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- PDB-2h1h: E. coli heptosyltransferase WaaC with ADP-2-deoxy-2-fluoro heptose -

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Basic information

Entry
Database: PDB / ID: 2h1h
TitleE. coli heptosyltransferase WaaC with ADP-2-deoxy-2-fluoro heptose
ComponentsLipopolysaccharide heptosyltransferase 1
KeywordsTRANSFERASE / Gt-B fold / absence of C-terminal alpha-helix
Function / homology
Function and homology information


ADP-heptose-lipopolysaccharide heptosyltransferase activity / lipopolysaccharide heptosyltransferase activity / Transferases / lipopolysaccharide core region biosynthetic process / 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
ADENOSINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUORO HEPTOSE / Lipopolysaccharide heptosyltransferase 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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
DepositionMay 16, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 30, 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
Remark 999SEQUENCE The difference in the sequence is due to the strain K1 (private strain) used in the study

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,9344
Polymers74,6912
Non-polymers1,2432
Water77543
1
A: Lipopolysaccharide heptosyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9672
Polymers37,3461
Non-polymers6211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lipopolysaccharide heptosyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9672
Polymers37,3461
Non-polymers6211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.530, 88.900, 90.800
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: 37345.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: RS218 / Gene: rfaC, rfa-2, waaC / Plasmid: pET-30b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P24173, Transferases
#2: Chemical ChemComp-AFH / ADENOSINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUORO HEPTOSE / [(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL (2S,3R,4S,5S,6R)-6-[(1S)-1,2-DIHYDROXYETHYL]-3-FLUORO-4,5-DIHYDROXYTETRAHYDRO-2H-PYRAN-2-YL DIHYDROGEN DIPHOSPHATE


Mass: 621.359 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H26FN5O15P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 42.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7
Details: 15% PEG 1500, 100 mM Hepes, 100 mM NaCl, 1 mM ADP-2F-heptose, pH 7.0, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9798 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 14, 2005 / Details: curvated mirrors
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 25227 / Num. obs: 25116 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rsym value: 0.106 / Net I/σ(I): 15.6
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 1645 / Rsym value: 0.417 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT2data extraction
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GT1

2gt1


Resolution: 2.4→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.269 1244 5 %RANDOM
Rwork0.222 ---
all-25114 --
obs-25058 99.8 %-
Solvent computationBsol: 20.846 Å2
Displacement parametersBiso mean: 31.536 Å2
Baniso -1Baniso -2Baniso -3
1-0.368 Å20 Å20 Å2
2--0.358 Å20 Å2
3----0.726 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5020 0 80 43 5143
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.373
LS refinement shellResolution: 2.4→2.51 Å
RfactorNum. reflection
Rfree0.351 150
Rwork0.273 -
obs-3079
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3afh.par

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