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- PDB-1hz4: CRYSTAL STRUCTURE OF TRANSCRIPTION FACTOR MALT DOMAIN III -

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Basic information

Entry
Database: PDB / ID: 1hz4
TitleCRYSTAL STRUCTURE OF TRANSCRIPTION FACTOR MALT DOMAIN III
ComponentsMALT REGULATORY PROTEIN
KeywordsTRANSCRIPTION ACTIVATOR / two-helix bundles / helix repeats / protein superhelix
Function / homology
Function and homology information


trisaccharide binding / positive regulation of carbohydrate metabolic process / DNA-binding transcription factor activity / positive regulation of DNA-templated transcription / DNA binding / ATP binding / identical protein binding
Similarity search - Function
Transcriptional regulator HTH-type, MalT / MalT-like TPR region / LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Signal transduction response regulator, C-terminal effector / Tetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat ...Transcriptional regulator HTH-type, MalT / MalT-like TPR region / LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Signal transduction response regulator, C-terminal effector / Tetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
BENZOIC ACID / HTH-type transcriptional regulator MalT
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.45 Å
AuthorsSteegborn, C. / Danot, O. / Clausen, T. / Huber, R.
CitationJournal: Structure / Year: 2001
Title: Crystal structure of transcription factor MalT domain III: a novel helix repeat fold implicated in regulated oligomerization.
Authors: Steegborn, C. / Danot, O. / Huber, R. / Clausen, T.
History
DepositionJan 23, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THE CRYSTALLOGRAPHIC TWOFOLD ROTATION AXIS GENERATES A DIMER WITH ABOUT 11 % OF THE SOLVENT ACCESSIBLE SURFACE OF EACH MONOMER COVERED BY THE INTERACTION. THE AUTHORS ASSUME THAT THIS INTERACTION IS A NON-PHYSIOLOGICAL CRYSTAL CONTACT EXPLOITING A PHYSIOLOGICAL PROTEIN/PROTEIN INTERACTION SITE, BUT CANNOT RULE OUT THE POSSIBILITY THAT THIS DIMER IS A BIOLOGICAL RELEVANT STATE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MALT REGULATORY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,99811
Polymers43,0161
Non-polymers98310
Water7,350408
1
A: MALT REGULATORY PROTEIN
hetero molecules

A: MALT REGULATORY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,99722
Polymers86,0312
Non-polymers1,96520
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area4920 Å2
ΔGint-219 kcal/mol
Surface area33190 Å2
MethodPISA
2
A: MALT REGULATORY PROTEIN
hetero molecules

A: MALT REGULATORY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,99722
Polymers86,0312
Non-polymers1,96520
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_674x-y+1,-y+2,-z-2/31
Buried area8220 Å2
ΔGint-226 kcal/mol
Surface area29900 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)87.845, 87.845, 110.036
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsThe biological assembly is a monomer or a dimer constructed from chain A and its symmetry partner generated by the two-fold rotation axis.

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Components

#1: Protein MALT REGULATORY PROTEIN


Mass: 43015.742 Da / Num. of mol.: 1 / Fragment: DOMAIN III (DT3)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P06993
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 408 / 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: 2.85 Å3/Da / Density % sol: 56.82 %
Crystal growTemperature: 291.2 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: ammonium sulphate, magnesium sulphate, MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.2K
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
17.5 mg/mlprotein1drop
250 mMMES/NaOH1reservoirpH6.5
31.6 Mammonium sulfate1reservoir
430 mMmagnesium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 3, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.45→20 Å / Num. all: 86426 / Num. obs: 86222 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.9 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 7.8
Reflection shellResolution: 1.45→1.47 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.386 / Num. unique all: 8340 / % possible all: 99.2
Reflection
*PLUS
% possible obs: 98.9 %
Reflection shell
*PLUS
% possible obs: 99.2 % / Rmerge(I) obs: 0.248

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Processing

Software
NameClassification
MLPHAREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.45→12 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.207 8654 RANDOM
Rwork0.189 --
all-87141 -
obs-86147 -
Refinement stepCycle: LAST / Resolution: 1.45→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2977 0 55 408 3440
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 12 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.2

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