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- PDB-1baz: ARC REPRESSOR MUTANT PHE10VAL -

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Basic information

Entry
Database: PDB / ID: 1baz
TitleARC REPRESSOR MUTANT PHE10VAL
ComponentsARC REPRESSOR
KeywordsTRANSCRIPTION REGULATION
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Arc-like DNA binding domain / Arc-like DNA binding domain / Met repressor-like / Arc Repressor Mutant / Arc-type ribbon-helix-helix / Ribbon-helix-helix / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcriptional repressor arc
Similarity search - Component
Biological speciesEnterobacteria phage P22 (virus)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsSchildbach, J.F. / Raumann, B.E. / Sauer, R.T.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Origins of DNA-binding specificity: role of protein contacts with the DNA backbone.
Authors: Schildbach, J.F. / Karzai, A.W. / Raumann, B.E. / Sauer, R.T.
#1: Journal: Nature / Year: 1994
Title: DNA Recognition by Beta-Sheets in the Arc Repressor-Operator Crystal Structure
Authors: Raumann, B.E. / Rould, M.A. / Pabo, C.O. / Sauer, R.T.
History
DepositionApr 21, 1998Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Other
Category: database_2 / pdbx_database_status / 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_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ARC REPRESSOR
B: ARC REPRESSOR
C: ARC REPRESSOR
D: ARC REPRESSOR


Theoretical massNumber of molelcules
Total (without water)24,7614
Polymers24,7614
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.900, 52.570, 47.320
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
ARC REPRESSOR / REGULATORY PROTEIN ARC


Mass: 6190.229 Da / Num. of mol.: 4 / Mutation: F10V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage P22 (virus) / Genus: P22-like viruses / Gene: ARC / Plasmid: PTA200-FV10 / Gene (production host): ARC / Production host: Escherichia coli (E. coli) / Strain (production host): UA2F / References: UniProt: P03050
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.31 Å3/Da / Density % sol: 46.69 %
Description: THE ARC MUTANT FV10 CRYSTALLIZED NEARLY ISOMORPHOUSLY WITH THE WILD TYPE WHEN CRYSTALLIZING USING MACROSEEDING. THEREFORE, THE WILD TYPE ARC STRUCTURE WAS USED AS THE INITIAL MODEL FOR THE MUTANT.
Crystal growpH: 8
Details: PROTEIN WAS CRYSTALLIZED FROM 40-45% SATURATED AMMONIUM PHOSPHATE, PH 8.0, BY MACROSEEDING USING CRYSTALS OF THE WILD TYPE PROTEIN
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
255 %satammonium phosphate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Oct 1, 1993 / Details: COLLIMATOR
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 1.9 Å / Num. obs: 16796 / % possible obs: 90 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Rmerge(I) obs: 0.087
Reflection shellResolution: 1.9→1.97 Å / % possible all: 50.7
Reflection
*PLUS
% possible obs: 89.9 %
Reflection shell
*PLUS
% possible obs: 50.7 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementResolution: 1.9→6 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: SCALE UNCONVENTIONAL ORTHORHOMBIC CELL, WITH A AND C SWAPPED.
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1633 10.1 %RANDOM
Rwork0.213 ---
obs0.213 16211 90 %-
Displacement parametersBiso mean: 31.1 Å2
Refinement stepCycle: LAST / Resolution: 1.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1530 0 0 67 1597
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg1.494
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.49
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.9→1.97 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.4641 98 10.8 %
Rwork0.3836 810 -
obs--50.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.49

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