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- PDB-1u6m: The crystal structure of acetyltransferase -

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Basic information

Entry
Database: PDB / ID: 1u6m
TitleThe crystal structure of acetyltransferase
Componentsacetyltransferase, GNAT family
KeywordsTRANSFERASE / acetyltransferase / GNAT family / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
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
Acetyltransferase, GNAT family
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsMin, T. / Gorman, J. / Shapiro, L. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: The crystal structure of acetyltransferase, GNAT family from Enterococcus faecalis
Authors: Min, T. / Gorman, J. / Shapiro, L.
History
DepositionJul 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 21, 2016Group: Other
Revision 1.4Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.classification / _software.name
Revision 1.5Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _struct_ref_seq_dif.details ..._audit_author.identifier_ORCID / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Feb 14, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,33012
Polymers89,5624
Non-polymers7698
Water10,971609
1
A: acetyltransferase, GNAT family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5833
Polymers22,3901
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: acetyltransferase, GNAT family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5833
Polymers22,3901
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: acetyltransferase, GNAT family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5833
Polymers22,3901
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: acetyltransferase, GNAT family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5833
Polymers22,3901
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.257, 115.257, 225.257
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
acetyltransferase, GNAT family


Mass: 22390.385 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q836Z8
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 609 / 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: 4.12 Å3/Da / Density % sol: 69.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 2.4M Ammonium Sulfate, 05M sodium Citrate, cryo Glycerol or Sucrose, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.979 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 24, 2004
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 59682 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.119
Reflection shellHighest resolution: 2.4 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→102.6 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.91 / SU B: 13.039 / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.204 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24676 3015 5.1 %RANDOM
Rwork0.20332 ---
all0.20558 ---
obs0.20558 59598 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.238 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20 Å20 Å2
2--0.48 Å20 Å2
3----0.96 Å2
Refinement stepCycle: LAST / Resolution: 2.4→102.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5835 0 40 609 6484
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0225961
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1431.9888069
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1075752
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.75424.275255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.236151043
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1441536
X-RAY DIFFRACTIONr_chiral_restr0.1450.2915
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024431
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2540.22770
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.23987
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2510.2595
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2430.264
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2670.229
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it2.1091.53868
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.525986
X-RAY DIFFRACTIONr_scbond_it3.96932387
X-RAY DIFFRACTIONr_scangle_it6.1674.52083
X-RAY DIFFRACTIONr_rigid_bond_restr2.8936255
X-RAY DIFFRACTIONr_sphericity_free8.4323615
X-RAY DIFFRACTIONr_sphericity_bonded3.64235865
LS refinement shellResolution: 2.4→2.466 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 215 -
Rwork0.22 4069 -
obs--99.56 %

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