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- PDB-1b4a: STRUCTURE OF THE ARGININE REPRESSOR FROM BACILLUS STEAROTHERMOPHILUS -

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Basic information

Entry
Database: PDB / ID: 1b4a
TitleSTRUCTURE OF THE ARGININE REPRESSOR FROM BACILLUS STEAROTHERMOPHILUS
ComponentsARGININE REPRESSOR
KeywordsREPRESSOR / ARGININE / HELIX TURN HELIX
Function / homology
Function and homology information


regulation of arginine biosynthetic process / L-arginine biosynthetic process / arginine binding / protein complex oligomerization / DNA-binding transcription factor activity / DNA 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-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A ...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-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsNi, J. / Sakanyan, V. / Charlier, D. / Glansdorff, N. / Van Duyne, G.D.
Citation
Journal: Nat.Struct.Biol. / Year: 1999
Title: Structure of the arginine repressor from Bacillus stearothermophilus.
Authors: Ni, J. / Sakanyan, V. / Charlier, D. / Glansdorff, N. / Van Duyne, G.D.
#1: Journal: Thesis, University of Pennsylvania / Year: 1998
Title: The Crystal Structure of Arginine Repressor
Authors: Ni, J.
History
DepositionDec 18, 1998Processing site: BNL
Revision 1.0Jun 15, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 2.0Aug 2, 2023Group: Atomic model / Database references ...Atomic model / Database references / Other / Refinement description
Category: atom_site / database_2 ...atom_site / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 2.1May 22, 2024Group: Advisory / Data collection / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_struct_special_symmetry / pdbx_validate_symm_contact

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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


Theoretical massNumber of molelcules
Total (without water)100,8576
Polymers100,8576
Non-polymers00
Water10,575587
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11280 Å2
ΔGint-43 kcal/mol
Surface area40360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.800, 121.900, 227.400
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
11B-168-

HOH

21D-150-

HOH

31E-203-

HOH

41E-229-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
/ NCS ensembles :
ID
1
2
3

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Components

#1: Protein
ARGININE REPRESSOR


Mass: 16809.545 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Geobacillus stearothermophilus (bacteria) / References: UniProt: O31408
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 587 / 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: 2.5 Å3/Da / Density % sol: 50 %
Crystal growpH: 5 / Details: pH 5
Crystal grow
*PLUS
Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein11
2100 mMsodium acetate11
310 mM2-mercaptoethanol11
40.35 M11NaCl
516 %PEG800011
620 %ehthylene glycol12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.9
DetectorDetector: CCD / Date: Dec 1, 1997 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.5→32 Å / Num. obs: 35454 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Rsym value: 0.064 / Net I/σ(I): 18
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 3 / Rsym value: 0.201 / % possible all: 100
Reflection
*PLUS
% possible obs: 98.4 % / Rmerge(I) obs: 0.054
Reflection shell
*PLUS
% possible obs: 99.5 % / Rmerge(I) obs: 0.167

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XXC

1xxc


Resolution: 2.5→8 Å / Rfactor Rfree error: 0.017 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.279 4137 10 %RANDOM
Rwork0.224 ---
obs0.224 35284 93 %-
Displacement parametersBiso mean: 48 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0 Å0 Å
Luzzati d res low-0 Å
Luzzati sigma a0 Å0 Å
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7451 0 0 587 8038
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d0
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.635
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.53
X-RAY DIFFRACTIONx_mcangle_it1.51.4
X-RAY DIFFRACTIONx_scbond_it43.8
X-RAY DIFFRACTIONx_scangle_it21.8
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Rms dev position: 1.5 Å / Weight Biso : 1

Ens-IDDom-IDNCS model detailsRms dev Biso (Å2)Weight position
11RESTRAINTS15280
2215250
3320250
LS refinement shellResolution: 2.5→2.6 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.37 560 10 %
Rwork0.32 4040 -
obs--87 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PROTEIN_REP.PARAM
X-RAY DIFFRACTION3PARAM19TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg0
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.635

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