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- PDB-4j09: Crystal Structure of LpxA bound to RJPXD33 -

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Basic information

Entry
Database: PDB / ID: 4j09
TitleCrystal Structure of LpxA bound to RJPXD33
Components
  • Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
  • Putative metabolite transport protein YjhB
KeywordsTRANSFERASE / acyltransferase / left-handed beta helix
Function / homology
Function and homology information


carboxylic acid transport / acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase / acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase activity / carboxylic acid transmembrane transporter activity / lipid A biosynthetic process / membrane => GO:0016020 / identical protein binding / plasma membrane / 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. / Major facilitator superfamily / Major Facilitator Superfamily ...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. / Major facilitator superfamily / Major Facilitator Superfamily / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / MFS transporter superfamily / 3 Solenoid / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase / Putative metabolite transport protein YjhB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsJenkins, R.J. / Meagher, J.L. / Stuckey, J.A. / Dotson, G.D.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structural Basis for the Recognition of Peptide RJPXD33 by Acyltransferases in Lipid A Biosynthesis.
Authors: Jenkins, R.J. / Heslip, K.A. / Meagher, J.L. / Stuckey, J.A. / Dotson, G.D.
History
DepositionJan 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2014Group: Database references
Revision 1.2Jun 18, 2014Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
B: Putative metabolite transport protein YjhB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3588
Polymers28,8712
Non-polymers4876
Water3,657203
1
A: Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
B: Putative metabolite transport protein YjhB
hetero molecules

A: Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
B: Putative metabolite transport protein YjhB
hetero molecules

A: Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
B: Putative metabolite transport protein YjhB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,07424
Polymers86,6136
Non-polymers1,46218
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area13070 Å2
ΔGint-80 kcal/mol
Surface area28250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.399, 96.399, 96.399
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#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) / Strain: K-12 / Gene: b0181, JW0176, lpxA / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(AI)
References: UniProt: P0A722, acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
#2: Protein/peptide Putative metabolite transport protein YjhB


Mass: 753.907 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: peptide synthesis / Source: (synth.) Escherichia coli (E. coli) / References: UniProt: P39352

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Non-polymers , 4 types, 209 molecules

#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 2.59 Å3/Da / Density % sol: 52.43 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 6.5
Details: 1.4 M Potassium Phosphate, 33% DMSO, pH 6.5, VAPOR DIFFUSION, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: Marmosaic 300 / Detector: CCD / Date: Apr 26, 2011 / Details: mirrors
RadiationMonochromator: Diamond (111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.9→48.2 Å / Num. all: 23834 / Num. obs: 23751 / % possible obs: 99.65 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 27.87 Å2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASERphasing
BUSTER-TNTBUSTER 2.10.0refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→21.46 Å / Cor.coef. Fo:Fc: 0.9588 / Cor.coef. Fo:Fc free: 0.9565 / Occupancy max: 1 / Occupancy min: 1 / SU R Cruickshank DPI: 0.131 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1771 1216 5.12 %RANDOM
Rwork0.172 ---
obs0.1723 23735 99.68 %-
all-23834 --
Displacement parametersBiso mean: 30.46 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→21.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2011 0 27 203 2241
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0112131HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.082909HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d974SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes46HARMONIC2
X-RAY DIFFRACTIONt_gen_planes325HARMONIC5
X-RAY DIFFRACTIONt_it2131HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.3
X-RAY DIFFRACTIONt_other_torsion2.61
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion281SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2655SEMIHARMONIC4
LS refinement shellResolution: 1.9→1.98 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.1944 149 5.24 %
Rwork0.1637 2697 -
all0.1654 2846 -
obs--99.68 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.01620.02970.361400.15140.0968-0.00020.00650.0007-0.00350.0010.00470.0043-0.0046-0.0008-0.0047-0.002-0.04250.0229-0.0074-0.0211-9.71491.7182-18.6411
20.9970.2848-0.00541.3580.19930.54310.01070.0580.09610.01820.0084-0.00180.00360.0064-0.0191-0.05560.02060.0043-0.02050.0291-0.03112.422216.763-3.8408
30.41860.7548-0.43310.90410.00090.0495-0.0012-0.00380.03220.0316-0.0022-0.0019-0.011900.0035-0.0887-0.0230.01-0.0407-0.00130.105916.773738.9129-0.38
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|1 - 16}A1 - 16
2X-RAY DIFFRACTION2{A|17 - 203}A17 - 203
3X-RAY DIFFRACTION3{A|204 - 262}A204 - 262

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