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- PDB-4eqy: Crystal structure of Acyl-[acyl-carrier-protein]--UDP-N-acetylglu... -

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Basic information

Entry
Database: PDB / ID: 4eqy
TitleCrystal structure of Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase from Burkholderia thailandensis
Components
  • Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
  • HIS-HIS-HIS peptide
KeywordsTRANSFERASE / SSGCID / beta helix / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
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-repeat containing-transferases signature. / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / 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-repeat containing-transferases signature. / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat / 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 speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Plos One / Year: 2013
Title: Combining functional and structural genomics to sample the essential Burkholderia structome.
Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C.
History
DepositionApr 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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: Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
C: Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
E: Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
F: Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
G: Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
X: HIS-HIS-HIS peptide


Theoretical massNumber of molelcules
Total (without water)181,6267
Polymers181,6267
Non-polymers00
Water21,3661186
1
A: Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
B: Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
C: Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase


Theoretical massNumber of molelcules
Total (without water)90,5973
Polymers90,5973
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6340 Å2
ΔGint-23 kcal/mol
Surface area28840 Å2
MethodPISA
2
E: Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
F: Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
G: Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase


Theoretical massNumber of molelcules
Total (without water)90,5973
Polymers90,5973
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6410 Å2
ΔGint-23 kcal/mol
Surface area28820 Å2
MethodPISA
3
X: HIS-HIS-HIS peptide


  • defined by author&software
  • 432 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)4321
Polymers4321
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.440, 90.490, 109.520
Angle α, β, γ (deg.)90.000, 111.030, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 30198.912 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / ATCC 700388 / DSM 13276 / CIP 106301 / Gene: 3848943, BTH_I2039, lpxA / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q2SWY6, acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
#2: Protein/peptide HIS-HIS-HIS peptide


Mass: 432.456 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / ATCC 700388 / DSM 13276 / CIP 106301 / Gene: 3848943, BTH_I2039, lpxA / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1186 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCHAIN X IS A PORTION OF N-TERMINAL EXPRESSION TAG WHICH CAN BE MODELED BUT NOT ASSIGNED.

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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: 2.79 Å3/Da / Density % sol: 55.87 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5
Details: EBS ProPlex screen h7: 15% MPD, 2% PEG4000, 100 mM sodium acetate/HCl pH 5.0, ButhA.00428.a.A1.PS01225 at 32 mg/mL, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 9, 2011
RadiationMonochromator: asymmetric curved crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 184689 / Num. obs: 183552 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 27.632 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 18.49
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
1.8-1.853.760.4722.9150902136451352699.1
1.85-1.93.770.3633.7449412132161311599.2
1.9-1.953.770.2655.1348221129031279799.2
1.95-2.013.770.2056.5346841125081243099.4
2.01-2.083.770.1677.9645508121491207899.4
2.08-2.153.770.12610.2544405118401178299.5
2.15-2.233.770.10112.3542343112851123499.5
2.23-2.323.770.08514.5341196109801093399.6
2.32-2.433.770.07816.139021103901034999.6
2.43-2.553.770.06917.6837806100701002799.6
2.55-2.683.760.05920.59358059542951099.7
2.68-2.853.750.04824.46336239004896299.5
2.85-3.043.730.0429.65316308531848599.5
3.04-3.293.710.03433.94290547871782899.5
3.29-3.63.660.02840.06265507292725499.5
3.6-4.023.610.02544.07236646605656099.3
4.02-4.653.530.02346.91205145859581799.3
4.65-5.693.640.02246.2180164969494399.5
5.69-8.053.690.02346.4140883836381899.5
8.05-503.530.01851.9474362194210495.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å19.94 Å
Translation3.5 Å19.94 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
BOSdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QIV

2qiv


Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.1828 / WRfactor Rwork: 0.1555 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.9083 / SU B: 3.769 / SU ML: 0.059 / SU R Cruickshank DPI: 0.0949 / SU Rfree: 0.0942 / Isotropic thermal model: ISOTROPIC, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1885 9208 5 %RANDOM
Rwork0.1592 ---
all0.1607 184689 --
obs0.1607 183526 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 62.26 Å2 / Biso mean: 22.4905 Å2 / Biso min: 9.29 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20.73 Å2
2--0.27 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11598 0 0 1186 12784
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01912009
X-RAY DIFFRACTIONr_bond_other_d0.0010.027784
X-RAY DIFFRACTIONr_angle_refined_deg1.5261.93716379
X-RAY DIFFRACTIONr_angle_other_deg0.956319028
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.92751628
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.03523.477512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.37151871
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7561588
X-RAY DIFFRACTIONr_chiral_restr0.0920.21886
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213848
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022412
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 669 -
Rwork0.242 12601 -
all-13270 -
obs--99.15 %
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)
11.0407-0.2013-0.07710.2792-0.05160.3542-0.02230.0537-0.0586-0.0340.04770.04120.0301-0.0362-0.02540.0257-0.0152-0.02680.04150.00490.0395-17.098-18.55930.343
20.7448-0.1992-0.19030.52270.25640.45570.0007-0.09870.016-0.02310.0059-0.0079-0.03990.0502-0.00660.00740.004-0.00330.0719-0.00510.01164.675-0.61341.497
30.65660.4526-0.75870.5865-0.39081.2139-0.0023-0.0884-0.02960.0864-0.0649-0.00330.12070.12810.06720.06780.0175-0.01590.05570.02550.0839-2.318-26.68155.925
40.6113-0.2918-0.05740.5332-0.03520.35090.02-0.0174-0.0283-0.0051-0.00940.02750.0080.0026-0.01060.0120.0014-0.00190.0624-0.0090.00936.196-0.40620.019
51.24510.3618-0.48170.4489-0.12670.40710.0311-0.14360.11310.0433-0.0495-0.0345-0.11280.08890.01840.0852-0.0288-0.02270.0612-0.01540.049350.70625.96617.623
60.6386-0.0709-0.33690.3520.18681.0114-0.00120.08480.0094-0.06770.01820.0363-0.0785-0.0946-0.0170.04740.01-0.01790.04860.01670.018732.68417.096-5.122
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 263
2X-RAY DIFFRACTION2B3 - 263
3X-RAY DIFFRACTION3C4 - 263
4X-RAY DIFFRACTION4E3 - 263
5X-RAY DIFFRACTION5F4 - 263
6X-RAY DIFFRACTION6G4 - 263

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