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- PDB-3lod: The crystal structure of the putative acyl-CoA N-acyltransferase ... -

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Basic information

Entry
Database: PDB / ID: 3lod
TitleThe crystal structure of the putative acyl-CoA N-acyltransferase from Klebsiella pneumoniae subsp.pneumoniae MGH 78578
ComponentsPutative acyl-CoA N-acyltransferase
KeywordsTRANSFERASE / acyl-CoA N-acyltransferase / structural genomics / PSI2 / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics / Acyltransferase
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
: / Acetyltransferase (GNAT) family / 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
Acyl-CoA N-acyltransferase
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsZhang, R. / Volkart, L. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the putative acyl-CoA N-acyltransferase from Klebsiella pneumoniae
Authors: Zhang, R. / Volkart, L. / Bearden, J. / Joachimiak, A.
History
DepositionFeb 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative acyl-CoA N-acyltransferase


Theoretical massNumber of molelcules
Total (without water)17,8501
Polymers17,8501
Non-polymers00
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.734, 86.734, 99.801
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsThis protein exists as monomer.

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Components

#1: Protein Putative acyl-CoA N-acyltransferase


Mass: 17850.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria)
Strain: ATCC 700721, MGH 78578 / Gene: KPN78578_16030, KPN_01633 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A6T8Z3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 3.04 Å3/Da / Density % sol: 59.48 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris, 16% PEG4000, , pH 8.5, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 8, 2008 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.5→75.11 Å / Num. all: 7754 / Num. obs: 7687 / % possible obs: 99.13 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 21.3 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 37.11
Reflection shellResolution: 2.5→2.565 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.664 / Mean I/σ(I) obs: 1 / Num. unique all: 570 / % possible all: 92.98

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.5→75.11 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.928 / SU B: 21.602 / SU ML: 0.217 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.352 / ESU R Free: 0.259
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26308 369 4.6 %RANDOM
Rwork0.22569 ---
obs0.22745 7687 99.13 %-
all-7754 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.88 Å2
Baniso -1Baniso -2Baniso -3
1--1.99 Å2-0.99 Å20 Å2
2---1.99 Å20 Å2
3---2.98 Å2
Refinement stepCycle: LAST / Resolution: 2.5→75.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1125 0 0 23 1148
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0221148
X-RAY DIFFRACTIONr_angle_refined_deg2.1271.9691559
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7965143
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.02824.15153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.08415188
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.334158
X-RAY DIFFRACTIONr_chiral_restr0.1560.2176
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021877
X-RAY DIFFRACTIONr_mcbond_it1.2251.5723
X-RAY DIFFRACTIONr_mcangle_it2.26221158
X-RAY DIFFRACTIONr_scbond_it2.8463425
X-RAY DIFFRACTIONr_scangle_it4.7544.5401
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.406 27 -
Rwork0.328 503 -
obs-530 92.98 %
Refinement TLS params.Method: refined / Origin x: -2.7558 Å / Origin y: 29.5146 Å / Origin z: 3.8747 Å
111213212223313233
T0.1758 Å20.0279 Å20.0088 Å2-0.2511 Å2-0.0174 Å2--0.2861 Å2
L5.844 °2-3.7607 °2-3.5666 °2-4.0592 °21.6562 °2--4.1715 °2
S-0.152 Å °-0.1078 Å °-0.0708 Å °-0.1609 Å °0.1277 Å °0.1353 Å °-0.0047 Å °0.2252 Å °0.0243 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 26
2X-RAY DIFFRACTION1A39 - 70
3X-RAY DIFFRACTION1A71 - 100
4X-RAY DIFFRACTION1A101 - 130
5X-RAY DIFFRACTION1A131 - 152

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