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- PDB-4yle: Crystal structure of an ABC transpoter solute binding protein (IP... -

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Basic information

Entry
Database: PDB / ID: 4yle
TitleCrystal structure of an ABC transpoter solute binding protein (IPR025997) from Burkholderia multivorans (Bmul_1631, Target EFI-511115) with an unknown ligand modelled as alpha-D-erythrofuranose
ComponentsPeriplasmic binding protein/LacI transcriptional regulator
KeywordsTRANSPORT PROTEIN / ABC TRANSPORTER SOLUTE BINDING PROTEIN / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics
Function / homology
Function and homology information


carbohydrate transport / periplasmic space
Similarity search - Function
Periplasmic binding protein / Periplasmic binding protein domain / Response regulator / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Unknown ligand / Periplasmic binding protein/LacI transcriptional regulator / Periplasmic binding protein/LacI transcriptional regulator
Similarity search - Component
Biological speciesBurkholderia multivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsVetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Koss, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. ...Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Koss, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Love, J. / Seidel, R.D. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM093342 United States
CitationJournal: To be published
Title: Crystal structure of an ABC transporter solute binding protein (IPR025997) from Burkholderia multivorans (Bmul_1631, Target EFI-511115) with an unknown ligand modelled as alpha-D-erythrofuranose
Authors: Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Koss, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Love, J. ...Authors: Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Koss, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Love, J. / Seidel, R.D. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C.
History
DepositionMar 5, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Periplasmic binding protein/LacI transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)34,0322
Polymers34,0321
Non-polymers01
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.966, 69.267, 115.060
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 Periplasmic binding protein/LacI transcriptional regulator / Simple sugar transport system substrate-binding protein


Mass: 34031.801 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia multivorans (bacteria) / Strain: ATCC 17616 / 249 / Gene: Bmul_1631, BMULJ_01611 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A9AIX1, UniProt: A0A0H3KJG7*PLUS
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 1.93 Å3/Da / Density % sol: 36.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein (10 mM HEPES pH 7.5, 5 mM DTT); Reservoir (MCSG1 G7, 0.1 M Tris pH 8.5, 25% (w/v) PEG 3350); Cryoprotection (20% glycerol, 80% Reservoir)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Feb 24, 2015 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.7→29.67 Å / Num. obs: 28926 / % possible obs: 96.8 % / Redundancy: 10.7 % / Biso Wilson estimate: 21.58 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.031 / Net I/σ(I): 15.4 / Num. measured all: 309119 / Scaling rejects: 127
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.7-1.73110.8162.81527313860.840.24988.6
9-29.678.20.07529.216251980.9920.02677.1

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Processing

Software
NameVersionClassification
Aimless0.5.1data scaling
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.7→26.437 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2109 1409 4.88 %
Rwork0.1711 27459 -
obs0.1731 28868 96.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.52 Å2 / Biso mean: 34.3261 Å2 / Biso min: 11.4 Å2
Refinement stepCycle: final / Resolution: 1.7→26.437 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2099 0 8 246 2353
Biso mean--16.87 38 -
Num. residues----283
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112130
X-RAY DIFFRACTIONf_angle_d1.3432881
X-RAY DIFFRACTIONf_chiral_restr0.054345
X-RAY DIFFRACTIONf_plane_restr0.006375
X-RAY DIFFRACTIONf_dihedral_angle_d14.413797
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.76080.23881260.22422484261089
1.7608-1.83120.2871340.20712569270391
1.8312-1.91460.26251440.20472633277795
1.9146-2.01550.22341350.18422684281997
2.0155-2.14170.21341540.17972749290398
2.1417-2.3070.2181340.17352815294999
2.307-2.53890.22131320.161428492981100
2.5389-2.90590.22091410.176528392980100
2.9059-3.65960.23991480.16829103058100
3.6596-26.44060.16651610.15492927308897
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)
12.66-0.756-0.63564.97412.07892.81350.123-0.11130.3622-0.51920.2271-0.7114-0.14230.334-0.3680.17450.00040.05620.2-0.03020.279711.2478-4.873411.3665
21.3416-0.2993-0.19526.61381.81332.97580.15740.19130.2484-0.7978-0.0763-0.5303-0.2204-0.0224-0.08060.2563-0.03870.16540.2159-0.05850.427212.7558-1.28068.3977
30.54041.17980.16783.04660.3523.6113-0.06410.34550.4228-1.4078-0.0327-0.0081-1.024-0.14860.00880.66160.06740.03130.23550.06140.30973.02635.55162.1659
42.9513-0.2145-0.0342.02191.45191.7829-0.0863-0.03180.0080.0408-0.21740.3466-0.0592-0.57360.25080.13770.0357-0.00420.2794-0.07860.2003-9.34017.819126.9741
50.2188-0.35650.343.40562.13582.830-0.08320.1216-0.10440.0327-0.0984-0.4191-0.3189-0.07610.18780.0645-0.02630.2096-0.05490.2275-0.368516.09729.3382
61.12410.2998-0.24212.06941.07472.3088-0.1852-0.27260.17030.50470.2763-0.33950.20530.1494-0.09120.21740.1083-0.05840.2261-0.07520.17460.616710.166534.5619
71.1597-0.7595-1.31173.46151.64435.3141-0.17190.0658-0.10470.0386-0.07860.1580.4497-0.30110.21980.1139-0.02260.02040.1212-0.00590.19430.6012-5.135315.8093
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 30:60 )A30 - 60
2X-RAY DIFFRACTION2( CHAIN A AND RESID 61:77 )A61 - 77
3X-RAY DIFFRACTION3( CHAIN A AND RESID 78:145 )A78 - 145
4X-RAY DIFFRACTION4( CHAIN A AND RESID 146:193 )A146 - 193
5X-RAY DIFFRACTION5( CHAIN A AND RESID 194:219 )A194 - 219
6X-RAY DIFFRACTION6( CHAIN A AND RESID 220:259 )A220 - 259
7X-RAY DIFFRACTION7( CHAIN A AND RESID 260:315 )A260 - 315

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