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- PDB-1r1u: Crystal structure of the metal-sensing transcriptional repressor ... -

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Basic information

Entry
Database: PDB / ID: 1r1u
TitleCrystal structure of the metal-sensing transcriptional repressor CzrA from Staphylococcus aureus in the apo-form
Componentsrepressor protein
KeywordsTRANSCRIPTION REPRESSOR / Zinc / DNA binding / Transcriptional regulation / winged HTH protein
Function / homology
Function and homology information


DNA-binding transcription factor activity / metal ion binding / identical protein binding
Similarity search - Function
: / Bacterial regulatory protein, arsR family / ArsR-type HTH domain profile. / helix_turn_helix, Arsenical Resistance Operon Repressor / HTH ArsR-type DNA-binding domain / ArsR-like helix-turn-helix domain / 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 ...: / Bacterial regulatory protein, arsR family / ArsR-type HTH domain profile. / helix_turn_helix, Arsenical Resistance Operon Repressor / HTH ArsR-type DNA-binding domain / ArsR-like helix-turn-helix domain / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ArsR family transcriptional regulator
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsEicken, C. / Pennella, M.A. / Chen, X. / Koshlap, K.M. / VanZile, M.L. / Sacchettini, J.C. / Giedroc, D.P.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: A metal-ligand-mediated intersubunit allosteric switch in related SmtB/ArsR zinc sensor proteins.
Authors: Eicken, C. / Pennella, M.A. / Chen, X. / Koshlap, K.M. / VanZile, M.L. / Sacchettini, J.C. / Giedroc, D.P.
History
DepositionSep 25, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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
A: repressor protein
B: repressor protein
C: repressor protein
D: repressor protein


Theoretical massNumber of molelcules
Total (without water)48,0314
Polymers48,0314
Non-polymers00
Water3,567198
1
A: repressor protein
B: repressor protein


Theoretical massNumber of molelcules
Total (without water)24,0152
Polymers24,0152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-23 kcal/mol
Surface area10250 Å2
MethodPISA
2
C: repressor protein
D: repressor protein


Theoretical massNumber of molelcules
Total (without water)24,0152
Polymers24,0152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-28 kcal/mol
Surface area10320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.110, 50.110, 153.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
DetailsThe biological assembly is a dimer. The asymmetric unit contains two dimers: A,B and C,D.

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Components

#1: Protein
repressor protein / CzrA


Mass: 12007.708 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O85142
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.32 Å3/Da / Density % sol: 46.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: NaCl, Na/K phosphate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 4, 2002 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→21 Å / Num. all: 29163 / Num. obs: 28209 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 3 % / Rsym value: 0.035 / Net I/σ(I): 13.6
Reflection shellResolution: 2→2.07 Å / Rsym value: 0.137 / % possible all: 74.1

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
CrystalClear(MSC/RIGAKU)data reduction
d*TREKdata scaling
MOLREPV. 7.3.01phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1R1T

1r1t


Resolution: 2→18.9 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.913 / SU B: 5.028 / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.211 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2559 2355 8.4 %RANDOM
Rwork0.20168 ---
all0.20625 25674 --
obs0.20625 25674 96.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.796 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20.37 Å20 Å2
2--0.74 Å20 Å2
3----1.12 Å2
Refinement stepCycle: LAST / Resolution: 2→18.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3016 0 0 198 3214
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0213062
X-RAY DIFFRACTIONr_bond_other_d0.0020.022819
X-RAY DIFFRACTIONr_angle_refined_deg1.8181.9384122
X-RAY DIFFRACTIONr_angle_other_deg1.03336583
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9745376
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.1250.2489
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023324
X-RAY DIFFRACTIONr_gen_planes_other0.0140.02552
X-RAY DIFFRACTIONr_nbd_refined0.250.2769
X-RAY DIFFRACTIONr_nbd_other0.250.23257
X-RAY DIFFRACTIONr_nbtor_other0.090.21830
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.2132
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2260.227
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2580.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2180.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.3411.51890
X-RAY DIFFRACTIONr_mcangle_it2.4123055
X-RAY DIFFRACTIONr_scbond_it3.08931172
X-RAY DIFFRACTIONr_scangle_it5.0534.51067
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.268 114
Rwork0.236 1382

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