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- PDB-3juw: Putative GnaT-family acetyltransferase from Bordetella pertussis. -

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Basic information

Entry
Database: PDB / ID: 3juw
TitlePutative GnaT-family acetyltransferase from Bordetella pertussis.
ComponentsProbable GnaT-family acetyltransferase
KeywordsTRANSFERASE / structural genomics / APC60242 / GnaT family / acetyltransferase / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
: / Acetyltransferase (GNAT) domain / 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
Probable GnaT-family acetyltransferase
Similarity search - Component
Biological speciesBordetella pertussis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.11 Å
AuthorsOsipiuk, J. / Wu, R. / Cobb, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: X-ray crystal structure of putative GnaT-family acetyltransferase from Bordetella pertussis.
Authors: Osipiuk, J. / Wu, R. / Cobb, G. / Joachimiak, A.
History
DepositionSep 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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: Probable GnaT-family acetyltransferase
B: Probable GnaT-family acetyltransferase
C: Probable GnaT-family acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6899
Polymers60,1123
Non-polymers5766
Water5,477304
1
A: Probable GnaT-family acetyltransferase
B: Probable GnaT-family acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5557
Polymers40,0752
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-79 kcal/mol
Surface area15950 Å2
MethodPISA
2
C: Probable GnaT-family acetyltransferase
hetero molecules

C: Probable GnaT-family acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2674
Polymers40,0752
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area2240 Å2
ΔGint-41 kcal/mol
Surface area15620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.211, 65.886, 64.375
Angle α, β, γ (deg.)90.000, 102.490, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-240-

HOH

Detailsauthors state that the biological unit is a dimer made of chains A and B

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Components

#1: Protein Probable GnaT-family acetyltransferase


Mass: 20037.498 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis (bacteria) / Strain: Tohama I / Gene: BP0858 / Plasmid: pMCSG19b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7VZN9
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.07 Å3/Da / Density % sol: 40.59 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M ammonium sulfate, 0.1 M MES buffer, 30% PEG 5000 MME, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 19, 2009
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: 2.1→30.6 Å / Num. all: 28544 / Num. obs: 28544 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 28.8 Å2 / Rmerge(I) obs: 0.164 / Χ2: 2.502 / Net I/σ(I): 7.6
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.831 / Mean I/σ(I) obs: 2.36 / Num. unique all: 1441 / Χ2: 2.124 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0102refinement
PDB_EXTRACT3.005data extraction
SBC-Collectdata collection
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.11→30.6 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.906 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 13.17 / SU ML: 0.156 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.265 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1441 5 %RANDOM
Rwork0.186 ---
all0.19 28541 --
obs0.19 28541 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 52.5 Å2 / Biso mean: 15.767 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å2-0.51 Å2
2---0.31 Å20 Å2
3---0.29 Å2
Refinement stepCycle: LAST / Resolution: 2.11→30.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3954 0 30 304 4288
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0214106
X-RAY DIFFRACTIONr_angle_refined_deg1.6811.9365538
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1815501
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.28221.509232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.47315657
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9281564
X-RAY DIFFRACTIONr_chiral_restr0.1120.2545
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213273
X-RAY DIFFRACTIONr_mcbond_it1.0911.52462
X-RAY DIFFRACTIONr_mcangle_it1.96123854
X-RAY DIFFRACTIONr_scbond_it3.0831644
X-RAY DIFFRACTIONr_scangle_it4.8464.51679
LS refinement shellResolution: 2.105→2.16 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 108 -
Rwork0.226 1950 -
all-2058 -
obs-2058 97.81 %
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)
11.43070.48231.41530.78440.24581.7920.025-0.00510.0901-0.2018-0.06080.01270.21190.16850.03580.12350.0604-0.00840.0927-0.0180.041634.866511.163916.8312
20.0417-0.08960.10571.63760.29210.53270.00360.00320.0064-0.22360.00340.11160.00460.0411-0.0070.0856-0.0089-0.03370.0368-0.01160.066926.378117.841312.8384
30.13210.55670.23344.7558-1.04932.5733-0.05330.05730.077-0.52730.1130.31290.23420.2104-0.05970.0988-0.0099-0.06430.03210.03380.139529.829229.78726.0709
40.3432-0.0952-0.4550.03940.01922.48410.02080.0537-0.10050.00740.00580.0328-0.0509-0.1349-0.02660.0555-0.00330.0130.0374-0.0080.078832.099926.472337.9381
50.46-0.0737-0.46520.11030.2540.8001-0.02420.0401-0.05350.03640.0263-0.01630.07460.0409-0.00210.0359-0.00190.00860.0678-0.00710.058934.130217.907339.2499
63.2811-0.4132-0.22720.2823-0.10580.78990.0224-0.0487-0.2030.00820.05370.04090.12970.1147-0.07610.04380.0144-0.00620.10640.02240.063442.160712.835947.4351
71.10230.52340.2380.5912-0.45711.1694-0.05310.02110.20610.01270.07850.0765-0.1395-0.1449-0.02540.06020.01830.00530.08060.0150.124544.371350.156823.0885
80.26960.20680.24130.82690.05040.2437-0.0626-0.02220.0498-0.1850.02650.0254-0.0211-0.03410.0360.077-0.0176-0.00760.07510.03810.092951.455249.025514.6018
91.7997-0.57110.27711.2221-1.59222.22440.08070.01610.138-0.0444-0.03560.0210.05160.0742-0.0450.04850.00050.02270.06010.02370.055958.563944.84438.7455
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 51
2X-RAY DIFFRACTION2A52 - 129
3X-RAY DIFFRACTION3A130 - 171
4X-RAY DIFFRACTION4B5 - 47
5X-RAY DIFFRACTION5B48 - 108
6X-RAY DIFFRACTION6B109 - 171
7X-RAY DIFFRACTION7C5 - 73
8X-RAY DIFFRACTION8C74 - 122
9X-RAY DIFFRACTION9C123 - 171

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