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- PDB-2qco: Crystal structure of the transcriptional regulator CmeR from Camp... -

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Basic information

Entry
Database: PDB / ID: 2qco
TitleCrystal structure of the transcriptional regulator CmeR from Campylobacter jejuni
ComponentsCmeR
KeywordsTRANSCRIPTION / transcriptional regulator protein
Function / homology
Function and homology information


Tetracycline Repressor, domain 2 / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.25 Å
AuthorsGu, R. / Su, C. / Shi, F. / Li, M. / McDermott, G. / Zhang, Q. / Yu, E.W.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal structure of the transcriptional regulator CmeR from Campylobacter jejuni.
Authors: Gu, R. / Su, C.C. / Shi, F. / Li, M. / McDermott, G. / Zhang, Q. / Yu, E.W.
History
DepositionJun 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CmeR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3552
Polymers24,2631
Non-polymers921
Water55831
1
A: CmeR
hetero molecules

A: CmeR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7104
Polymers48,5262
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area4510 Å2
ΔGint-36 kcal/mol
Surface area20310 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)93.125, 37.587, 57.789
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe second part of the biological assembly is generated by the two fold axis: -x,-y,z.

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Components

#1: Protein CmeR


Mass: 24262.896 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: cmeR / Plasmid: PQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q7B8P6
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.08 Å3/Da / Density % sol: 40.98 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 23, 2006
RadiationMonochromator: Si 111 Channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 10172 / Num. obs: 10132 / % possible obs: 99.6 % / Observed criterion σ(F): 3.9 / Observed criterion σ(I): 3.9 / Rsym value: 0.055 / Net I/σ(I): 16.6
Reflection shellResolution: 2.25→2.33 Å / Mean I/σ(I) obs: 4.7 / Rsym value: 0.262 / % possible all: 97.7

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Processing

Software
NameClassification
HKL-2000data collection
SnBphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.25→50 Å / σ(F): 3.9 / σ(I): 3.9 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.243 506 -random
Rwork0.219 ---
obs0.23 10132 99.6 %-
all-10172 --
Refinement stepCycle: LAST / Resolution: 2.25→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1649 0 6 31 1686
Refine LS restraintsType: c_angle_d / Dev ideal: 0.8

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