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- PDB-3pmo: The structure of LpxD from Pseudomonas aeruginosa at 1.3 A resolution -

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Basic information

Entry
Database: PDB / ID: 3pmo
TitleThe structure of LpxD from Pseudomonas aeruginosa at 1.3 A resolution
ComponentsUDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase
KeywordsTRANSFERASE / Lipid A biosynthesis pathway
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 / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Hexapeptide repeat proteins / Hexapeptide repeat ...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 / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / 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
UDP-3-O-acylglucosamine N-acyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsBadger, J. / Chie-Leon, B. / Logan, C. / Sridhar, V. / Sankaran, B. / Zwart, P.H. / Nienaber, V.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: The structure of LpxD from Pseudomonas aeruginosa at 1.3 A resolution.
Authors: Badger, J. / Chie-Leon, B. / Logan, C. / Sridhar, V. / Sankaran, B. / Zwart, P.H. / Nienaber, V.
History
DepositionNov 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4264
Polymers38,2661
Non-polymers1603
Water8,035446
1
A: UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase
hetero molecules

A: UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase
hetero molecules

A: UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,27712
Polymers114,7993
Non-polymers4799
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area21030 Å2
ΔGint-148 kcal/mol
Surface area38430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.190, 106.190, 93.380
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-450-

HOH

21A-477-

HOH

31A-509-

HOH

41A-517-

HOH

51A-597-

HOH

61A-654-

HOH

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Components

#1: Protein UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase


Mass: 38266.184 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: lpxD, PA3646 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9HXY6, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 446 / 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: 2.65 Å3/Da / Density % sol: 53.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10 mM Tris HCl, 1mM DTT, 500mM NaCl, 2 uL of 100 mM Tris, 1.5 M lithium sulfate, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 27, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→26.85 Å / Num. all: 96539 / Num. obs: 96539 / % possible obs: 99.9 % / Observed criterion σ(I): -4 / Redundancy: 9 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 14.1
Reflection shellResolution: 1.3→1.37 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.644 / Mean I/σ(I) obs: 3.2 / Num. unique all: 14084 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→26.85 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.125 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.18532 4827 5 %RANDOM
Rwork0.1644 ---
all0.16546 91655 --
obs0.16546 91655 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.634 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.3→26.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2577 0 9 446 3032
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0212715
X-RAY DIFFRACTIONr_angle_refined_deg1.1711.9463674
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.045357
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.15123.661112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.70915447
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4441519
X-RAY DIFFRACTIONr_chiral_restr0.0750.2418
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212043
X-RAY DIFFRACTIONr_mcbond_it0.99621754
X-RAY DIFFRACTIONr_mcangle_it1.5382.52806
X-RAY DIFFRACTIONr_scbond_it1.8313961
X-RAY DIFFRACTIONr_scangle_it2.8424.5867
X-RAY DIFFRACTIONr_rigid_bond_restr0.94832715
X-RAY DIFFRACTIONr_sphericity_free3.2423447
X-RAY DIFFRACTIONr_sphericity_bonded2.89432669
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.389 346
Rwork0.376 6765

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