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- PDB-1td5: Crystal Structure of the Ligand Binding Domain of E. coli IclR. -

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Basic information

Entry
Database: PDB / ID: 1td5
TitleCrystal Structure of the Ligand Binding Domain of E. coli IclR.
ComponentsAcetate operon repressor
KeywordsTRANSCRIPTION / MIDWEST CENTER FOR STRUCTURAL GENOMICS / ALPHA/BETA DOMAIN / LIGAND BINDING DOMAIN / TRANSCRIPTION REGULATOR / PSI / Protein Structure Initiative / MCSG
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 / IclR helix-turn-helix domain / Transcription regulator IclR, N-terminal / Transcription regulator IclR, C-terminal / : / IclR-type HTH domain profile. / IclR effector binding domain profile. / GAF domain / GAF-like domain superfamily ...helix_turn_helix isocitrate lyase regulation / Bacterial transcriptional regulator / IclR helix-turn-helix domain / Transcription regulator IclR, N-terminal / Transcription regulator IclR, C-terminal / : / 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
Transcriptional repressor IclR
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsWalker, J.R. / Evdokimova, L. / Zhang, R.-G. / Bochkarev, A. / Joachimiak, A. / Arrowsmith, C. / Edwards, A. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
Citation
Journal: To be Published
Title: Structural Analyses of the Ligand Binding Sites of the IclR family of transcriptional regulators
Authors: Walker, J.R. / Evdokimova, L. / Zhang, R.-G. / Bochkarev, A. / Arrowsmith, C. / Edwards, A. / Savchenko, A.
#1: Journal: J.Biol.Chem. / Year: 2002
Title: Crystal Structure of Thermotoga maritima 0065, a member of the IclR transcriptional factor family
Authors: Zhang, R.-G. / Youngchang, K. / Skarina, T. / Beasley, S. / Laskowski, R. / Arrowsmith, C. / Edwards, A. / Joachimiak, A. / Savchenko, A.
#2: Journal: To be Published
Title: Crystal Structure Analysis of the E. coli Glyoxylate Regulatory Protein Ligand Binding Domain
Authors: Walker, J.R. / Skarina, T. / Kudrytska, M. / Arrowsmith, C. / Edwards, A. / Savchenko, A.
History
DepositionMay 21, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_remark / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_remark.text / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Remark 300BIOMOLECULE: 1, 2, 3, 4 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF ...BIOMOLECULE: 1, 2, 3, 4 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). GEL FILTRATION STUDIES SHOW THAT THE LIGAND BINDING DOMAIN OF ICLR IS A MONOMER IN SOLUTION.

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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


Theoretical massNumber of molelcules
Total (without water)90,8674
Polymers90,8674
Non-polymers00
Water6,035335
1
A: Acetate operon repressor


Theoretical massNumber of molelcules
Total (without water)22,7171
Polymers22,7171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Acetate operon repressor


Theoretical massNumber of molelcules
Total (without water)22,7171
Polymers22,7171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Acetate operon repressor


Theoretical massNumber of molelcules
Total (without water)22,7171
Polymers22,7171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Acetate operon repressor


Theoretical massNumber of molelcules
Total (without water)22,7171
Polymers22,7171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.098, 82.911, 157.316
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Acetate operon repressor / APC5050


Mass: 22716.697 Da / Num. of mol.: 4 / Fragment: ligand binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ICLR, B4018 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P16528
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.3 Å3/Da / Density % sol: 46.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: HEPES pH 7.5, Potassium acetate, PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934,0.9791,0.96110
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 4, 2002 / Details: mirrors
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979341
20.97911
30.96111
ReflectionResolution: 2.3→20 Å / Num. all: 31820 / Num. obs: 31820 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.96 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 19.9
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 4 / Num. unique all: 3100 / % possible all: 98.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→19.91 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 187632.18 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.299 1076 1.9 %RANDOM
Rwork0.23 ---
obs0.23 31820 96.1 %-
all-31820 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.2132 Å2 / ksol: 0.332517 e/Å3
Displacement parametersBiso mean: 37.7 Å2
Baniso -1Baniso -2Baniso -3
1--6.49 Å20 Å20 Å2
2--12.83 Å20 Å2
3----6.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5499 0 0 335 5834
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.93
X-RAY DIFFRACTIONc_mcbond_it1.551.5
X-RAY DIFFRACTIONc_mcangle_it2.572
X-RAY DIFFRACTIONc_scbond_it2.442
X-RAY DIFFRACTIONc_scangle_it3.512.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.393 160 1.8 %
Rwork0.289 8793 -
obs-8953 88.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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