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- PDB-1sb9: Crystal structure of Pseudomonas aeruginosa UDP-N-acetylglucosami... -

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Basic information

Entry
Database: PDB / ID: 1sb9
TitleCrystal structure of Pseudomonas aeruginosa UDP-N-acetylglucosamine 4-epimerase complexed with UDP-glucose
ComponentswbpP
KeywordsISOMERASE / WbpP / epimerase / 4-epimerase / UDP-GlcNAc / SDR / GalE / NAD / SYK / pseudomonas aeruginosa / UDP / N-acetylglucosamine / UDP-Glc / glucose / galactose
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-5'-DIPHOSPHATE-GLUCOSE / : / WbpP
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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

Downloads & links

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Assembly

Deposited unit
A: wbpP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3103
Polymers39,0801
Non-polymers1,2302
Water2,558142
1
A: wbpP
hetero molecules

A: wbpP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,6196
Polymers78,1602
Non-polymers2,4594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area6820 Å2
ΔGint-41 kcal/mol
Surface area25480 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)60.989, 95.704, 141.165
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


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 566.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N2O17P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.69 Å3/Da / Density % sol: 53.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: PEG 600, phosphate-citrate buffer , pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 24, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.5→45.32 Å / Num. all: 14683 / Num. obs: 14274 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 30.5 Å2 / Rsym value: 0.096 / Net I/σ(I): 7.8
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 5.6 % / Num. unique all: 1458 / Rsym value: 0.38 / % possible all: 91.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XEL

1xel


Resolution: 2.5→45.32 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 341340.93 / Data cutoff high rms absF: 341340.93 / 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
Rfree0.255 1429 10 %RANDOM
Rwork0.195 ---
all-14683 --
obs-14274 97.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.9454 Å2 / ksol: 0.392513 e/Å3
Displacement parametersBiso mean: 33.1 Å2
Baniso -1Baniso -2Baniso -3
1-19.28 Å20 Å20 Å2
2---11.31 Å20 Å2
3----7.97 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2.5→45.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2654 0 80 142 2876
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_mcbond_it1.161.5
X-RAY DIFFRACTIONc_mcangle_it1.862
X-RAY DIFFRACTIONc_scbond_it1.952
X-RAY DIFFRACTIONc_scangle_it2.782.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.265 220 9.8 %
Rwork0.196 2021 -
obs-2241 93 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2NAD_NI.PARNAD_NI.TOP
X-RAY DIFFRACTION3UPG_NI.PARUPG_NI.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMWATER.TOP

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