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- PDB-4bmh: Crystal structure of SsHAT -

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Basic information

Entry
Database: PDB / ID: 4bmh
TitleCrystal structure of SsHAT
ComponentsACETYLTRANSFERASE
KeywordsTRANSFERASE / O-GLCNACASE / HAT
Function / homology
Function and homology information


N-acetyltransferase activity
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
Biological speciesSTREPTOMYCES SVICEUS ATCC 29083 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.5 Å
AuthorsHe, Y. / Turkenburg, J.P. / Davies, G.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Three-Dimensional Structure of a Streptomyces Sviceus Gnat Acetyltransferase with Similarity to the C-Terminal Domain of the Human Gh84 O-Glcnacase
Authors: He, Y. / Roth, C. / Turkenburg, J.P. / Davies, G.J.
History
DepositionMay 8, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2014Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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Assembly

Deposited unit
A: ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7152
Polymers28,6791
Non-polymers351
Water5,405300
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.885, 75.885, 76.517
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-2215-

HOH

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Components

#1: Protein ACETYLTRANSFERASE / / PUTATIVE N-ACETYLTRANSFERASE


Mass: 28679.330 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES SVICEUS ATCC 29083 (bacteria)
Plasmid: PETYSBLIC-3C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: B5HKU0
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 300 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE NCBI REFERENCE NUMBER FOR THIS SEQUENCE IS ZP_05014886

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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: 2.3 Å3/Da / Density % sol: 46 % / Description: NONE
Crystal growDetails: 0.2 M MGCL2, 0.1 M IMIDAZOLE PH8.0 AND 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 26, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.5→65.72 Å / Num. obs: 40822 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 12.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 20.8
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 4.9 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.6.0086refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 1.5→65.72 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.803 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 246-247 ARE DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.17457 2050 5 %RANDOM
Rwork0.14633 ---
obs0.14769 38757 98.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.44 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20.08 Å20 Å2
2--0.16 Å20 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.5→65.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1580 0 1 300 1881
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221632
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2551.9632233
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6885200
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.86821.15478
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.13815222
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1721520
X-RAY DIFFRACTIONr_chiral_restr0.080.2235
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0221313
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.98134603
X-RAY DIFFRACTIONr_sphericity_free8.4915301
X-RAY DIFFRACTIONr_sphericity_bonded9.20151580
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.19 151 -
Rwork0.179 2827 -
obs--98.12 %

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