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- PDB-3efa: Crystal structure of putative N-acetyltransferase from Lactobacil... -

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Basic information

Entry
Database: PDB / ID: 3efa
TitleCrystal structure of putative N-acetyltransferase from Lactobacillus plantarum
ComponentsPutative Acetyltransferase
KeywordsTRANSFERASE / acetyltransferase / Lactobacillus plantarum / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


glucosamine 6-phosphate N-acetyltransferase activity / UDP-N-acetylglucosamine biosynthetic process / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
Similarity search - Function
Acetyltransferase (GNAT) domain / Glucosamine 6-phosphate N-acetyltransferase / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / PHOSPHATE ION / Acetyltransferase, GNAT family / :
Similarity search - Component
Biological speciesLactobacillus plantarum WCFS1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.423 Å
AuthorsChang, C. / Li, H. / Cobb, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of putative N-acetyltransferase from Lactobacillus plantarum
Authors: Chang, C. / Li, H. / Cobb, G. / Joachimiak, A.
History
DepositionSep 8, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative Acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0957
Polymers16,7231
Non-polymers3716
Water1,18966
1
A: Putative Acetyltransferase
hetero molecules

A: Putative Acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,18914
Polymers33,4472
Non-polymers74212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/61
Buried area3360 Å2
ΔGint-20 kcal/mol
Surface area15400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.673, 84.673, 174.074
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-206-

PO4

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Components

#1: Protein Putative Acetyltransferase /


Mass: 16723.426 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus plantarum WCFS1 (bacteria)
Gene: lp_1797 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) derivatives / References: UniProt: Q88W61, UniProt: F9UPE4*PLUS
#2: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / 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

Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Bis-TRIS 0.5M Magnesium formate, pH 6.5, 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: 0.97931 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 27, 2008
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 14713 / Num. obs: 14578 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 12.2 % / Biso Wilson estimate: 54 Å2 / Rmerge(I) obs: 0.112 / Net I/σ(I): 48.35
Reflection shellResolution: 2.4→2.42 Å / Redundancy: 13.8 % / Rmerge(I) obs: 0.537 / Mean I/σ(I) obs: 6.9 / Num. unique all: 332 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHARPphasing
PHENIX(phenix.refine)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.423→35.877 Å / SU ML: 0.3 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2366 733 5.05 %RANDOM
Rwork0.2062 ---
all0.2077 15250 --
obs0.2077 14517 98.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 68.757 Å2 / ksol: 0.343 e/Å3
Refinement stepCycle: LAST / Resolution: 2.423→35.877 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1160 0 23 66 1249
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.01
X-RAY DIFFRACTIONf_angle_deg1.156
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.4231-2.61010.25451560.22432626303498
2.6101-2.87270.26821560.213227182921100
2.8727-3.28810.27631420.218127642906100
3.2881-4.14170.2141580.19452763287499
4.1417-35.88120.21211210.19312913278296
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)
10.29890.2907-0.75361.0026-1.76161.11680.05840.30080.0169-0.29810.05550.04920.22640.1463-0.00010.4035-0.0320.00330.2916-0.03760.3403-3.256452.84278.7287
21.33670.0187-0.75011.314-0.62932.56130.0345-0.0140.164-0.00720.0747-0.0347-0.28760.3513-0.00020.3665-0.0250.03750.2977-0.02580.32281.065161.6962.3665
31.3028-0.76380.45741.61620.82243.1740.2585-0.20590.0713-0.1214-0.36510.3884-0.2681-0.5562-0.00010.43340.11550.01280.4941-0.07990.3734-3.184457.8125-11.7629
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 1-43
2X-RAY DIFFRACTION2chain A and resid 44-107
3X-RAY DIFFRACTION3chain A and resid 108-144

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