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- PDB-1xxa: C-TERMINAL DOMAIN OF ESCHERICHIA COLI ARGININE REPRESSOR/ L-ARGIN... -

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Basic information

Entry
Database: PDB / ID: 1xxa
TitleC-TERMINAL DOMAIN OF ESCHERICHIA COLI ARGININE REPRESSOR/ L-ARGININE COMPLEX; PB DERIVATIVE
ComponentsARGININE REPRESSOR
KeywordsCOMPLEX (DNA BINDING PROTEIN/PEPTIDE) / COMPLEX (DNA BINDING PROTEIN-PEPTIDE) / COMPLEX (DNA BINDING PROTEIN-PEPTIDE) complex
Function / homology
Function and homology information


regulation of arginine catabolic process / plasmid recombination / regulation of arginine biosynthetic process / negative regulation of DNA-templated transcription initiation / : / positive regulation of DNA-templated transcription initiation / L-arginine biosynthetic process / arginine binding / protein complex oligomerization / cis-regulatory region sequence-specific DNA binding ...regulation of arginine catabolic process / plasmid recombination / regulation of arginine biosynthetic process / negative regulation of DNA-templated transcription initiation / : / positive regulation of DNA-templated transcription initiation / L-arginine biosynthetic process / arginine binding / protein complex oligomerization / cis-regulatory region sequence-specific DNA binding / transcription regulator complex / DNA-binding transcription factor activity / identical protein binding / cytoplasm
Similarity search - Function
Arginine repressor / Arginine repressor, C-terminal / Arginine repressor, DNA-binding domain / Arginine repressor, C-terminal domain superfamily / Arginine repressor, DNA binding domain / Arginine repressor, C-terminal domain / Gyrase A; domain 2 - #40 / Gyrase A; domain 2 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily ...Arginine repressor / Arginine repressor, C-terminal / Arginine repressor, DNA-binding domain / Arginine repressor, C-terminal domain superfamily / Arginine repressor, DNA binding domain / Arginine repressor, C-terminal domain / Gyrase A; domain 2 - #40 / Gyrase A; domain 2 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ARGININE / LEAD (II) ION / Arginine repressor
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsVan Duyne, G.D. / Ghosh, G. / Maas, W.K. / Sigler, P.B.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: Structure of the oligomerization and L-arginine binding domain of the arginine repressor of Escherichia coli.
Authors: Van Duyne, G.D. / Ghosh, G. / Maas, W.K. / Sigler, P.B.
#1: Journal: Mol.Microbiol. / Year: 1994
Title: The Arginine Repressor of Escherichia Coli
Authors: Maas, W.K.
#2: Journal: J.Mol.Biol. / Year: 1987
Title: Nucleotide Sequence of the Argr Gene of Escherichia Coli K-12 and Isolation of its Product, the Arginine Repressor
Authors: Lim, D.B. / Oppenheim, J.D. / Eckhardt, T. / Maas, W.K.
History
DepositionNov 3, 1995Processing site: BNL
Revision 1.0Mar 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ARGININE REPRESSOR
B: ARGININE REPRESSOR
C: ARGININE REPRESSOR
D: ARGININE REPRESSOR
E: ARGININE REPRESSOR
F: ARGININE REPRESSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,98916
Polymers50,1096
Non-polymers1,88010
Water7,476415
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9130 Å2
ΔGint-48 kcal/mol
Surface area17630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.500, 83.800, 217.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11E-219-

HOH

21F-452-

HOH

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Components

#1: Protein
ARGININE REPRESSOR / ARGR


Mass: 8351.467 Da / Num. of mol.: 6 / Fragment: INITIATOR MET PLUS C-TERMINAL RESIDUES 80 - 156
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Description: T7 PROMOTER SYSTEM (NOVAGEN) / Gene: T7 / Plasmid: PET3A / Gene (production host): T7 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6D0
#2: Chemical
ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H15N4O2
#3: Chemical
ChemComp-PB / LEAD (II) ION / ARG


Mass: 207.200 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Pb
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.3 %
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
210 mML-arginine1drop
350 mMNaHepes1drop
4100 mM1dropNaCl
520 mM1dropCaCl2
620-25 %MPD1drop

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9
DetectorType: FUJI / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 24878 / % possible obs: 95 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Rmerge(I) obs: 0.089
Reflection
*PLUS
Rmerge(I) obs: 0.089

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8model building
X-PLOR3.8refinement
X-PLOR3.8phasing
RefinementResolution: 2.2→8 Å / σ(F): 3 /
RfactorNum. reflection
Rfree0.33 -
Rwork0.2 -
obs0.2 23025
Displacement parametersBiso mean: 42 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3286 0 4 415 3705
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_deg2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.4
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Num. reflection all: 23025 / Num. reflection obs: 19076 / Rfactor all: 0.241 / Rfactor obs: 0.195
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4

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