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- PDB-5jg7: Crystal structure of putative periplasmic binding protein from Sa... -

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Basic information

Entry
Database: PDB / ID: 5jg7
TitleCrystal structure of putative periplasmic binding protein from Salmonella typhimurium LT2
ComponentsFur regulated Salmonella iron transporter
KeywordsMETAL TRANSPORT / structural genomics / CSGID / periplasmic binding protein / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


metal ion transport / cell envelope / cell adhesion / metal ion binding
Similarity search - Function
Adhesin B / Adhesion lipoprotein / : / Periplasmic solute binding protein, ZnuA-like / Zinc-uptake complex component A periplasmic / Nitrogenase molybdenum iron protein domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Fur regulated Salmonella iron transporter
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsChang, C. / Zhou, M. / Shatsman, S. / Joachimiak, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Crystal structure of putative periplasmic binding protein from Salmonella typhimurium LT2
Authors: Chang, C. / Zhou, M. / Shatsman, S. / Joachimiak, A. / Anderson, W.F.
History
DepositionApr 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Experimental preparation
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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fur regulated Salmonella iron transporter
B: Fur regulated Salmonella iron transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1745
Polymers35,8982
Non-polymers2763
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6730 Å2
ΔGint-48 kcal/mol
Surface area15950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.057, 84.582, 91.049
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Fur regulated Salmonella iron transporter / periplasmic binding protein


Mass: 17948.754 Da / Num. of mol.: 2 / Fragment: UNP residues 28-187
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: sitA, STM2861 / Plasmid: pMCSG53
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q7CPX8
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 234 / 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: 2.56 Å3/Da / Density % sol: 51.99 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M proline, 0.1 M HEPES, 10% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 6, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 37084 / % possible obs: 96.8 % / Redundancy: 5.4 % / Biso Wilson estimate: 12.88 Å2 / Rmerge(I) obs: 0.03 / Rpim(I) all: 0.014 / Rrim(I) all: 0.033 / Χ2: 0.725 / Net I/av σ(I): 45.947 / Net I/σ(I): 11.3 / Num. measured all: 199870
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.7-1.734.50.3215650.920.1570.3580.77582.8
1.73-1.764.50.2816560.9420.1380.3130.7987.5
1.76-1.794.30.23817260.9630.1210.2680.76593.5
1.79-1.834.80.20317690.9690.0980.2260.74492.8
1.83-1.875.30.17318240.980.0790.1910.75697.6
1.87-1.915.40.14618370.9830.0660.1610.74596.3
1.91-1.965.50.11818400.990.0540.130.75999.7
1.96-2.025.50.10118780.9910.0460.1110.74697.6
2.02-2.075.40.08218940.9910.0380.090.73799.8
2.07-2.145.30.06718510.9920.0310.0740.70698.5
2.14-2.225.20.05918570.9930.0270.0650.71597.1
2.22-2.315.80.0519080.9960.0220.0540.70299.9
2.31-2.415.80.04118720.9970.0180.0450.63999.3
2.41-2.545.80.04119170.9960.0180.0450.67899.4
2.54-2.75.70.03618830.9960.0160.040.66699.3
2.7-2.915.50.03318990.9960.0150.0360.66398.3
2.91-3.260.02819310.9970.0120.0310.70899.7
3.2-3.665.90.02419620.9980.0110.0260.71399.9
3.66-4.615.60.02219400.9980.010.0240.75898.7
4.61-505.70.02320750.9950.010.0250.80398.5

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Processing

Software
NameVersionClassification
PHENIXdev_2328refinement
SCALEPACKdata scaling
PDB_EXTRACT3.2data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→30.984 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.39 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2133 1828 5.09 %
Rwork0.1718 34052 -
obs0.174 35880 93.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 159.56 Å2 / Biso mean: 23.0094 Å2 / Biso min: 2.59 Å2
Refinement stepCycle: final / Resolution: 1.7→30.984 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2228 0 30 234 2492
Biso mean--24.29 32.34 -
Num. residues----290
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062409
X-RAY DIFFRACTIONf_angle_d0.7343268
X-RAY DIFFRACTIONf_chiral_restr0.05359
X-RAY DIFFRACTIONf_plane_restr0.004428
X-RAY DIFFRACTIONf_dihedral_angle_d15.7131472
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6995-1.74550.2565950.20831843193867
1.7455-1.79680.24481110.18632102221376
1.7968-1.85480.22291250.17742443256889
1.8548-1.92110.23081380.17172647278596
1.9211-1.9980.211310.17332733286498
1.998-2.08890.20931420.16242739288199
2.0889-2.1990.2161270.15672723285098
2.199-2.33680.22141490.15362756290599
2.3368-2.51710.21731520.158527552907100
2.5171-2.77030.20641500.17622788293899
2.7703-3.17080.20771700.17862772294299
3.1708-3.99350.18811450.171228563001100
3.9935-30.98950.22091930.18092895308898

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