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- PDB-1tf1: Crystal Structure of the E. coli Glyoxylate Regulatory Protein Li... -

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Basic information

Entry
Database: PDB / ID: 1tf1
TitleCrystal Structure of the E. coli Glyoxylate Regulatory Protein Ligand Binding Domain
ComponentsNegative regulator of allantoin and glyoxylate utilization operons
KeywordsTRANSCRIPTION / Midwest Center for Structural Genomics / GlcR / ligand binding domain / transcriptional regulator / PSI / Protein Structure Initiative / MCSG
Function / homology
Function and homology information


DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA damage response / DNA binding / identical protein binding / cytosol
Similarity search - Function
helix_turn_helix isocitrate lyase regulation / IclR helix-turn-helix domain / Transcription regulator IclR, N-terminal / Transcription regulator IclR, C-terminal / : / Bacterial transcriptional 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 / IclR helix-turn-helix domain / Transcription regulator IclR, N-terminal / Transcription regulator IclR, C-terminal / : / Bacterial transcriptional 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
HTH-type transcriptional repressor AllR
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWalker, J.R. / Skarina, T. / Kudrytska, M. / Joachimiak, A. / Arrowsmith, C. / Edwards, A. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
Citation
Journal: J.Mol.Biol. / Year: 2006
Title: Structural and biochemical study of effector molecule recognition by the E.coli glyoxylate and allantoin utilization regulatory protein AllR.
Authors: Walker, J.R. / Altamentova, S. / Ezersky, A. / Lorca, G. / Skarina, T. / Kudritska, M. / Ball, L.J. / Bochkarev, 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. / Kim, Y. / Skarina, T. / Beasley, S. / Laskowski, R. / Arrowsmith, C. / Edwards, A. / Joachimiak, A. / Savchenko, A.
#2: 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. / Joachimiak, A. / Arrowsmith, C. / Edwards, A. / Savchenko, A.
History
DepositionMay 26, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 300BIOMOLECULE GEL FILTRATION STUDIES SHOW THAT THE GLCR LIGAND BINDING DOMAIN FORMS A MONOMER IN SOLUTION.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Negative regulator of allantoin and glyoxylate utilization operons
B: Negative regulator of allantoin and glyoxylate utilization operons
C: Negative regulator of allantoin and glyoxylate utilization operons
D: Negative regulator of allantoin and glyoxylate utilization operons


Theoretical massNumber of molelcules
Total (without water)85,8664
Polymers85,8664
Non-polymers00
Water10,719595
1
A: Negative regulator of allantoin and glyoxylate utilization operons


Theoretical massNumber of molelcules
Total (without water)21,4671
Polymers21,4671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Negative regulator of allantoin and glyoxylate utilization operons


Theoretical massNumber of molelcules
Total (without water)21,4671
Polymers21,4671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Negative regulator of allantoin and glyoxylate utilization operons


Theoretical massNumber of molelcules
Total (without water)21,4671
Polymers21,4671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Negative regulator of allantoin and glyoxylate utilization operons


Theoretical massNumber of molelcules
Total (without water)21,4671
Polymers21,4671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.796, 97.538, 144.488
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly is a tetramer generated by applying the translation -46.4850, -48.8411, 0.0000 to molecule C.

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Components

#1: Protein
Negative regulator of allantoin and glyoxylate utilization operons / Transcriptional regulator allR / APC5051


Mass: 21466.574 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: glxa3 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ACN4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 595 / 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: 2.18 Å3/Da / Density % sol: 43.56 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.5
Details: MgCl2, PEG3350, Tris PH 8.5, ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 100K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 12, 2004
RadiationMonochromator: CONFOCAL MULTILAYER OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 59628 / Num. obs: 59628 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 20.7 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 15.1
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.277 / Num. unique all: 5986 / % possible all: 98.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1T9L

1t9l
PDB Unreleased entry


Resolution: 1.8→19.73 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2980696.7 / 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
Rfree0.257 3033 5.1 %RANDOM
Rwork0.214 ---
obs0.214 59563 97.7 %-
all-59563 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.8659 Å2 / ksol: 0.363963 e/Å3
Displacement parametersBiso mean: 27.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.76 Å20 Å20 Å2
2---10.08 Å20 Å2
3---8.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.8→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5457 0 0 595 6052
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d1.2
X-RAY DIFFRACTIONc_mcbond_it1.411.5
X-RAY DIFFRACTIONc_mcangle_it2.022
X-RAY DIFFRACTIONc_scbond_it2.482
X-RAY DIFFRACTIONc_scangle_it3.552.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.284 529 5.3 %
Rwork0.242 9374 -
obs--98.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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