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- PDB-3r0s: UDP-N-acetylglucosamine acyltransferase from Campylobacter jejuni -

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Basic information

Entry
Database: PDB / ID: 3r0s
TitleUDP-N-acetylglucosamine acyltransferase from Campylobacter jejuni
ComponentsAcyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
KeywordsTRANSFERASE / structural genomics / Center for Structural Genomics of Infectious Diseases / CSGID / lipid A biosynthesis
Function / homology
Function and homology information


acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase / acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase activity / lipid A biosynthetic process / 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. / Hexapeptide repeat proteins / Hexapeptide repeat ...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. / Hexapeptide repeat proteins / Hexapeptide repeat / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
Similarity search - Component
Biological speciesCampylobacter jejuni subsp. jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsOsipiuk, J. / Zhou, M. / Papazisi, L. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: UDP-N-acetylglucosamine acyltransferase from Campylobacter jejuni.
Authors: Osipiuk, J. / Zhou, M. / Papazisi, L. / Anderson, W.F. / Joachimiak, A.
History
DepositionMar 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1852
Polymers29,1501
Non-polymers351
Water61334
1
A: Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
hetero molecules

A: Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
hetero molecules

A: Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,5556
Polymers87,4493
Non-polymers1063
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 area6120 Å2
ΔGint-55 kcal/mol
Surface area29940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.959, 98.959, 157.463
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase / UDP-N-acetylglucosamine acyltransferase


Mass: 29149.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni subsp. jejuni (Campylobacter)
Strain: NCTC 11168 / Gene: Cj0274, lpxA / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9PIM1, acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
#2: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.55 Å3/Da / Density % sol: 51.67 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 20% PEG MME 5000, 0.1 M Bis-tris buffer, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 10, 2009
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.22→41.3 Å / Num. all: 14945 / Num. obs: 14945 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 24 % / Biso Wilson estimate: 48.3 Å2 / Rmerge(I) obs: 0.124 / Χ2: 2.063 / Net I/σ(I): 7.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.22-2.2619.70.8234.417161.16898.8
2.26-2.320.60.8867391.20599.3
2.3-2.3421.70.6687301.26399.2
2.34-2.3922.70.6667301.21998.9
2.39-2.4423.60.6847351.2299.3
2.44-2.524.30.5317491.26799.3
2.5-2.5624.80.4747281.20299.3
2.56-2.63250.4157451.22899.2
2.63-2.7125.40.3467451.31199.7
2.71-2.825.50.3017481.31999.5
2.8-2.925.60.2357341.49599.5
2.9-3.0125.50.1927601.61199.6
3.01-3.1525.50.1697351.69699.6
3.15-3.3225.30.1287542.00999.6
3.32-3.5225.10.1137572.3399.6
3.52-3.824.80.0967422.75599.6
3.8-4.1824.40.0837533.14299.9
4.18-4.78240.0777633.54498.3
4.78-6.0223.80.0797733.72899.4
6.02-5022.70.0728096.02799.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J2Z

1j2z


Resolution: 2.3→41.4 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.931 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 14.457 / SU ML: 0.161 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2395 654 4.9 %RANDOM
Rwork0.1957 ---
all0.1978 13358 --
obs0.1978 13358 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 97.07 Å2 / Biso mean: 52.2621 Å2 / Biso min: 25.85 Å2
Baniso -1Baniso -2Baniso -3
1--1.3 Å2-0.65 Å20 Å2
2---1.3 Å20 Å2
3---1.95 Å2
Refinement stepCycle: LAST / Resolution: 2.3→41.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1925 0 1 34 1960
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222035
X-RAY DIFFRACTIONr_bond_other_d0.0010.021406
X-RAY DIFFRACTIONr_angle_refined_deg1.5851.9522756
X-RAY DIFFRACTIONr_angle_other_deg0.92333431
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7325271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.87823.87898
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.02115370
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.551518
X-RAY DIFFRACTIONr_chiral_restr0.0890.2313
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022313
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02421
X-RAY DIFFRACTIONr_mcbond_it0.8281.51272
X-RAY DIFFRACTIONr_mcbond_other0.2171.5533
X-RAY DIFFRACTIONr_mcangle_it1.45522052
X-RAY DIFFRACTIONr_scbond_it2.2233763
X-RAY DIFFRACTIONr_scangle_it3.4914.5693
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 48 -
Rwork0.217 920 -
all-968 -
obs-968 98.98 %
Refinement TLS params.Method: refined / Origin x: 7.9921 Å / Origin y: 16.2569 Å / Origin z: 32.9904 Å
111213212223313233
T0.0738 Å20.0011 Å2-0.0118 Å2-0.1115 Å20.0185 Å2--0.2384 Å2
L1.7652 °20.4085 °20.1173 °2-1.8634 °2-2.054 °2--4.3444 °2
S-0.0271 Å °0.4085 Å °0.2548 Å °-0.1553 Å °0.0053 Å °-0.0857 Å °0.1061 Å °0.1778 Å °0.0218 Å °

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