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- PDB-3kkw: Crystal structure of His-tagged form of PA4794 protein -

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Basic information

Entry
Database: PDB / ID: 3kkw
TitleCrystal structure of His-tagged form of PA4794 protein
ComponentsPutative uncharacterized protein
KeywordsTRANSFERASE / acetyltransferase / GNAT family / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
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 PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsMajorek, K.A. / Chruszcz, M. / 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
DepositionNov 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 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
Revision 1.4Sep 6, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,62220
Polymers20,3751
Non-polymers1,24719
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.534, 76.145, 39.454
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Putative uncharacterized protein


Mass: 20375.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: PA4794 / Plasmid: p11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) real / References: UniProt: Q9HV14
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.12 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.5 M Ammonium Sulfate, 0.1 M Tris pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 12, 2009 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.41→50 Å / Num. all: 34174 / Num. obs: 34174 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 14.6 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 47.19
Reflection shellResolution: 1.41→1.43 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 4.18 / Num. unique all: 1658 / Rsym value: 0.391 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-3000MOLREPphasing
REFMAC5.5.0072refinement
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2i6c

2i6c
PDB Unreleased entry


Resolution: 1.41→45.9 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.962 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.056 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17922 1727 5.1 %RANDOM
Rwork0.15628 ---
all0.15749 32398 --
obs0.15749 32398 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.124 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å20 Å2
2---0.28 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.41→45.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1326 0 78 210 1614
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0211421
X-RAY DIFFRACTIONr_bond_other_d00.021010
X-RAY DIFFRACTIONr_angle_refined_deg1.8181.9621894
X-RAY DIFFRACTIONr_angle_other_deg4.10332413
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7435170
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.08522.568
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.40515213
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2341513
X-RAY DIFFRACTIONr_chiral_restr0.1120.2193
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211562
X-RAY DIFFRACTIONr_gen_planes_other0.0140.02305
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_it1.1691.5841
X-RAY DIFFRACTIONr_mcbond_other01.5342
X-RAY DIFFRACTIONr_mcangle_it1.97421334
X-RAY DIFFRACTIONr_scbond_it2.8773580
X-RAY DIFFRACTIONr_scangle_it4.4284.5560
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.41→1.447 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.207 115 -
Rwork0.196 2345 -
obs--99.31 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.7758-0.3503-3.67693.5813-2.65718.3749-0.3062-0.36780.0373-0.3887-0.2205-0.55440.69970.9440.52660.11620.06890.04860.12390.05450.1116-8.38838.08223.604
20.55170.20090.43290.8025-0.05951.30240.015-0.00760.03750.05210.00470.0319-0.01030.099-0.01970.0532-0.020.00530.0562-0.0110.027916.53515.08317.474
30.3293-0.11650.00360.52980.47491.7393-0.02190.01120.0461-0.04510.03750.0668-0.01890.041-0.01560.0608-0.02410.00540.04760.00050.035511.22915.2666.886
40.26570.3567-0.00161.1655-0.39630.7317-0.0050.0191-0.01140.03010.0466-0.0158-0.03170.0551-0.04160.0638-0.0125-0.00160.0471-0.00420.03227.1694.7066.824
54.05892.601-4.944.3628-2.56276.15810.09190.32460.2784-0.16030.24470.2575-0.2215-0.365-0.33660.1569-0.0541-0.01040.10870.03080.05135.50911.203-3.133
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-19 - -13
2X-RAY DIFFRACTION2A1 - 66
3X-RAY DIFFRACTION3A67 - 104
4X-RAY DIFFRACTION4A105 - 153
5X-RAY DIFFRACTION5A154 - 159

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