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- PDB-2iu9: Chlamydia trachomatis LpxD with 100mM UDPGlcNAc (Complex II) -

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Basic information

Entry
Database: PDB / ID: 2iu9
TitleChlamydia trachomatis LpxD with 100mM UDPGlcNAc (Complex II)
ComponentsUDP-3-O-[3-HYDROXYMYRISTOYL] GLUCOSAMINE N-ACYLTRANSFERASE
KeywordsTRANSFERASE / UDP-3- O-ACYL-GLUCOSAMINE N-ACYLTRANSFERASE / ACYLTRANSFERASE / LIPID A BIOSYNTHESIS / LEFT-HANDED BETA HELIX / COMPLEX WITH UDPGLCNAC / ENZYME / HOMOTRIMER / LIPID SYNTHESIS
Function / homology
Function and homology information


UDP-3-O-(3-hydroxyacyl)glucosamine N-acyltransferase / N-acyltransferase activity / lipid A biosynthetic process / membrane
Similarity search - Function
UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase LpxD / UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, non-repeat region / UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD / MurE/MurF, N-terminal domain / Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Hexapeptide repeat / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Bacterial transferase hexapeptide (six repeats) ...UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase LpxD / UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, non-repeat region / UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD / MurE/MurF, N-terminal domain / Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Hexapeptide repeat / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / PALMITIC ACID / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / UDP-3-O-acylglucosamine N-acyltransferase / UDP-3-O-acylglucosamine N-acyltransferase
Similarity search - Component
Biological speciesCHLAMYDIA TRACHOMATIS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsBuetow, L. / Smith, T.K. / Dawson, A. / Fyffe, S. / Hunter, W.N.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2007
Title: Structure and Reactivity of Lpxd, the N-Acyltransferase of Lipid a Biosynthesis
Authors: Buetow, L. / Smith, T.K. / Dawson, A. / Fyffe, S. / Hunter, W.N.
History
DepositionMay 30, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 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_conn
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_conn.pdbx_leaving_atom_flag
Revision 1.4Oct 1, 2025Group: Derived calculations / Structure summary / Category: pdbx_entry_details / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-3-O-[3-HYDROXYMYRISTOYL] GLUCOSAMINE N-ACYLTRANSFERASE
B: UDP-3-O-[3-HYDROXYMYRISTOYL] GLUCOSAMINE N-ACYLTRANSFERASE
C: UDP-3-O-[3-HYDROXYMYRISTOYL] GLUCOSAMINE N-ACYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,52615
Polymers121,8883
Non-polymers2,63812
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)98.871, 98.872, 283.053
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.5021, -0.2844, 0.8167), (0.7161, -0.3927, -0.577), (0.4848, 0.8746, 0.006493)25.79, -193.2, 27.33
2given(0.4425, 0.7393, 0.5076), (-0.2444, -0.4452, 0.8614), (0.8628, -0.5053, -0.01635)117.9, -99.8, -127.8
3given(0.4768, 0.7171, 0.5084), (-0.21, -0.4687, 0.858), (0.8536, -0.5159, -0.07292)114.6, -103.2, -130.6

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein UDP-3-O-[3-HYDROXYMYRISTOYL] GLUCOSAMINE N-ACYLTRANSFERASE / LPXD


Mass: 40629.332 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CHLAMYDIA TRACHOMATIS (bacteria) / Variant: SEROVAR B / Plasmid: PET 15B (NOVAGEN) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O84245, UniProt: P0CD76*PLUS, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups

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Non-polymers , 5 types, 111 molecules

#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H32O2
#5: Chemical ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 607.354 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H27N3O17P2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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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: 2.99 Å3/Da / Density % sol: 58.5 %
Crystal growpH: 6.5
Details: PROTEIN INCUBATED WITH 100MM UDPGLCNAC AND CRYSTALLIZED FROM 1.2M AMMONIUM SULFATE, 0.1M MES, PH 6.5, 2% DIOXANE, 1MM TCEP, AND 2MM UDPGLCNAC.

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU R-AXIS IV / Detector: IMAGE PLATE / Date: Aug 25, 2004 / Details: OSMIC MIRRORS
RadiationMonochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.1→28.5 Å / Num. obs: 26254 / % possible obs: 98.9 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 11.1
Reflection shellResolution: 3.1→3.19 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IU8

2iu8


Resolution: 3.1→28.5 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.89 / SU B: 46.63 / SU ML: 0.407 / Cross valid method: THROUGHOUT / ESU R Free: 0.513 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.281 1323 5.1 %RANDOM
Rwork0.221 ---
obs0.224 24769 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 76.21 Å2
Baniso -1Baniso -2Baniso -3
1-3.87 Å20 Å20 Å2
2--3.87 Å20 Å2
3----7.73 Å2
Refinement stepCycle: LAST / Resolution: 3.1→28.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7911 0 166 99 8176
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0228319
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0391.96211256
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.18351034
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.1823.955354
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.727151424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8111547
X-RAY DIFFRACTIONr_chiral_restr0.0710.21302
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.026110
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1880.24195
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.25586
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2323
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1460.264
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1931.55267
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.34228338
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.40233310
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.6924.52918
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: 3.1→3.18 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.396 104
Rwork0.294 1787

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