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- PDB-2gk3: Cytoplasmic Protein STM3548 from Salmonella typhimurium -

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Basic information

Entry
Database: PDB / ID: 2gk3
TitleCytoplasmic Protein STM3548 from Salmonella typhimurium
Componentsputative cytoplasmic protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Salmonella typhimurium / STM3548 / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologySTM3548-like / Putative glutamine amidotransferase / Putative glutamine amidotransferase / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Cytoplasmic protein
Function and homology information
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.25 Å
AuthorsPetrova, T. / Cuff, M.E. / Wu, R.Y. / Holzle, D. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: J.Struct.Funct.Genom. / Year: 2007
Title: Novel hexamerization motif is discovered in a conserved cytoplasmic protein from Salmonella typhimurium.
Authors: Petrova, T. / Cuff, M.E. / Wu, R. / Kim, Y. / Holzle, D. / Joachimiak, A.
History
DepositionMar 31, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 3, 2011Group: Database references
Revision 1.4Oct 30, 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
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 6 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 6 CHAIN(S) FORMING A STRIKING HEXAMER WITH D3 SYMMETRY. ADDITIONAL EXPERIMENTS ARE REQUIRED TO DETERMINE WHETHER THIS IS THE BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE. SEE REMARK 350 FOR INFORMATION ON GENERATING THE ASSUMED BIOLOGICAL MOLECULE(S).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: putative cytoplasmic protein
B: putative cytoplasmic protein
C: putative cytoplasmic protein
D: putative cytoplasmic protein
E: putative cytoplasmic protein
F: putative cytoplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,94412
Polymers175,3916
Non-polymers5536
Water9,872548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23430 Å2
ΔGint-98 kcal/mol
Surface area46660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.892, 79.367, 115.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsNot experimentally determined, D3 hexamer in the asymmetric unit

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Components

#1: Protein
putative cytoplasmic protein


Mass: 29231.891 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: DUF1355 / Plasmid: PMCSG7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ZLF9
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 548 / 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: 2.41 Å3/Da / Density % sol: 49.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris, pH 8.5, 1.2M tri-sodium citrate dehydrate, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979809, 0.979522
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Jun 28, 2004
RadiationMonochromator: sagitally focused Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9798091
20.9795221
ReflectionResolution: 2.25→115.47 Å / Num. all: 72006 / Num. obs: 72006 / % possible obs: 93.92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.25→2.34 Å / % possible all: 61.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-2000data scaling
autoSHARPphasing
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 2.25→115.47 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.937 / SU B: 6.693 / SU ML: 0.163 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.308 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22643 3815 5 %RANDOM
Rwork0.17717 ---
all0.17967 72006 --
obs0.17967 72006 93.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.456 Å2
Baniso -1Baniso -2Baniso -3
1--1.26 Å20 Å20 Å2
2--1.15 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.25→115.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11736 0 36 548 12320
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02212178
X-RAY DIFFRACTIONr_angle_refined_deg1.4171.94816552
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.91751494
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.125.026573
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.912151991
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7251532
X-RAY DIFFRACTIONr_chiral_restr0.1150.21788
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029344
X-RAY DIFFRACTIONr_nbd_refined0.2140.25891
X-RAY DIFFRACTIONr_nbtor_refined0.3090.28210
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2833
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2620.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2050.234
X-RAY DIFFRACTIONr_mcbond_it0.6791.57592
X-RAY DIFFRACTIONr_mcangle_it1.119211973
X-RAY DIFFRACTIONr_scbond_it1.64735307
X-RAY DIFFRACTIONr_scangle_it2.4864.54578
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 204 -
Rwork0.244 3707 -
obs--66.05 %

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