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- PDB-4m3s: Crystal structure of a GNAT superfamily acetyltransferase PA4794 ... -

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Basic information

Entry
Database: PDB / ID: 4m3s
TitleCrystal structure of a GNAT superfamily acetyltransferase PA4794 in complex with HEPES
ComponentsUncharacterized protein
KeywordsTRANSFERASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / GNAT / acetyltransferase
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups / metal ion binding
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
N-acetyltransferase domain-containing protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å
AuthorsMajorek, K.A. / Chruszcz, M. / Xu, X. / Cymborowski, M. / Zheng, H. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Protein Sci. / Year: 2014
Title: Double trouble-Buffer selection and His-tag presence may be responsible for nonreproducibility of biomedical experiments.
Authors: Majorek, K.A. / Kuhn, M.L. / Chruszcz, M. / Anderson, W.F. / Minor, W.
History
DepositionAug 6, 2013Deposition site: RCSB / Processing site: RCSB
SupersessionAug 21, 2013ID: 2I6C
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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
Revision 1.2Aug 9, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8548
Polymers18,2821
Non-polymers5727
Water5,621312
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.950, 75.513, 39.481
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-4237-

HOH

21A-4307-

HOH

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Components

#1: Protein Uncharacterized protein


Mass: 18281.975 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA4794 / Plasmid: p11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: Q9HV14
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 2.32 Å3/Da / Density % sol: 47.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M NaHepes pH 7.5, 2%PEG400, 2M NH4SO4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97932 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 12, 2006 / Details: MIRRORS
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. all: 42543 / Num. obs: 42543 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.8 % / Biso Wilson estimate: 12.9 Å2 / Rmerge(I) obs: 0.103 / Rsym value: 0.103 / Net I/σ(I): 37.2
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.779 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2085 / Rsym value: 0.779 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-3000SOLVE/RESOLVEphasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMmodel building
ARP/wARPmodel building
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.3→29.83 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.339 / SU ML: 0.028 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.044 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16942 2142 5 %RANDOM
Rwork0.1332 ---
obs0.13501 40351 99.84 %-
all-40351 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.084 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20 Å2-0 Å2
2---0.2 Å2-0 Å2
3----0.37 Å2
Refinement stepCycle: LAST / Resolution: 1.3→29.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1245 0 29 312 1586
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0191392
X-RAY DIFFRACTIONr_bond_other_d0.0020.021317
X-RAY DIFFRACTIONr_angle_refined_deg1.7391.9771900
X-RAY DIFFRACTIONr_angle_other_deg1.3993.0022993
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.775179
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.05622.35368
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.80615201
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8861516
X-RAY DIFFRACTIONr_chiral_restr0.1120.2196
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211641
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02351
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_restr6.40531392
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded11.98451356
LS refinement shellResolution: 1.301→1.335 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 161 -
Rwork0.206 2904 -
obs-2904 98.78 %

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