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- PDB-2i79: The crystal structure of the acetyltransferase of GNAT family fro... -

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Basic information

Entry
Database: PDB / ID: 2i79
TitleThe crystal structure of the acetyltransferase of GNAT family from Streptococcus pneumoniae
ComponentsAcetyltransferase, GNAT family
KeywordsTRANSFERASE / acetyltransferase / GNAT family / acetyl Coenzyme *A / Structural Genomics / 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
ACETYL COENZYME *A / Acetyltransferase, GNAT family / Acetyltransferase, GNAT family
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsZhang, R.G. / Zhou, M. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the acetyltransferase of GNAT family from Streptococcus pneumoniae
Authors: Zhang, R.G. / Zhou, M. / Abdullah, J. / Joachimiak, A.
History
DepositionAug 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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, GNAT family
B: Acetyltransferase, GNAT family
C: Acetyltransferase, GNAT family
D: Acetyltransferase, GNAT family
E: Acetyltransferase, GNAT family
F: Acetyltransferase, GNAT family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,01812
Polymers116,1616
Non-polymers4,8576
Water6,107339
1
A: Acetyltransferase, GNAT family
E: Acetyltransferase, GNAT family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3394
Polymers38,7202
Non-polymers1,6192
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5550 Å2
ΔGint-8 kcal/mol
Surface area15890 Å2
MethodPISA
2
B: Acetyltransferase, GNAT family
C: Acetyltransferase, GNAT family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3394
Polymers38,7202
Non-polymers1,6192
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint-8 kcal/mol
Surface area16070 Å2
MethodPISA
3
D: Acetyltransferase, GNAT family
F: Acetyltransferase, GNAT family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3394
Polymers38,7202
Non-polymers1,6192
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5430 Å2
ΔGint-5 kcal/mol
Surface area15380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.131, 174.792, 56.573
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThis protein existed as dimer. MolA/MolE, MolB/MolC, MolD/MolF represent three dimers in asymmetric unit.

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Components

#1: Protein
Acetyltransferase, GNAT family


Mass: 19360.102 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Plasmid: PDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q97NS4, UniProt: A0A0H2URR1*PLUS, amino-acid N-acetyltransferase
#2: Chemical
ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / 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: 2.83 Å3/Da / Density % sol: 56.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 35%MPD, MES pH6.0, 0.2M LiSO4, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9798 Å
DetectorType: SBC-2 / Detector: CCD / Date: Apr 23, 2006 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 73580 / Num. obs: 68790 / % possible obs: 93.49 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.8 % / Biso Wilson estimate: 39.8 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 26.3
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 6 % / Mean I/σ(I) obs: 2 / Num. unique all: 5664 / Rsym value: 0.396 / % possible all: 62.52

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.1→44.7 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.936 / SU B: 11.284 / SU ML: 0.161 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.231 / ESU R Free: 0.196
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25133 3647 5 %RANDOM
Rwork0.20823 ---
obs0.21045 68790 93.49 %-
all-73580 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.864 Å2
Baniso -1Baniso -2Baniso -3
1--1.5 Å20 Å20 Å2
2---0.81 Å20 Å2
3---2.31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.04 Å0.034 Å
Luzzati d res low-6 Å
Luzzati sigma a0.5 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.1→44.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8061 0 306 339 8706
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0228489
X-RAY DIFFRACTIONr_bond_other_d0.0010.025678
X-RAY DIFFRACTIONr_angle_refined_deg1.5932.00611484
X-RAY DIFFRACTIONr_angle_other_deg0.966313828
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.751008
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.49324.514401
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.446151515
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3721560
X-RAY DIFFRACTIONr_chiral_restr0.0870.21298
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029258
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021720
X-RAY DIFFRACTIONr_nbd_refined0.2040.21545
X-RAY DIFFRACTIONr_nbd_other0.2030.26009
X-RAY DIFFRACTIONr_nbtor_refined0.1730.24062
X-RAY DIFFRACTIONr_nbtor_other0.0890.24432
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2334
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1160.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1940.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1380.213
X-RAY DIFFRACTIONr_mcbond_it1.11.56542
X-RAY DIFFRACTIONr_mcbond_other0.1621.52104
X-RAY DIFFRACTIONr_mcangle_it1.28727996
X-RAY DIFFRACTIONr_scbond_it2.14133985
X-RAY DIFFRACTIONr_scangle_it3.1494.53488
LS refinement shellResolution: 2.1→2.16 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 176 -
Rwork0.239 3365 -
obs-3647 62.52 %
Refinement TLS params.Method: refined / Origin x: 77.755 Å / Origin y: 42.637 Å / Origin z: 13.547 Å
111213212223313233
T-0.1799 Å2-0.0093 Å20.0058 Å2--0.0545 Å20.0343 Å2--0.0143 Å2
L0.4153 °2-0.2194 °2-0.0361 °2-0.3772 °20.0003 °2--0.0739 °2
S-0.0228 Å °-0.0453 Å °0.0057 Å °-0.0036 Å °0.0116 Å °0.0131 Å °-0.0307 Å °-0.0117 Å °0.0112 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 501 - 50
2X-RAY DIFFRACTION1AA51 - 10051 - 100
3X-RAY DIFFRACTION1AA101 - 140101 - 140
4X-RAY DIFFRACTION1AA141 - 171141 - 171
5X-RAY DIFFRACTION1BB3 - 503 - 50
6X-RAY DIFFRACTION1BB51 - 10051 - 100
7X-RAY DIFFRACTION1BB101 - 140101 - 140
8X-RAY DIFFRACTION1BB141 - 171141 - 171
9X-RAY DIFFRACTION1CC1 - 501 - 50
10X-RAY DIFFRACTION1CC51 - 10051 - 100
11X-RAY DIFFRACTION1CC101 - 140101 - 140
12X-RAY DIFFRACTION1CC141 - 171141 - 171
13X-RAY DIFFRACTION1DD5 - 505 - 50
14X-RAY DIFFRACTION1DD51 - 10051 - 100
15X-RAY DIFFRACTION1DD101 - 140101 - 140
16X-RAY DIFFRACTION1DD141 - 172141 - 172
17X-RAY DIFFRACTION1EE5 - 505 - 50
18X-RAY DIFFRACTION1EE51 - 10051 - 100
19X-RAY DIFFRACTION1EE101 - 140101 - 140
20X-RAY DIFFRACTION1EE141 - 171141 - 171
21X-RAY DIFFRACTION1FF4 - 504 - 50
22X-RAY DIFFRACTION1FF51 - 10051 - 100
23X-RAY DIFFRACTION1FF101 - 140101 - 140
24X-RAY DIFFRACTION1FF141 - 172141 - 172

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