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- PDB-4kzk: The structure of the periplasmic L-arabinose binding protein from... -

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Basic information

Entry
Database: PDB / ID: 4kzk
TitleThe structure of the periplasmic L-arabinose binding protein from Burkholderia thailandensis
ComponentsL-arabinose ABC transporter, periplasmic L-arabinose-binding protein
KeywordsSUGAR BINDING PROTEIN / L-arabinose / BETA-D-GALACTOSE / ABC transporter / periplasmic binding protein / SSGCID / Seattle Structural Genomics Center for Infectious Disease / NIAID / National Institute of Allergy and Infectious Diseases / Sugar binding
Function / homology
Function and homology information


L-arabinose transmembrane transport / outer membrane-bounded periplasmic space / carbohydrate binding
Similarity search - Function
L-arabinose-binding periplasmic protein / Periplasmic binding protein/LacI sugar binding domain / Periplasmic binding proteins and sugar binding domain of LacI family / : / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
beta-D-galactopyranose / L-arabinose-binding periplasmic protein
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: The structure of the periplasmic L-arabinose binding protein from Burkholderia thailandensis
Authors: Clifton, M.C. / Fairman, J.W.
History
DepositionMay 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2016Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: L-arabinose ABC transporter, periplasmic L-arabinose-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7502
Polymers35,5691
Non-polymers1801
Water6,197344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.770, 51.820, 59.220
Angle α, β, γ (deg.)90.000, 107.340, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein L-arabinose ABC transporter, periplasmic L-arabinose-binding protein


Mass: 35569.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / Gene: BTH_II1196 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2T607
#2: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / 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: 1.88 Å3/Da / Density % sol: 34.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 50% MPD, 200mM Ammonium Phosphate, 100mM Tris pH8.5, 14.8mg/ml, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 10, 2013
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.5→43.73 Å / Num. obs: 11596 / % possible obs: 100 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 20.707 Å2 / Rmerge(I) obs: 0.111 / Net I/σ(I): 21.42
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.95-20.4376.7511845836100
2-2.060.3747.8911425800100
2.06-2.120.3069.7411224787100
2.12-2.180.27410.8610931770100
2.18-2.250.22912.8410432738100
2.25-2.330.21113.7410496739100
2.33-2.420.18814.989785694100
2.42-2.520.16517.359445671100
2.52-2.630.14718.979168650100
2.63-2.760.13619.878790629100
2.76-2.910.10625.18438603100
2.91-3.080.09227.57822566100
3.08-3.30.08130.797418539100
3.3-3.560.06337.776814504100
3.56-3.90.05839.346208462100
3.9-4.360.0543.375701440100
4.36-5.040.04647.915029380100
5.04-6.170.0637.294349337100
6.17-8.720.0540.843380273100
8.720.03847.33183917898.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.95 Å48.01 Å
Translation1.95 Å48.01 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.2phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ABP

5abp


Resolution: 1.5→43.73 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.1688 / WRfactor Rwork: 0.1405 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8886 / SU B: 2.578 / SU ML: 0.051 / SU R Cruickshank DPI: 0.113 / SU Rfree: 0.1108 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1925 2142 5.1 %RANDOM
Rwork0.1696 ---
obs0.1708 -99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 48.77 Å2 / Biso mean: 17.7108 Å2 / Biso min: 6.31 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å2-0 Å2-0.84 Å2
2---0.25 Å2-0 Å2
3---0.55 Å2
Refinement stepCycle: LAST / Resolution: 1.5→43.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2235 0 12 344 2591
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192328
X-RAY DIFFRACTIONr_bond_other_d0.0010.022223
X-RAY DIFFRACTIONr_angle_refined_deg1.2721.9533180
X-RAY DIFFRACTIONr_angle_other_deg0.76635095
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3055312
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.81123.91897
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.44815355
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9241516
X-RAY DIFFRACTIONr_chiral_restr0.0720.2364
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212706
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02528
X-RAY DIFFRACTIONr_mcbond_it0.4580.8281215
X-RAY DIFFRACTIONr_mcbond_other0.4460.8271214
X-RAY DIFFRACTIONr_mcangle_it0.7721.2411520
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 157 -
Rwork0.243 2976 -
all-3133 -
obs--99.78 %
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)
12.01580.58981.16481.76860.6371.5290.1786-0.3481-0.11380.2209-0.0953-0.09470.0857-0.2201-0.08330.0561-0.0240.00050.08670.03310.0266-2.8423.198171.8225
21.71780.59361.47032.45040.60042.17030.1610.0269-0.2410.1964-0.0047-0.53770.14190.125-0.15630.03580.015-0.05730.03060.00960.16527.585318.408867.5127
31.04130.26520.12070.97360.11421.2324-0.0540.1054-0.0305-0.15070.05360.0011-0.05260.01090.00050.0421-0.00830.00120.0222-0.00040.0364-9.225719.640843.755
41.38610.98470.51810.89180.69320.74680.196-0.1475-0.25240.2233-0.1053-0.16680.2161-0.0502-0.09070.1179-0.0212-0.04740.04520.0610.1224-7.26339.299266.171
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A33 - 107
2X-RAY DIFFRACTION2A108 - 138
3X-RAY DIFFRACTION3A139 - 288
4X-RAY DIFFRACTION4A289 - 333

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