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- PDB-5ixp: Crystal structure of Extracellular solute-binding protein family 1 -

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Basic information

Entry
Database: PDB / ID: 5ixp
TitleCrystal structure of Extracellular solute-binding protein family 1
ComponentsExtracellular solute-binding protein family 1
KeywordsTRANSPORT PROTEIN / Structural Genomics / Midwest Center for Structural Genomics / MCSG / ABC transporter / solute-binding protein
Function / homology: / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Prokaryotic membrane lipoprotein lipid attachment site profile. / FORMIC ACID / Extracellular solute-binding protein family 1
Function and homology information
Biological speciesKribbella flavida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.73 Å
AuthorsChang, C. / Cuff, M. / Chhor, G. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To Be Published
Title: Crystal structure of Extracellular solute-binding protein family 1
Authors: Chang, C. / Cuff, M. / Chhor, G. / Endres, M. / Joachimiak, A.
History
DepositionMar 23, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Structure summary
Revision 1.2Oct 23, 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

Downloads & links

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Assembly

Deposited unit
A: Extracellular solute-binding protein family 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9744
Polymers43,8361
Non-polymers1383
Water5,927329
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.967, 115.184, 59.976
Angle α, β, γ (deg.)90.000, 131.170, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Extracellular solute-binding protein family 1


Mass: 43836.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kribbella flavida (strain DSM 17836 / JCM 10339 / NBRC 14399) (bacteria)
Strain: DSM 17836 / JCM 10339 / NBRC 14399 / Gene: Kfla_2403 / Plasmid: pMCSG68
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: D2PV11
#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 329 / 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: 2.67 Å3/Da / Density % sol: 53.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: Bis-Tris propane, tacsimate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 7, 2012
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.73→50 Å / Num. obs: 47739 / % possible obs: 99.7 % / Redundancy: 4.4 % / Biso Wilson estimate: 17.78 Å2 / Rmerge(I) obs: 0.044 / Net I/av σ(I): 27.638 / Net I/σ(I): 13.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.73-1.763.40.562197.9
1.76-1.793.50.494198.7
1.79-1.833.70.418199.1
1.83-1.863.90.344199.9
1.86-1.94.10.2961100
1.9-1.954.50.2291100
1.95-24.60.1951100
2-2.054.60.1591100
2.05-2.114.60.131100
2.11-2.184.70.1121100
2.18-2.264.60.0931100
2.26-2.354.70.0811100
2.35-2.454.70.0681100
2.45-2.584.70.0581100
2.58-2.754.70.0491100
2.75-2.964.70.041100
2.96-3.264.70.0331100
3.26-3.734.70.0281100
3.73-4.694.60.0261100
4.69-504.40.034198.7

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACT3.2data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.73→33.862 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.4
RfactorNum. reflection% reflection
Rfree0.1715 3987 4.96 %
Rwork0.1303 --
obs0.1324 46831 84.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 65.09 Å2 / Biso mean: 23.916 Å2 / Biso min: 7.21 Å2
Refinement stepCycle: final / Resolution: 1.73→33.862 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3068 0 9 329 3406
Biso mean--46.33 34.4 -
Num. residues----393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073322
X-RAY DIFFRACTIONf_angle_d0.8154537
X-RAY DIFFRACTIONf_chiral_restr0.049476
X-RAY DIFFRACTIONf_plane_restr0.004601
X-RAY DIFFRACTIONf_dihedral_angle_d14.8411960
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7289-1.750.2481590.17611341140041
1.75-1.77220.2847820.161415149745
1.7722-1.79550.2369730.16161584165749
1.7955-1.82010.2141940.15681702179653
1.8201-1.84610.1899900.15281766185656
1.8461-1.87360.19551240.14792044216862
1.8736-1.90290.20681000.14882055215566
1.9029-1.93410.18581090.13442419252872
1.9341-1.96740.19661290.13142506263579
1.9674-2.00320.18381330.12582732286585
2.0032-2.04170.19291390.12232877301688
2.0417-2.08340.20351420.11652959310192
2.0834-2.12870.17841870.11543000318795
2.1287-2.17820.17151640.11913131329597
2.1782-2.23270.15911980.11753162336099
2.2327-2.2930.16011670.11713198336599
2.293-2.36050.16951840.11863191337599
2.3605-2.43660.1791780.119731863364100
2.4366-2.52370.18381400.118132363376100
2.5237-2.62470.15631630.127732213384100
2.6247-2.74410.16611950.143631763371100
2.7441-2.88870.18841520.148732143366100
2.8887-3.06960.20782040.148331913395100
3.0696-3.30640.18411300.134832703400100
3.3064-3.63880.12341580.124132163374100
3.6388-4.16450.13761740.112832073381100
4.1645-5.24370.14291760.120232273403100
5.2437-33.86880.21951430.16083170331398

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