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- PDB-2iu8: Chlamydia trachomatis LpxD with 25mM UDPGlcNAc (Complex I) -

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Basic information

Entry
Database: PDB / ID: 2iu8
TitleChlamydia trachomatis LpxD with 25mM UDPGlcNAc (Complex I)
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 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
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
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)123,98115
Polymers121,8883
Non-polymers2,09312
Water8,917495
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)98.805, 98.805, 283.082
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(0.5116, -0.2776, 0.8132), (0.7121, -0.3927, -0.582), (0.4809, 0.8768, -0.003197)25.9, -193.3, 27.15
2given(0.4546, 0.7373, 0.4997), (-0.245, -0.4359, 0.866), (0.8563, -0.5161, -0.01755)116.7, -98.55, -128.5
3given(0.4792, 0.7136, 0.511), (-0.2165, -0.4681, 0.8567), (0.8506, -0.5212, -0.06981)114.2, -103, -130.9

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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 , 6 types, 507 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 256.424 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H32O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#6: Chemical ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


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


Mass: 18.015 Da / Num. of mol.: 495 / 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: 2.84 Å3/Da / Density % sol: 56.35 %
Description: MOLECULAR REPLACEMENT WAS DONE USING A MODEL OBTAINED FROM A SAD EXPERIMENT ON A SELENOMETHIONINE- INCORPORATED CRYSTAL.
Crystal growpH: 6.5
Details: PROTEIN INCUBATED WITH 25MM UDPGLCNAC AND CRYSTALLIZED FROM 1.3M AMMONIUM SULFATE, 0.1M MES, PH 6.5, 2% PEG 400, AND 1MM TCEP.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97563
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 7, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97563 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 65635 / % possible obs: 91.1 % / Redundancy: 4.3 % / Biso Wilson estimate: 47.8 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.9
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.3 / % possible all: 95.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / SU B: 17.086 / SU ML: 0.207 / Cross valid method: THROUGHOUT / ESU R: 0.27 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.256 3302 5.1 %RANDOM
Rwork0.206 ---
obs0.209 61869 90.4 %-
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: 61.87 Å2
Baniso -1Baniso -2Baniso -3
1-3.71 Å20 Å20 Å2
2--3.71 Å20 Å2
3----7.41 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7911 0 131 495 8537
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0228336
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3441.95711264
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.34951034
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.73523.944360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.933151447
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5481549
X-RAY DIFFRACTIONr_chiral_restr0.0870.21299
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026122
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.24203
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.25564
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2532
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.297
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4561.55294
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.70928362
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.11533313
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.6664.52902
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: 2.2→2.26 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.379 239
Rwork0.325 4688

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