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- PDB-1b4b: STRUCTURE OF THE OLIGOMERIZATION DOMAIN OF THE ARGININE REPRESSOR... -

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Basic information

Entry
Database: PDB / ID: 1b4b
TitleSTRUCTURE OF THE OLIGOMERIZATION DOMAIN OF THE ARGININE REPRESSOR FROM BACILLUS STEAROTHERMOPHILUS
ComponentsARGININE REPRESSOR
KeywordsREPRESSOR / ARGININE / CORE / OLIGOMERIZATION DOMAIN / 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 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 / Arginine repressor
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 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 1.4Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4486
Polymers22,9233
Non-polymers5263
Water3,603200
1
A: ARGININE REPRESSOR
B: ARGININE REPRESSOR
C: ARGININE REPRESSOR
hetero molecules

A: ARGININE REPRESSOR
B: ARGININE REPRESSOR
C: ARGININE REPRESSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,89712
Polymers45,8466
Non-polymers1,0516
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Unit cell
Length a, b, c (Å)82.000, 82.000, 67.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-160-

HOH

21A-211-

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: 7640.941 Da / Num. of mol.: 3 / Fragment: OLIGOMERIZATION DOMAIN, L-ARGININE BINDING DOMAIN / Source method: isolated from a natural source / Source: (natural) Geobacillus stearothermophilus (bacteria) / References: UniProt: O31408
#2: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H15N4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.3 Å3/Da / Density % sol: 50 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein11
210 mML-arginine11
3100 mMsodium cacodylate11
410 mM2-mercaptoethanol11
5100 mM11NaCl
620 mM11CaCl2
730 %PEG40011

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1996 / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 12146 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Rsym value: 0.052 / Net I/σ(I): 18
Reflection shellResolution: 2.2→2.26 Å / Mean I/σ(I) obs: 3 / Rsym value: 0.216 / % possible all: 100
Reflection
*PLUS
Rmerge(I) obs: 0.052
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.216

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8model building
X-PLOR3.8refinement
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XXC

1xxc


Resolution: 2.2→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
Rfree0.266 4137 10 %RANDOM
Rwork0.218 ---
obs0.218 12097 95 %-
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: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1835 0 0 200 2035
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.005
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_deg1.2
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_d0.596
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: 2.2→2.3 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_deg0.596

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