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- PDB-2zcn: Crystal structure of IcaR, a repressor of the TetR family -

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Basic information

Entry
Database: PDB / ID: 2zcn
TitleCrystal structure of IcaR, a repressor of the TetR family
ComponentsBiofilm operon icaABCD HTH-type negative transcriptional regulator icaR
KeywordsTRANSCRIPTION / helix-turn-helix / biofilm / TetR family / repressor / polysaccharide intercellular adhesin (PIA) / DNA-binding / Transcription regulation
Function / homology
Function and homology information


IcaR, C-terminal / Tetracyclin repressor-like, C-terminal domain / : / Tetracycline Repressor, domain 2 / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biofilm operon icaADBC HTH-type negative transcriptional regulator IcaR
Similarity search - Component
Biological speciesStaphylococcus epidermidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsJeng, W.Y. / Ko, T.P. / Liu, C.I. / Guo, R.T. / Liu, C.L. / Wang, A.H.J.
CitationJournal: Nucleic Acids Res. / Year: 2008
Title: Crystal structure of IcaR, a repressor of the TetR family implicated in biofilm formation in Staphylococcus epidermidis
Authors: Jeng, W.Y. / Ko, T.P. / Liu, C.I. / Guo, R.T. / Liu, C.L. / Shr, H.L. / Wang, A.H.J.
History
DepositionNov 10, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Biofilm operon icaABCD HTH-type negative transcriptional regulator icaR
B: Biofilm operon icaABCD HTH-type negative transcriptional regulator icaR
C: Biofilm operon icaABCD HTH-type negative transcriptional regulator icaR
D: Biofilm operon icaABCD HTH-type negative transcriptional regulator icaR


Theoretical massNumber of molelcules
Total (without water)92,6334
Polymers92,6334
Non-polymers00
Water13,331740
1
A: Biofilm operon icaABCD HTH-type negative transcriptional regulator icaR
B: Biofilm operon icaABCD HTH-type negative transcriptional regulator icaR


Theoretical massNumber of molelcules
Total (without water)46,3162
Polymers46,3162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-21.9 kcal/mol
Surface area16850 Å2
MethodPISA
2
C: Biofilm operon icaABCD HTH-type negative transcriptional regulator icaR
D: Biofilm operon icaABCD HTH-type negative transcriptional regulator icaR


Theoretical massNumber of molelcules
Total (without water)46,3162
Polymers46,3162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-21.5 kcal/mol
Surface area16940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.11, 86.14, 113.85
Angle α, β, γ (deg.)90, 99.15, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Biofilm operon icaABCD HTH-type negative transcriptional regulator icaR / Intercellular adhesion protein R / intercellular adhesion regulator / IcaR repressor


Mass: 23158.199 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus epidermidis (bacteria) / Strain: RP62A / Gene: IcaR / Plasmid: pET-21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL-21 (DE3) / References: UniProt: Q5HKQ1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 740 / 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: 2.04 Å3/Da / Density % sol: 39.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 4~6% (w/v) PEG 1500, 1.4~1.8 M NaCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 10, 2005
Details: Vertically Collimating Premirror, Toroidal Focusing Mirror
RadiationMonochromator: LN2-Cooled Fixed-Exit Double Crystal Si(111) Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 58755 / Num. obs: 57448 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 6.2 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 17.6
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 3.5 / Num. unique all: 5881 / % possible all: 89.1

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZCM

2zcm


Resolution: 1.9→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.211 2855 -random
Rwork0.172 ---
all-58755 --
obs-56361 95.9 %-
Displacement parametersBiso mean: 35.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6174 0 0 740 6914
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_deg1.5
LS refinement shellResolution: 1.9→1.97 Å / Rfactor Rfree error: 0.067
RfactorNum. reflection% reflection
Rfree0.317 264 -
Rwork0.25 --
obs-5094 86.63 %

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