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- PDB-2o99: The crystal structure of E.coli IclR C-terminal fragment in compl... -

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Basic information

Entry
Database: PDB / ID: 2o99
TitleThe crystal structure of E.coli IclR C-terminal fragment in complex with glyoxylate
ComponentsAcetate operon repressor
KeywordsDNA BINDING PROTEIN / IclR
Function / homology
Function and homology information


glyoxylate cycle / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA binding / cytosol
Similarity search - Function
helix_turn_helix isocitrate lyase regulation / Bacterial transcriptional regulator / Transcription regulator IclR, N-terminal / Transcription regulator IclR, C-terminal / IclR helix-turn-helix domain / IclR-type HTH domain profile. / IclR effector binding domain profile. / GAF domain / GAF-like domain superfamily / Beta-Lactamase ...helix_turn_helix isocitrate lyase regulation / Bacterial transcriptional regulator / Transcription regulator IclR, N-terminal / Transcription regulator IclR, C-terminal / IclR helix-turn-helix domain / IclR-type HTH domain profile. / IclR effector binding domain profile. / GAF domain / GAF-like domain superfamily / Beta-Lactamase / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
GLYCOLIC ACID / Transcriptional repressor IclR
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLunin, V.V. / Ezersky, A. / Evdokimova, E. / Kudritska, M. / Savchenko, A.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Glyoxylate and Pyruvate Are Antagonistic Effectors of the Escherichia coli IclR Transcriptional Regulator.
Authors: Lorca, G.L. / Ezersky, A. / Lunin, V.V. / Walker, J.R. / Altamentova, S. / Evdokimova, E. / Vedadi, M. / Bochkarev, A. / Savchenko, A.
History
DepositionDec 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_close_contact / struct_conn / struct_ref_seq_dif / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_validate_close_contact.auth_atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_label_atom_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 ...BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). Although there are two dimers in the asymmetric unit, the dimer might not represent the biological unit since only the fragment of the protein is present in the crystal.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetate operon repressor
B: Acetate operon repressor
C: Acetate operon repressor
D: Acetate operon repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,92112
Polymers81,3694
Non-polymers5528
Water11,295627
1
A: Acetate operon repressor
D: Acetate operon repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9616
Polymers40,6842
Non-polymers2764
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint3 kcal/mol
Surface area16420 Å2
MethodPISA
2
B: Acetate operon repressor
C: Acetate operon repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9616
Polymers40,6842
Non-polymers2764
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint3 kcal/mol
Surface area16320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.538, 81.483, 154.693
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a dimer, there are two of them in the asymmetric unit, chains A and D form first dimer and chain B and C form second dimer.

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Components

#1: Protein
Acetate operon repressor


Mass: 20342.150 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: Pet15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P16528
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-GOA / GLYCOLIC ACID / HYDROXYACETIC ACID / HYDROXYETHANOIC ACID / Glycolic acid


Mass: 76.051 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H4O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 627 / 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: 2.07 Å3/Da / Density % sol: 40.66 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M Potassium Acetate, pH 7.0, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 16, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→50.59 Å / Num. all: 73139 / Num. obs: 73139 / % possible obs: 97.1 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 5.93 % / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 13.7
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 3.9 / Rsym value: 3.9 / % possible all: 85.5

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Phasing

Phasing MRRfactor: 0.586 / Cor.coef. Fo:Fc: 0.159
Highest resolutionLowest resolution
Rotation3 Å38.73 Å
Translation3 Å38.73 Å

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Processing

Software
NameVersionClassificationNB
d*TREK9.2SSIdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT2data extraction
CrystalClear(MSC/RIGAKU)data collection
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.109 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26116 3677 5 %RANDOM
Rwork0.20371 ---
obs0.20661 69414 97.12 %-
all-62684 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.338 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2--0.34 Å20 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5664 0 36 627 6327
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0215806
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8611.9667834
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6695754
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.47623.145248
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.006151063
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0521548
X-RAY DIFFRACTIONr_chiral_restr0.1290.2886
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024336
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2360.23149
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2970.23978
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2563
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2390.2114
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1850.251
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3031.53813
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.90925878
X-RAY DIFFRACTIONr_scbond_it3.43232228
X-RAY DIFFRACTIONr_scangle_it4.5054.51947
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 242 -
Rwork0.302 4325 -
obs--83.43 %

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