DIFFRACTIONc_scangle_it2.832.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.264 358 10.1 %
Rwork0.204 3202 -
obs-3202 90.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2NAD_NI.PARNAD_NI.TOP
X-RAY DIFFRACTION3UD2_NI.PARUD2_NI.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMWATER.TOP

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