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- PDB-2gt1: E. coli heptosyltransferase WaaC. -

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Basic information

Entry
Database: PDB / ID: 2gt1
TitleE. coli heptosyltransferase WaaC.
ComponentsLipopolysaccharide heptosyltransferase-1
KeywordsTRANSFERASE / Gt-B fold
Function / homology
Function and homology information


lipopolysaccharide heptosyltransferase I / ADP-heptose-lipopolysaccharide heptosyltransferase activity / lipopolysaccharide core region biosynthetic process / plasma membrane / cytosol
Similarity search - Function
Lipopolysaccharide heptosyltransferase I / : / Glycosyl transferase, family 9 / Glycosyltransferase family 9 (heptosyltransferase) / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Lipopolysaccharide heptosyltransferase 1
Similarity search - Component
Biological speciesEscherichia coli UTI89 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsGrizot, S. / Salem, M. / Vongsouthi, V. / Durand, L. / Moreau, F. / Dohi, H. / Vincent, S. / Escaich, S. / Ducruix, A.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structure of the Escherichia coli Heptosyltransferase WaaC: Binary Complexes with ADP AND ADP-2-deoxy-2-fluoro Heptose.
Authors: Grizot, S. / Salem, M. / Vongsouthi, V. / Durand, L. / Moreau, F. / Dohi, H. / Vincent, S. / Escaich, S. / Ducruix, A.
History
DepositionApr 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipopolysaccharide heptosyltransferase-1
B: Lipopolysaccharide heptosyltransferase-1


Theoretical massNumber of molelcules
Total (without water)72,5492
Polymers72,5492
Non-polymers00
Water7,062392
1
A: Lipopolysaccharide heptosyltransferase-1


Theoretical massNumber of molelcules
Total (without water)36,2751
Polymers36,2751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lipopolysaccharide heptosyltransferase-1


Theoretical massNumber of molelcules
Total (without water)36,2751
Polymers36,2751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.650, 88.790, 89.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Lipopolysaccharide heptosyltransferase-1


Mass: 36274.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli UTI89 (bacteria) / Species: Escherichia coli / Strain: RS218 / Plasmid: BL21(DE3) / Production host: Escherichia coli (E. coli) / References: GenBank: 91213139, UniProt: Q1R4X0*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / 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: 2.16 Å3/Da / Density % sol: 43.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7
Details: 15% PEG 1500, 100 mM Hepes (pH 7.O), 100 mM NaCl, pH 7.0, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 30, 2004
RadiationMonochromator: Diamond (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 49550 / Num. obs: 49489 / % possible obs: 99.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 26 Å2 / Rsym value: 0.076 / Net I/σ(I): 22.4
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 4874 / Rsym value: 0.438 / % possible all: 99.6

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT1.701data extraction
ADSCdata collection
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.245 2507 5 %RANDOM
Rwork0.214 ---
all-49489 --
obs-49489 --
Solvent computationBsol: 40.875 Å2
Displacement parametersBiso mean: 31.442 Å2
Baniso -1Baniso -2Baniso -3
1--3.567 Å20 Å20 Å2
2--3.011 Å20 Å2
3---0.556 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4930 0 0 392 5322
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.441
LS refinement shellResolution: 1.9→1.99 Å
RfactorNum. reflection
Rfree0.272 283
Rwork0.232 -
obs-5552
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param

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