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- PDB-2aac: ESCHERCHIA COLI GENE REGULATORY PROTEIN ARAC COMPLEXED WITH D-FUCOSE -

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Basic information

Entry
Database: PDB / ID: 2aac
TitleESCHERCHIA COLI GENE REGULATORY PROTEIN ARAC COMPLEXED WITH D-FUCOSE
ComponentsARAC
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. / Helix-turn-helix domain / DNA binding HTH domain, AraC-type / 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. / Helix-turn-helix domain / DNA binding HTH domain, AraC-type / 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
ACETIC ACID / beta-D-fucopyranose / Arabinose operon regulatory protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / RIGID-BODY REFINEMENT, DIFFERENCE FOURIER MAPS / Resolution: 1.6 Å
AuthorsSoisson, S.M. / Wolberger, C.
CitationJournal: J.Mol.Biol. / Year: 1997
Title: The 1.6 A crystal structure of the AraC sugar-binding and dimerization domain complexed with D-fucose.
Authors: Soisson, S.M. / MacDougall-Shackleton, B. / Schleif, R. / Wolberger, C.
History
DepositionOct 31, 1996Processing site: BNL
Revision 1.0Nov 12, 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 1.4Aug 9, 2023Group: Database references / Refinement description / Structure summary
Category: chem_comp / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ARAC
B: ARAC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5436
Polymers41,0942
Non-polymers4484
Water7,296405
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.247, 93.682, 49.915
Angle α, β, γ (deg.)90.00, 95.57, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.191475, 0.4722, -0.860444), (0.516994, -0.696666, -0.497367), (-0.834299, -0.540078, -0.110731)
Vector: 53.0876, 41.8669, 74.9226)

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Components

#1: Protein ARAC


Mass: 20547.184 Da / Num. of mol.: 2 / Fragment: SUGAR-BINDING/DIMERIZATION
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ARAC / Gene (production host): ARAC / Production host: Escherichia coli (E. coli) / References: UniProt: P0A9E0
#2: Sugar ChemComp-FCB / beta-D-fucopyranose / beta-D-fucose / 6-deoxy-beta-D-galactopyranose / D-fucose / fucose


Type: D-saccharide, beta linking / Mass: 164.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
DFucpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-fucopyranoseCOMMON NAMEGMML 1.0
b-D-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / 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: 2.23 Å3/Da / Density % sol: 45 %
Crystal growpH: 5.5
Details: PROTEIN WAS CRYSTALLIZED BY MICROSEEDING FROM 24% PEG 4000, 100 MM SODIUM CITRATE PH 5.5 200 MM AMMONIUM ACETATE
Crystal grow
*PLUS
pH: 7.25 / Method: vapor diffusion, hanging drop
Details: used to seeding, Soisson, S.M., (1997) Science, 276, 421.
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: 1.6→30 Å / Num. obs: 47363 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Biso Wilson estimate: 12.31 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 9.7
Reflection shellResolution: 1.6→1.67 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.08 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.39 / % possible all: 99
Reflection
*PLUS
Num. obs: 57378 / Num. measured all: 293876 / Rmerge(I) obs: 0.09

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: RIGID-BODY REFINEMENT, DIFFERENCE FOURIER MAPS
Starting model: PDB ENTRY 2ARC

2arc


Resolution: 1.6→7 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.01 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.222 4112 10 %RANDOM
Rwork0.176 ---
obs0.176 46103 98 %-
Displacement parametersBiso mean: 12.48 Å2
Baniso -1Baniso -2Baniso -3
1--0.4819 Å20 Å20.3233 Å2
2--1.3664 Å20 Å2
3----0.8845 Å2
Refine analyzeLuzzati coordinate error obs: 0.15 Å / Luzzati d res low obs: 30 Å
Refinement stepCycle: LAST / Resolution: 1.6→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2617 0 30 405 3052
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_deg1.58
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.29
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.762.64
X-RAY DIFFRACTIONx_mcangle_it1.683.37
X-RAY DIFFRACTIONx_scbond_it2.984.47
X-RAY DIFFRACTIONx_scangle_it2.975.94
LS refinement shellResolution: 1.6→1.67 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.284 583 10 %
Rwork0.249 5111 -
obs--96 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2ACY.PARAMTOPH19.SOL
X-RAY DIFFRACTION3PARAM19.SOLFCB_ACY.TOP
X-RAY DIFFRACTION4PARAM3.CHO
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.29

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