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- PDB-4e6u: Structure of LpxA from Acinetobacter baumannii at 1.4A resolution... -

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Basic information

Entry
Database: PDB / ID: 4e6u
TitleStructure of LpxA from Acinetobacter baumannii at 1.4A resolution (P63 form)
ComponentsAcyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
KeywordsTRANSFERASE / lipopolysaccaride synthesis
Function / homology
Function and homology information


Udp N-acetylglucosamine O-acyltransferase; Domain 2 / Udp N-acetylglucosamine O-acyltransferase, C-terminal domain / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / 3 Solenoid / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
UDP-N-acetylglucosamine acyltransferase / UDP-N-acetylglucosamine acyltransferase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 4E6T / Resolution: 1.41 Å
AuthorsBadger, J. / Chie-Leon, B. / Logan, C. / Sridhar, V. / Sankaran, B. / Zwart, P.H. / Nienaber, V.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Structure determination of LpxA from the lipopolysaccharide-synthesis pathway of Acinetobacter baumannii.
Authors: Badger, J. / Chie-Leon, B. / Logan, C. / Sridhar, V. / Sankaran, B. / Zwart, P.H. / Nienaber, V.
History
DepositionMar 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 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

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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)29,22312
Polymers28,4721
Non-polymers75111
Water5,278293
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)87,66936
Polymers85,4173
Non-polymers2,25233
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area11980 Å2
ΔGint-4 kcal/mol
Surface area28300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.751, 75.751, 119.063
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-457-

HOH

21A-459-

HOH

31A-526-

HOH

41A-561-

HOH

51A-601-

HOH

61A-668-

HOH

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Components

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


Mass: 28472.334 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: lpxA, ABTW07_2294 / Cell line (production host): BL21 (DE3) / Production host: Escherichia coli (E. coli)
References: UniProt: F0QHB3, UniProt: A0A7U4DSW1*PLUS, acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 3.46 Å3/Da / Density % sol: 64.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2ul of 25mg/ml protein, 2uL of 1.8M LiSO4, 0.1M Hepes 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.979 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 6, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.41→50 Å / Num. all: 73881 / Num. obs: 73881 / % possible obs: 99.8 % / Observed criterion σ(I): -4 / Redundancy: 11.3 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 36.1
Reflection shellResolution: 1.41→1.46 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.591 / Mean I/σ(I) obs: 5 / Num. unique all: 63291 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: 4E6T / Resolution: 1.41→36.09 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.968 / SU B: 0.758 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.049 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19147 3720 5 %RANDOM
Rwork0.17507 ---
obs0.17591 70122 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.799 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20.08 Å20 Å2
2--0.16 Å20 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 1.41→36.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1931 0 46 293 2270
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0212060
X-RAY DIFFRACTIONr_angle_refined_deg1.2911.9482772
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3445257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.26825.22290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.77315354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.73157
X-RAY DIFFRACTIONr_chiral_restr0.0890.2316
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211511
X-RAY DIFFRACTIONr_mcbond_it0.88521269
X-RAY DIFFRACTIONr_mcangle_it1.5562.52063
X-RAY DIFFRACTIONr_scbond_it2.0553791
X-RAY DIFFRACTIONr_scangle_it3.3654.5709
LS refinement shellResolution: 1.412→1.449 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 230 -
Rwork0.251 5150 -
obs--100 %

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