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- PDB-4h89: The Structure of a GCN5-Related N-Acetyltransferase from Kribbell... -

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Basic information

Entry
Database: PDB / ID: 4h89
TitleThe Structure of a GCN5-Related N-Acetyltransferase from Kribbella flavida
ComponentsGCN5-related N-acetyltransferase
KeywordsTRANSFERASE / N-Acyltransferase superfamily / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / PFAM:PF00583 / putative acetyltransferase
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
GCN5-related N-acetyltransferase
Similarity search - Component
Biological speciesKribbella flavida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.37 Å
AuthorsCuff, M.E. / Mcknight, S.M. / Mack, J.C. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: The Structure of a GCN5-Related N-Acetyltransferase from Kribbella flavida.
Authors: Cuff, M.E. / Mcknight, S.M. / Mack, J.C. / Endres, M. / Joachimiak, A.
History
DepositionSep 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2012Provider: 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GCN5-related N-acetyltransferase


Theoretical massNumber of molelcules
Total (without water)18,9621
Polymers18,9621
Non-polymers00
Water4,990277
1
A: GCN5-related N-acetyltransferase

A: GCN5-related N-acetyltransferase


Theoretical massNumber of molelcules
Total (without water)37,9252
Polymers37,9252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2240 Å2
ΔGint-15 kcal/mol
Surface area15590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.482, 64.913, 56.569
Angle α, β, γ (deg.)90.000, 100.680, 90.000
Int Tables number5
Space group name H-MC121
DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN, BUT A POSSIBLE DIMER FORMED WITH CRYSTAL SYMMETRY MATES X,Y,Z AND -X,-Y,-Z

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Components

#1: Protein GCN5-related N-acetyltransferase


Mass: 18962.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kribbella flavida (bacteria) / Strain: DSM 17836 / Gene: Kfla_6915 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: D2Q3N2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / 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: 2.02 Å3/Da / Density % sol: 39.14 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES:NaOH pH 7.5, 1.4M Sodium Citrate, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931, 0.97945
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 8, 2012
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979311
20.979451
ReflectionResolution: 1.37→50 Å / Num. all: 30480 / Num. obs: 30480 / % possible obs: 95.8 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 16.4 Å2 / Rmerge(I) obs: 0.1 / Χ2: 4.434 / Net I/σ(I): 10.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.37-1.393.90.35114670.664192.5
1.39-1.424.30.30214890.812194.2
1.42-1.454.70.27815010.862194.8
1.45-1.484.80.26414801.082194.7
1.48-1.514.70.23815171.23195.1
1.51-1.544.70.21715051.517195.6
1.54-1.584.80.20615121.81195.4
1.58-1.624.70.18815522.105195.9
1.62-1.674.70.1815192.451196
1.67-1.734.70.16415022.815196.5
1.73-1.794.70.15115373.354196.4
1.79-1.864.70.13815484.04196.9
1.86-1.944.70.12815534.666196.9
1.94-2.054.70.11815315.7197.3
2.05-2.174.70.10515616.278197.4
2.17-2.344.70.1115327.945197.8
2.34-2.584.70.10815768.873198
2.58-2.954.60.09715739.519198.4
2.95-3.724.50.07915748.896198.6
3.72-504.40.092145113.789188.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.37→18.45 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.973 / WRfactor Rfree: 0.17 / WRfactor Rwork: 0.1215 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.9433 / SU B: 1.817 / SU ML: 0.033 / SU R Cruickshank DPI: 0.058 / SU Rfree: 0.0541 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.054
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1587 1541 5.1 %RANDOM
Rwork0.1175 ---
all0.1196 30373 --
obs0.1196 30373 95.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 106.32 Å2 / Biso mean: 22.4968 Å2 / Biso min: 11.47 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å2-1.65 Å2
2--0.86 Å20 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.37→18.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1283 0 0 277 1560
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191447
X-RAY DIFFRACTIONr_bond_other_d0.0010.021333
X-RAY DIFFRACTIONr_angle_refined_deg1.6891.9411989
X-RAY DIFFRACTIONr_angle_other_deg0.88133052
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1885190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.30721.71470
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.54815196
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1851518
X-RAY DIFFRACTIONr_chiral_restr0.1130.2208
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211743
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02375
X-RAY DIFFRACTIONr_rigid_bond_restr3.76332779
X-RAY DIFFRACTIONr_sphericity_free38.871558
X-RAY DIFFRACTIONr_sphericity_bonded11.72752951
LS refinement shellResolution: 1.37→1.405 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.206 107 -
Rwork0.162 2061 -
all-2168 -
obs--93.13 %

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