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- PDB-2jf3: Nucleotide substrate binding by UDP-N-acetylglucosamine acyltrans... -

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Basic information

Entry
Database: PDB / ID: 2jf3
TitleNucleotide substrate binding by UDP-N-acetylglucosamine acyltransferase
ComponentsACYL-[ACYL-CARRIER-PROTEIN]--UDP-N-ACETYLGLUCOSAMINE O-ACYLTRANSFERASE
KeywordsTRANSFERASE / LIPID A BIOSYNTHESIS / ACYLTRANSFERASE / LIPID SYNTHESIS
Function / homology
Function and homology information


acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase / acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase activity / lipid A biosynthetic process / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Udp N-acetylglucosamine O-acyltransferase; Domain 2 / Udp N-acetylglucosamine O-acyltransferase, C-terminal domain / UDP N-acetylglucosamine O-acyltransferase, C-terminal / UDP-N-acetylglucosamine O-acyltransferase, C-terminal domain superfamily / Udp N-acetylglucosamine O-acyltransferase; Domain 2 / Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat proteins / Hexapeptide repeat ...Udp N-acetylglucosamine O-acyltransferase; Domain 2 / Udp N-acetylglucosamine O-acyltransferase, C-terminal domain / UDP N-acetylglucosamine O-acyltransferase, C-terminal / UDP-N-acetylglucosamine O-acyltransferase, C-terminal domain superfamily / Udp N-acetylglucosamine O-acyltransferase; Domain 2 / Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat proteins / Hexapeptide repeat / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsUlaganathan, V. / Buetow, L. / Hunter, W.N.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Nucleotide Substrate Recognition by Udp-N-Acetylglucosamine Acyltransferase (Lpxa) in the First Step of Lipid a Biosynthesis.
Authors: Ulaganathan, V. / Buetow, L. / Hunter, W.N.
History
DepositionJan 25, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2013Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Source and taxonomy / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: ACYL-[ACYL-CARRIER-PROTEIN]--UDP-N-ACETYLGLUCOSAMINE O-ACYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7242
Polymers28,1171
Non-polymers6071
Water52229
1
A: ACYL-[ACYL-CARRIER-PROTEIN]--UDP-N-ACETYLGLUCOSAMINE O-ACYLTRANSFERASE
hetero molecules

A: ACYL-[ACYL-CARRIER-PROTEIN]--UDP-N-ACETYLGLUCOSAMINE O-ACYLTRANSFERASE
hetero molecules

A: ACYL-[ACYL-CARRIER-PROTEIN]--UDP-N-ACETYLGLUCOSAMINE O-ACYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,1736
Polymers84,3513
Non-polymers1,8223
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation5_555z,x,y1
Buried area8300 Å2
ΔGint-42.5 kcal/mol
Surface area29880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.740, 97.740, 97.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein ACYL-[ACYL-CARRIER-PROTEIN]--UDP-N-ACETYLGLUCOSAMINE O-ACYLTRANSFERASE / UDP-N-ACETYLGLUCOSAMINE ACYLTRANSFERASE


Mass: 28117.018 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0A722, acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
#2: Chemical ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


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


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.77 Å3/Da / Density % sol: 56 %
Crystal growpH: 6.5 / Details: 10% PEG 10000, 0.1M MES PH6.5, pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARRESEARCH / Detector: CCD / Date: May 20, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 3→69.17 Å / Num. obs: 6451 / % possible obs: 99.8 % / Observed criterion σ(I): 2.5 / Redundancy: 3.2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 7.6
Reflection shellResolution: 3→3.16 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LXA

1lxa


Resolution: 3→69.17 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.84 / SU B: 20.514 / SU ML: 0.381 / Cross valid method: THROUGHOUT / ESU R Free: 0.476 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27 299 4.6 %RANDOM
Rwork0.218 ---
obs0.22 6136 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.41 Å2
Refinement stepCycle: LAST / Resolution: 3→69.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1975 0 39 29 2043
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222058
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.941.9662794
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4955262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.86123.48389
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.44215329
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2981515
X-RAY DIFFRACTIONr_chiral_restr0.0610.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.021551
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1570.2927
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2940.21388
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3470.266
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1280.245
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1141.51326
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.20522079
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.0623800
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.1164.5714
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.08 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.235 23
Rwork0.275 459

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