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- PDB-1bdt: WILD TYPE GENE-REGULATING PROTEIN ARC/DNA COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1bdt
TitleWILD TYPE GENE-REGULATING PROTEIN ARC/DNA COMPLEX
Components
  • DNA (5'-D(*AP*AP*TP*GP*AP*TP*AP*GP*AP*AP*GP*CP*AP*CP*TP*CP*TP*AP*CP*TP*AP*T)-3')
  • DNA (5'-D(*TP*AP*TP*AP*GP*TP*AP*GP*AP*GP*TP*GP*CP*TP*TP*CP*TP*AP*TP*CP*AP*T)-3')
  • PROTEIN (GENE-REGULATING PROTEIN ARC)
KeywordsGENE REGULATION/DNA / GENE-REGULATING PROTEIN / GENE REGULATION-DNA COMPLEX
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
DNA / DNA (> 10) / Transcriptional repressor arc
Similarity search - Component
Biological speciesEnterobacteria phage P22 (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSchilbach, J.F. / Karzai, A.W. / Raumann, B.E. / Sauer, R.T.
CitationJournal: 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.
History
DepositionMay 11, 1998Deposition site: BNL / Processing site: NDB
Revision 1.0Feb 16, 1999Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Category: struct_conf / struct_conf_type
Revision 1.4Aug 2, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: DNA (5'-D(*TP*AP*TP*AP*GP*TP*AP*GP*AP*GP*TP*GP*CP*TP*TP*CP*TP*AP*TP*CP*AP*T)-3')
F: DNA (5'-D(*AP*AP*TP*GP*AP*TP*AP*GP*AP*AP*GP*CP*AP*CP*TP*CP*TP*AP*CP*TP*AP*T)-3')
A: PROTEIN (GENE-REGULATING PROTEIN ARC)
B: PROTEIN (GENE-REGULATING PROTEIN ARC)
C: PROTEIN (GENE-REGULATING PROTEIN ARC)
D: PROTEIN (GENE-REGULATING PROTEIN ARC)


Theoretical massNumber of molelcules
Total (without water)38,4536
Polymers38,4536
Non-polymers00
Water1,49583
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.130, 56.410, 52.330
Angle α, β, γ (deg.)90.00, 104.14, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.5118, 0.1127, -0.8517), (0.1307, -0.9696, -0.2068), (-0.8491, -0.2172, 0.4815)63.4547, -8.0355, 35.2145
2given(0.5356, 0.0395, -0.8435), (0.0426, -0.9989, -0.0198), (-0.8434, -0.0253, -0.5367)58.0827, -4.3397, 105.3471
3given(0.0146, 0.1199, -0.9927), (0.1004, -0.9879, -0.1179), (-0.9948, -0.098, -0.0264)70.372, -5.9028, 71.2235

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Components

#1: DNA chain DNA (5'-D(*TP*AP*TP*AP*GP*TP*AP*GP*AP*GP*TP*GP*CP*TP*TP*CP*TP*AP*TP*CP*AP*T)-3')


Mass: 6756.387 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*AP*AP*TP*GP*AP*TP*AP*GP*AP*AP*GP*CP*AP*CP*TP*CP*TP*AP*CP*TP*AP*T)-3')


Mass: 6743.404 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein
PROTEIN (GENE-REGULATING PROTEIN ARC)


Mass: 6238.272 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage P22 (virus) / Genus: P22-like viruses / Description: SYNTHETIC GENE / Production host: Escherichia coli (E. coli) / References: UniProt: P03050
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.28 Å3/Da / Density % sol: 46.1 %
Crystal growpH: 4.5 / Details: pH 4.5
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 40011
2MGCL211
Crystal grow
*PLUS
pH: 8 / 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: 200 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Aug 7, 1996 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 12055 / % possible obs: 98.3 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Rmerge(I) obs: 0.075
Reflection shellResolution: 2.5→2.6 Å / % possible all: 80.9
Reflection shell
*PLUS
% possible obs: 80.9 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PAR

1par


Resolution: 2.5→20 Å / Rfactor Rfree error: 0.0081 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.282 -10 %RANDOM
Rwork0.2364 ---
obs0.2364 12055 98.3 %-
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1697 896 0 83 2676
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.41
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.12
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.26
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: 2.5→2.6 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.514 -10 %
Rwork0.4482 979 -
obs--89.75 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.236 / Rfactor Rwork: 0.236
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.339
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.12
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.26

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