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- PDB-1f6d: THE STRUCTURE OF UDP-N-ACETYLGLUCOSAMINE 2-EPIMERASE FROM E. COLI. -

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Basic information

Entry
Database: PDB / ID: 1f6d
TitleTHE STRUCTURE OF UDP-N-ACETYLGLUCOSAMINE 2-EPIMERASE FROM E. COLI.
ComponentsUDP-N-ACETYLGLUCOSAMINE 2-EPIMERASE
KeywordsISOMERASE / sugar-nucleotide epimerase / Rossmann fold / two domains / glycogen phosphorylase superfamily / UDP / dimer
Function / homology
Function and homology information


enterobacterial common antigen biosynthetic process / UDP-N-acetylglucosamine 2-epimerase (non-hydrolysing) / UDP-N-acetylglucosamine 2-epimerase activity / protein homodimerization activity / cytosol
Similarity search - Function
UDP-N-acetylglucosamine 2-epimerase WecB / UDP-N-acetylglucosamine 2-epimerase WecB-like / UDP-N-acetylglucosamine 2-epimerase domain / UDP-N-acetylglucosamine 2-epimerase / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE / UDP-N-acetylglucosamine 2-epimerase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsCampbell, R.E. / Mosimann, S.C. / Tanner, M.E. / Strynadka, N.C.J.
CitationJournal: Biochemistry / Year: 2000
Title: The structure of UDP-N-acetylglucosamine 2-epimerase reveals homology to phosphoglycosyl transferases.
Authors: Campbell, R.E. / Mosimann, S.C. / Tanner, M.E. / Strynadka, N.C.
History
DepositionJun 21, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-N-ACETYLGLUCOSAMINE 2-EPIMERASE
B: UDP-N-ACETYLGLUCOSAMINE 2-EPIMERASE
C: UDP-N-ACETYLGLUCOSAMINE 2-EPIMERASE
D: UDP-N-ACETYLGLUCOSAMINE 2-EPIMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,91216
Polymers171,0624
Non-polymers1,85012
Water13,781765
1
A: UDP-N-ACETYLGLUCOSAMINE 2-EPIMERASE
B: UDP-N-ACETYLGLUCOSAMINE 2-EPIMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,4568
Polymers85,5312
Non-polymers9256
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-83 kcal/mol
Surface area30750 Å2
MethodPISA
2
C: UDP-N-ACETYLGLUCOSAMINE 2-EPIMERASE
D: UDP-N-ACETYLGLUCOSAMINE 2-EPIMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,4568
Polymers85,5312
Non-polymers9256
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-83 kcal/mol
Surface area30740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.008, 94.541, 100.970
Angle α, β, γ (deg.)90.00, 109.13, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe asymetric unit contains two copies of the biological assembly which is a dimer constructed from chains A and B or chains C and D.

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Components

#1: Protein
UDP-N-ACETYLGLUCOSAMINE 2-EPIMERASE / UDP-GLCNAC-2-EPIMERASE / BACTERIOPHAGE N4 ADSORPTION PROTEIN C


Mass: 42765.441 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PKI86 / Production host: Escherichia coli (E. coli)
References: UniProt: P27828, UDP-N-acetylglucosamine 2-epimerase (non-hydrolysing)
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 765 / 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: 2.4 Å3/Da / Density % sol: 48.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.3
Details: 13 % PEG 8000, 0.3 M NaCl, 0.1 M sodium citrate, pH 5.3, VAPOR DIFFUSION, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14 mg/mlprotein1drop
213 %PEG80001reservoir
30.3 Msodium chloride1reservoir
40.1 Msodium citrate1reservoir
50.1 MUDP-GlcNAc1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONNSLS X12C10.979
SYNCHROTRONNSLS X12C20.9787
SYNCHROTRONNSLS X12C30.94
Detector
TypeIDDetectorDate
BRANDEIS1CCDFeb 20, 1999
BRANDEIS2CCDFeb 20, 1999
BRANDEIS3CCDFeb 20, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.97871
30.941
ReflectionResolution: 2.5→30 Å / Num. all: 50792 / Num. obs: 50775 / % possible obs: 93.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 29.3 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 21.6
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.21 / Num. unique all: 2386 / % possible all: 89
Reflection
*PLUS
Num. measured all: 163518
Reflection shell
*PLUS
% possible obs: 89 % / Num. possible: 6804 / Num. unique obs: 2386 / Mean I/σ(I) obs: 3.6

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.5→30.32 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2116010.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Structure was refined against the remote wavelenght data set (0.9400)
RfactorNum. reflection% reflectionSelection details
Rfree0.271 4955 10.1 %RANDOM
Rwork0.198 ---
all0.198 50775 --
obs0.198 49090 87.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.11 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 35.8 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.5→30.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11801 0 108 765 12674
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_mcbond_it1.411.5
X-RAY DIFFRACTIONc_mcangle_it2.392
X-RAY DIFFRACTIONc_scbond_it2.032
X-RAY DIFFRACTIONc_scangle_it2.932.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.332 670 10.5 %
Rwork0.255 5693 -
obs--68.3 %
Xplor fileSerial no: 1 / Param file: UGE_REFI.PARAM / Topol file: UGE_REFI.TOPOLOGY
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.94

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