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- PDB-4fe7: structure of xylose-binding transcription activator xylR -

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Basic information

Entry
Database: PDB / ID: 4fe7
Titlestructure of xylose-binding transcription activator xylR
ComponentsXylose operon regulatory protein
KeywordsDNA BINDING PROTEIN / HTH_ARAC / Helix-turn-helix / PBP / periplasmic binding protein / DNA-binding transcription regulator / DNA xylose
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription
Similarity search - Function
Bacterial regulatory helix-turn-helix proteins, AraC family / Transcription regulator HTH, AraC- type / HTH domain AraC-type, conserved site / Bacterial regulatory proteins, araC family signature. / DNA binding HTH domain, AraC-type / Helix-turn-helix domain / Bacterial regulatory proteins, araC family DNA-binding domain profile. / helix_turn_helix, arabinose operon control protein / Transcriptional regulator LacI/GalR-like, sensor domain / Periplasmic binding protein-like domain ...Bacterial regulatory helix-turn-helix proteins, AraC family / Transcription regulator HTH, AraC- type / HTH domain AraC-type, conserved site / Bacterial regulatory proteins, araC family signature. / DNA binding HTH domain, AraC-type / Helix-turn-helix domain / Bacterial regulatory proteins, araC family DNA-binding domain profile. / helix_turn_helix, arabinose operon control protein / Transcriptional regulator LacI/GalR-like, sensor domain / Periplasmic binding protein-like domain / Homeodomain-like / Response regulator / Periplasmic binding protein-like I / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
alpha-D-xylopyranose / Xylose operon regulatory protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsNi, L. / Schumacher, M.A.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: Structures of the Escherichia coli transcription activator and regulator of diauxie, XylR: an AraC DNA-binding family member with a LacI/GalR ligand-binding domain.
Authors: Ni, L. / Tonthat, N.K. / Chinnam, N. / Schumacher, M.A.
History
DepositionMay 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2013Group: Database references
Revision 1.2Feb 20, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jul 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 1.5Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
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: Xylose operon regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2522
Polymers47,1011
Non-polymers1501
Water93752
1
A: Xylose operon regulatory protein
hetero molecules

A: Xylose operon regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,5034
Polymers94,2032
Non-polymers3002
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area5290 Å2
ΔGint-24 kcal/mol
Surface area33130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.071, 70.071, 215.403
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Xylose operon regulatory protein


Mass: 47101.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: DH5 alpha / Gene: xylR / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0ACI3
#2: Sugar ChemComp-XYS / alpha-D-xylopyranose / alpha-D-xylose / D-xylose / xylose / XYLOPYRANOSE


Type: D-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
DXylpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-xylopyranoseCOMMON NAMEGMML 1.0
a-D-XylpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
XylSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.81 Å3/Da / Density % sol: 56.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.3 M Li2SO4 100 mM Tris pH=8.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.95689 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 14, 2009
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95689 Å / Relative weight: 1
ReflectionResolution: 2.9→107.83 Å / Num. all: 12704 / Num. obs: 12704 / % possible obs: 100 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 2 / Redundancy: 8.6 % / Biso Wilson estimate: 70.333 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 29.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2.9-3.068.70.3857.617891100
9.17-107.838.70.0359.2501199.9

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SOLVEphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→66.67 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.865 / SU B: 29.4 / SU ML: 0.302 / Cross valid method: THROUGHOUT / ESU R Free: 0.42 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27916 615 4.9 %RANDOM
Rwork0.2193 ---
all0.22204 12022 --
obs0.22204 12022 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.101 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2--0.07 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.9→66.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3067 0 10 52 3129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223139
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2751.9534252
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8575377
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.73323.567157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.35915540
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2161526
X-RAY DIFFRACTIONr_chiral_restr0.0880.2469
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022390
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2270.21436
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.22151
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.286
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.275
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2410.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4871.51923
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.81623054
X-RAY DIFFRACTIONr_scbond_it1.1531355
X-RAY DIFFRACTIONr_scangle_it1.9094.51198
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 58 -
Rwork0.298 828 -
obs--100 %
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)
12.1411-1.3356-3.15571.53773.03366.2612-0.0403-0.220.07210.40410.3861-0.27980.06930.917-0.34580.15540.117-0.05690.1976-0.07140.118545.83825.935112.858
26.8077-2.2663-1.3521.93070.18471.1261-0.03610.0205-0.60460.138-0.04820.04340.2488-0.21520.0842-0.0609-0.0254-0.05960.2416-0.21020.090629.60912.71185.19
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 272
2X-RAY DIFFRACTION2A285 - 389

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