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- PDB-5hqj: Crystal structure of ABC transporter Solute Binding Protein B1G1H... -

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Basic information

Entry
Database: PDB / ID: 5hqj
TitleCrystal structure of ABC transporter Solute Binding Protein B1G1H7 from Burkholderia graminis C4D1M, target EFI-511179, in complex with D-arabinose
ComponentsPeriplasmic binding protein/LacI transcriptional regulator
KeywordsSOLUTE-BINDING PROTEIN / ABC TRANSPORTER SOLUTE BINDING PROTEIN / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics
Function / homology
Function and homology information


outer membrane-bounded periplasmic space / carbohydrate binding
Similarity search - Function
: / Periplasmic binding protein / Periplasmic binding protein domain / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-D-arabinopyranose / Periplasmic binding protein/LacI transcriptional regulator
Similarity search - Component
Biological speciesBurkholderia graminis C4D1M (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.55 Å
AuthorsRoth, Y. / Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Koss, J. / Wasserman, S.R. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be published
Title: Crystal structure of ABC transporter Solute Binding Protein B1G1H7 from Burkholderia graminis C4D1M, target EFI-511179, in complex with D-arabinose
Authors: Roth, Y. / Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Koss, J. / Wasserman, S.R. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionJan 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_chem_comp_identifier / pdbx_prerelease_seq / pdbx_struct_oper_list / pdbx_validate_close_contact / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.type / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_close_contact.auth_atom_id_2
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Periplasmic binding protein/LacI transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9193
Polymers33,7341
Non-polymers1862
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.094, 37.403, 62.429
Angle α, β, γ (deg.)90.000, 113.610, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Periplasmic binding protein/LacI transcriptional regulator


Mass: 33733.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia graminis C4D1M (bacteria) / Strain: C4D1M / Gene: BgramDRAFT_3172 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B1G1H7
#2: Sugar ChemComp-64K / alpha-D-arabinopyranose / alpha-D-arabinose / D-arabinose / arabinose


Type: D-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
DArapaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-arabinopyranoseCOMMON NAMEGMML 1.0
a-D-ArapIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
AraSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 1.94 Å3/Da / Density % sol: 36.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein (10 mM HEPES pH 7.5, 5 mM DTT, 10 mM D-Arabinose); Reservoir (MCSG2 B2)(0.2 M Potassium Acetate 20 %(w/v) PEG 3350); Cryoprotection (20% Ethylene Glycol, 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: Oct 20, 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: 1.55→50 Å / Num. obs: 37889 / % possible obs: 99.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 12.81 Å2 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.022 / Rrim(I) all: 0.061 / Χ2: 0.892 / Net I/av σ(I): 27.917 / Net I/σ(I): 10.3 / Num. measured all: 282195
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.55-1.617.40.65637480.910.2580.7050.792100
1.61-1.677.40.4737490.9450.1850.5060.799100
1.67-1.757.40.34137840.9660.1340.3670.795100
1.75-1.847.50.23237620.980.0910.2490.777100
1.84-1.957.50.15737720.9890.0610.1680.834100
1.95-2.17.50.10337860.9930.040.1110.879100
2.1-2.327.50.08937760.9940.0350.0961.23100
2.32-2.657.50.07538120.9940.0290.0811.311100
2.65-3.347.50.04438170.9980.0170.0470.833100
3.34-507.20.03338830.9980.0130.0350.65298.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data scaling
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
MLPHAREphasing
RefinementMethod to determine structure: SAD / Resolution: 1.55→27.991 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.254 1721 4.8 %
Rwork0.2057 34159 -
obs0.2081 35880 94.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 331.42 Å2 / Biso mean: 32.4823 Å2 / Biso min: 4.84 Å2
Refinement stepCycle: final / Resolution: 1.55→27.991 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2149 0 21 270 2440
Biso mean--21.27 32.46 -
Num. residues----289
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122227
X-RAY DIFFRACTIONf_angle_d1.3553017
X-RAY DIFFRACTIONf_chiral_restr0.055358
X-RAY DIFFRACTIONf_plane_restr0.006394
X-RAY DIFFRACTIONf_dihedral_angle_d14.817852
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5492-1.59480.2996820.24551875195763
1.5948-1.64630.3141200.26042424254481
1.6463-1.70510.31511370.27232851298895
1.7051-1.77340.30961500.269829763126100
1.7734-1.85410.30081320.265429973129100
1.8541-1.95180.33171440.258629823126100
1.9518-2.07410.2841570.23232985314299
2.0741-2.23410.26921610.22172956311799
2.2341-2.45880.24141730.208629953168100
2.4588-2.81430.28741810.201229713152100
2.8143-3.54470.1951420.179430493191100
3.5447-27.99540.2061420.15083098324099
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)
10.1495-0.0001-0.23861.2281-0.20360.64890.1520.09310.1015-0.8622-0.27010.50970.8763-0.51390.11330.5183-0.1545-0.15060.2869-0.03540.039917.53278.347843.0824
20.44160.03030.08940.5965-0.19340.3711-0.0331-0.1346-0.15580.21410.0535-0.1625-0.0391-0.09460.00260.06220.00340.00330.07860.03330.112847.665510.609138.8083
31.00030.41760.13650.52120.08150.3024-0.022-0.16820.3159-0.0887-0.02310.19640.2527-0.0210.02560.14180.05930.04720.1638-0.02030.08633.199417.642349.6958
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 25 through 133 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 134 through 243 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 244 through 313 )A0

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