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- PDB-2arc: ESCHERICHIA COLI REGULATORY PROTEIN ARAC COMPLEXED WITH L-ARABINOSE -

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Basic information

Entry
Database: PDB / ID: 2arc
TitleESCHERICHIA COLI REGULATORY PROTEIN ARAC COMPLEXED WITH L-ARABINOSE
ComponentsARABINOSE OPERON REGULATORY PROTEIN
KeywordsTRANSCRIPTION FACTOR / CARBOHYDRATE BINDING / COILED-COIL / JELLY ROLL
Function / homology
Function and homology information


arabinose catabolic process / DNA-binding transcription repressor activity / protein-DNA complex / transcription cis-regulatory region binding / identical protein binding / cytosol
Similarity search - Function
Regulatory protein AraC / Transcription regulator HTH-like / AraC-type arabinose-binding/dimerisation domain / AraC-like ligand binding domain / 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. ...Regulatory protein AraC / Transcription regulator HTH-like / AraC-type arabinose-binding/dimerisation domain / AraC-like ligand binding domain / 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 / Homeobox-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
alpha-L-arabinopyranose / Arabinose operon regulatory protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SINGLE ISOMORPHOUS REPLACEMENT / Resolution: 1.5 Å
AuthorsSoisson, S.M. / Wolberger, C.
CitationJournal: Science / Year: 1997
Title: Structural basis for ligand-regulated oligomerization of AraC.
Authors: Soisson, S.M. / MacDougall-Shackleton, B. / Schleif, R. / Wolberger, C.
History
DepositionOct 29, 1996Processing site: BNL
Revision 1.0May 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.process_site / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Feb 14, 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: ARABINOSE OPERON REGULATORY PROTEIN
B: ARABINOSE OPERON REGULATORY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4414
Polymers38,1412
Non-polymers3002
Water7,422412
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.750, 93.840, 50.330
Angle α, β, γ (deg.)90.00, 95.62, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.259135, 0.450464, -0.85436), (0.508354, -0.688524, -0.517215), (-0.821234, -0.568346, -0.050574)
Vector: 56.4191, 42.4771, 73.7901)

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Components

#1: Protein ARABINOSE OPERON REGULATORY PROTEIN / ARAC


Mass: 19070.564 Da / Num. of mol.: 2 / Fragment: SUGAR-BINDING/DIMERIZATION DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A9E0
#2: Sugar ChemComp-ARA / alpha-L-arabinopyranose / alpha-L-arabinose / L-arabinose / arabinose / Arabinose


Type: L-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
LArapaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-arabinopyranoseCOMMON NAMEGMML 1.0
a-L-ArapIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
AraSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 412 / 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: 2.28 Å3/Da / Density % sol: 46 %
Crystal growpH: 7.25
Details: PROTEIN WAS CRYSTALLIZED BY MICROSEEDING FROM 18-20% PEG 8000, 100 MM TRIS-HCL, PH 7.25, 40 MM MAGNESIUM ACETATE AND 0.2% (W/V) L-ARABINOSE
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: used to seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
118 %PEG80001reservoir
2100 mMTris-HCl1reservoir
340 mMmagnesium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.689
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Sep 1, 1995 / Details: SPHERICAL RH COATED MIRROR
RadiationMonochromator: SAGITALLY FOCUSED SI(111) DOUBLE CRYSTAL MONOCHROMATOR
Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.689 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 58716 / % possible obs: 94.7 % / Observed criterion σ(I): 1.5 / Redundancy: 5 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.051 / Net I/σ(I): 10.9
Reflection shellResolution: 1.5→1.57 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.292 / % possible all: 90.2

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: SINGLE ISOMORPHOUS REPLACEMENT
Resolution: 1.5→12 Å / Rfactor Rfree error: 0.321 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1.5
RfactorNum. reflection% reflectionSelection details
Rfree0.232 5193 10 %RANDOM
Rwork0.179 ---
obs0.179 50892 86.9 %-
Displacement parametersBiso mean: 20.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.1722 Å20 Å20.2994 Å2
2--0.0844 Å20 Å2
3----0.2566 Å2
Refine analyzeLuzzati coordinate error obs: 0.12 Å / Luzzati d res low obs: 12 Å
Refinement stepCycle: LAST / Resolution: 1.5→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2692 0 20 412 3124
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.483
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.811.87
X-RAY DIFFRACTIONx_mcangle_it3.731.87
X-RAY DIFFRACTIONx_scbond_it4.993.32
X-RAY DIFFRACTIONx_scangle_it7.123.56
LS refinement shellResolution: 1.5→1.57 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.273 480 9.4 %
Rwork0.267 3696 -
obs--67.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM3.CHOTOPH19.SOL
X-RAY DIFFRACTION3PARAM19.SOLARABINOSE.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.483

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