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- PDB-2iua: C. trachomatis LpxD -

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Basic information

Entry
Database: PDB / ID: 2iua
TitleC. trachomatis LpxD
ComponentsUDP-3-O-[3-HYDROXYMYRISTOYL] GLUCOSAMINE N-ACYLTRANSFERASE
KeywordsTRANSFERASE / UDP-3- O-ACYL-GLUCOSAMINE N-ACYLTRANSFERASE / LEFT-HANDED BETA HELIX / ACYLTRANSFERASE / LIPID A BIOSYNTHESIS / 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 proteins / Hexapeptide repeat / 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 proteins / Hexapeptide repeat / 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
PALMITIC ACID / 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: 2.7 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 / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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)123,62115
Polymers121,8883
Non-polymers1,73312
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)98.679, 98.679, 284.505
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(0.5174, -0.2711, 0.8116), (0.7095, -0.3943, -0.584), (0.4784, 0.8781, -0.01165)26.26, -193.1, 26.83
2given(0.4633, 0.7305, 0.5016), (-0.2412, -0.4407, 0.8646), (0.8527, -0.5216, -0.02803)115.6, -98.97, -129.1
3given(0.4834, 0.712, 0.5093), (-0.2044, -0.4739, 0.8565), (0.8512, -0.5181, -0.08355)113.6, -103.5, -131.2

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Components

#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
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.99 Å3/Da / Density % sol: 58.54 %
Crystal growpH: 6.5
Details: PROTEIN WAS CRYSTALLIZED FROM 1.2M AMMONIUM SULFATE, 0.1M MES, PH 6.5, 2% PEG 400, AND 1MM DTT.

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU-MSC R-AXIS-4++ / Detector: IMAGE PLATE / Date: Mar 1, 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: 2.7→40 Å / Num. obs: 38280 / % possible obs: 96.5 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.3
Reflection shellResolution: 2.7→2.78 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2 / % possible all: 90.4

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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: 2.7→93.25 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.885 / SU B: 13.262 / SU ML: 0.271 / Cross valid method: THROUGHOUT / ESU R: 0.933 / ESU R Free: 0.362 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1910 5 %RANDOM
Rwork0.209 ---
obs0.212 36293 96.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.55 Å2
Baniso -1Baniso -2Baniso -3
1-1.06 Å20 Å20 Å2
2--1.06 Å20 Å2
3----2.12 Å2
Refinement stepCycle: LAST / Resolution: 2.7→93.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7911 0 106 154 8171
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0228261
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3871.95211163
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.50851036
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.77523.807352
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.112151433
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6591549
X-RAY DIFFRACTIONr_chiral_restr0.0910.21279
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026084
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2190.24179
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.25570
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2395
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.267
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2140.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5781.55246
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.02928335
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.18733245
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.9584.52827
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: 2.7→2.77 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.387 125
Rwork0.285 2416

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