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- PDB-3ey5: Putative acetyltransferase from GNAT family from Bacteroides thet... -

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Basic information

Entry
Database: PDB / ID: 3ey5
TitlePutative acetyltransferase from GNAT family from Bacteroides thetaiotaomicron.
ComponentsAcetyltransferase-like, GNAT family
KeywordsTRANSFERASE / structural genomics / APC60148 / acetyltransferase / GNAT family / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


N-acetyltransferase activity / 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
Acetyltransferase-like, GNAT family
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å
AuthorsOsipiuk, J. / Bigelow, L. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: X-ray crystal structure of putative acetyltransferase from GNAT family from Bacteroides thetaiotaomicron.
Authors: Osipiuk, J. / Bigelow, L. / Clancy, S. / Joachimiak, A.
History
DepositionOct 17, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / 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_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

Downloads & links

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Assembly

Deposited unit
A: Acetyltransferase-like, GNAT family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3853
Polymers22,1931
Non-polymers1922
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.798, 50.785, 73.765
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsauthors state that the biological unit is the same as asymmetric unit based on PISA prediction.

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Components

#1: Protein Acetyltransferase-like, GNAT family


Mass: 22193.189 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: VPI-5482 / Gene: BT_2051 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8A635
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 1.81 Å3/Da / Density % sol: 31.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 0.2 M lithium sulfate, 0.1 M CAPS buffer, 1.2 M sodium/potassium phosphate, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: SBC-3 / Detector: CCD / Date: Oct 8, 2008
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: 2.15→21.3 Å / Num. all: 9184 / Num. obs: 9184 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 38.9 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 22.3
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 5.54 % / Rmerge(I) obs: 0.549 / Mean I/σ(I) obs: 3.17 / Num. unique all: 442 / % possible all: 99.3

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.006data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.15→21.3 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.909 / WRfactor Rfree: 0.253 / WRfactor Rwork: 0.225 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.821 / SU B: 15.417 / SU ML: 0.182 / SU R Cruickshank DPI: 0.442 / SU Rfree: 0.264 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.371 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.267 435 4.8 %RANDOM
Rwork0.198 ---
all0.201 9139 --
obs0.201 9139 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 54.81 Å2 / Biso mean: 24.739 Å2 / Biso min: 9.97 Å2
Baniso -1Baniso -2Baniso -3
1--1.39 Å20 Å20 Å2
2--2.03 Å20 Å2
3----0.64 Å2
Refinement stepCycle: LAST / Resolution: 2.15→21.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1517 0 10 40 1567
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221638
X-RAY DIFFRACTIONr_angle_refined_deg1.5191.952231
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4495190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.07823.564101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.69815276
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1961513
X-RAY DIFFRACTIONr_chiral_restr0.1050.2218
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211320
X-RAY DIFFRACTIONr_mcbond_it0.8161.5908
X-RAY DIFFRACTIONr_mcangle_it1.53321485
X-RAY DIFFRACTIONr_scbond_it2.4253730
X-RAY DIFFRACTIONr_scangle_it4.0034.5739
LS refinement shellResolution: 2.149→2.204 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 40 -
Rwork0.214 609 -
all-649 -
obs-649 96.15 %
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)
15.1009-1.7596-1.68273.9066-1.02228.5524-0.1034-0.1739-0.4802-0.23730.14770.68460.5547-0.6841-0.04430.1035-0.0687-0.04280.08880.03120.1298-8.4347-7.91557.4422
24.508-1.03520.62225.4205-3.03815.24260.19370.6312-0.0713-0.3495-0.18950.01840.2722-0.2472-0.00420.07270.0198-0.01230.1274-0.01960.0444-0.2085-2.3278-2.6807
33.9091-0.1030.03361.3856-0.13352.12590.0311-0.1463-0.2633-0.01070.02510.07460.2368-0.1581-0.05620.0752-0.0110.00420.02840.02320.02990.4999-4.177710.6923
42.9099-2.51691.50242.8618-0.32332.2105-0.0842-0.1987-0.0463-0.17680.04740.129-0.4616-0.30870.03680.16070.03360.02470.1040.03370.169-8.0967.164712.1043
51.7031.637-0.60966.729-3.04622.34270.0096-0.035-0.0225-0.0255-0.0070.14180.0243-0.023-0.00260.01230.01480.01430.04810.00920.03195.86155.398413.9066
68.9048-4.20655.57843.84760.42168.51650.0180.07740.374-0.099-0.034-0.3128-0.1470.03850.0160.0409-0.01540.00140.0130.02770.11191.622920.03424.9422
72.349-0.2496-0.89181.64720.27361.93380.0084-0.1296-0.0466-0.03070.0213-0.0492-0.03190.0598-0.02970.00820.00520.01180.01220.01060.018611.71859.35639.1751
89.63450.01250.16775.76770.14298.0872-0.03150.0575-0.1604-0.17980.0464-0.29730.34470.5674-0.01490.03830.02140.02270.0405-0.00530.029516.8471-1.17574.3603
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 18
2X-RAY DIFFRACTION2A19 - 41
3X-RAY DIFFRACTION3A42 - 74
4X-RAY DIFFRACTION4A75 - 96
5X-RAY DIFFRACTION5A97 - 110
6X-RAY DIFFRACTION6A111 - 118
7X-RAY DIFFRACTION7A119 - 165
8X-RAY DIFFRACTION8A166 - 177

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