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- PDB-4ius: GCN5-related N-acetyltransferase from Kribbella flavida. -

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Basic information

Entry
Database: PDB / ID: 4ius
TitleGCN5-related N-acetyltransferase from Kribbella flavida.
ComponentsGCN5-related N-acetyltransferase
KeywordsTRANSFERASE / structural genomics / GNAT family / PSI-Biology / 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) 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
MALONATE ION / GCN5-related N-acetyltransferase
Similarity search - Component
Biological speciesKribbella flavida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å
AuthorsOsipiuk, J. / Chhor, G. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: GCN5-related N-acetyltransferase from Kribbella flavida.
Authors: Osipiuk, J. / Chhor, G. / Endres, M. / Joachimiak, A.
History
DepositionJan 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Nov 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_ref_seq_dif / 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_ref_seq_dif.details / _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: GCN5-related N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7606
Polymers27,3421
Non-polymers4185
Water6,089338
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.993, 55.812, 104.702
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asymmetric unit (based on PISA)

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Components

#1: Protein GCN5-related N-acetyltransferase


Mass: 27342.150 Da / Num. of mol.: 1 / Mutation: G71D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kribbella flavida (bacteria) / Strain: DSM 17836 / Gene: Kfla_0359 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: D2PUG5, ribosomal-protein-alanine N-acetyltransferase
#2: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 2.14 Å3/Da / Density % sol: 42.44 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 2 M ammonium sulfate, 0.1 M Tris-HCl, 0.1 M sodium malonate , pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 2, 2012
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: 1.3→32.5 Å / Num. all: 57044 / Num. obs: 57044 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.066 / Χ2: 2.773 / Net I/σ(I): 14.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.3-1.322.20.3792.2321620.88875.6
1.32-1.352.50.35224990.8286.6
1.35-1.3730.36227361.02994.8
1.37-1.43.80.34328501.31699.5
1.4-1.434.50.30529101.251100
1.43-1.465.10.25328521.412100
1.46-1.55.20.20828831.281100
1.5-1.545.20.18528951.473100
1.54-1.595.20.15828831.506100
1.59-1.645.20.14228961.773100
1.64-1.75.20.1228991.922100
1.7-1.765.20.1129082.307100
1.76-1.845.20.09829102.753100
1.84-1.945.20.08629123.40699.9
1.94-2.065.10.07529233.751100
2.06-2.225.10.06929534.403100
2.22-2.4550.06929375.09799.8
2.45-2.84.90.06529595.56999.7
2.8-3.534.80.04829924.78299.7
3.53-504.60.0430854.63196.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.3→32.5 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.972 / Occupancy max: 1 / Occupancy min: 0.13 / SU B: 1.299 / SU ML: 0.025 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.047 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1556 2890 5.1 %RANDOM
Rwork0.1281 ---
all0.1295 56966 --
obs0.1295 56966 97.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 79.07 Å2 / Biso mean: 17.1247 Å2 / Biso min: 5.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å20 Å20 Å2
2---0.61 Å20 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.3→32.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1891 0 25 338 2254
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022137
X-RAY DIFFRACTIONr_bond_other_d0.0010.021425
X-RAY DIFFRACTIONr_angle_refined_deg1.6381.9792953
X-RAY DIFFRACTIONr_angle_other_deg0.96533487
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7495302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.43123.40297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.76415320
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9621521
X-RAY DIFFRACTIONr_chiral_restr0.0910.2334
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212495
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02438
X-RAY DIFFRACTIONr_rigid_bond_restr3.09833562
X-RAY DIFFRACTIONr_sphericity_free31.622591
X-RAY DIFFRACTIONr_sphericity_bonded10.25353749
LS refinement shellResolution: 1.301→1.335 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 147 -
Rwork0.233 2991 -
all-3138 -
obs-3138 76.7 %

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