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- PDB-3qqa: Crystal structures of CmeR-bile acid complexes from Campylobacter... -

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Basic information

Entry
Database: PDB / ID: 3qqa
TitleCrystal structures of CmeR-bile acid complexes from Campylobacter jejuni
ComponentsCmeR
KeywordsTRANSCRIPTION / Alpha-helical / Helix-Turn-Helix / DNA-binding / Transcription regulation / Transcription repressor / drug binding
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
TAUROCHOLIC ACID / CmeR
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLei, H.T. / Routh, M.D. / Shen, Z. / Su, C.-C. / Zhang, Q. / Yu, E.W.
CitationJournal: Protein Sci. / Year: 2011
Title: Crystal structures of CmeR-bile acid complexes from Campylobacter jejuni.
Authors: Lei, H.T. / Shen, Z. / Surana, P. / Routh, M.D. / Su, C.C. / Zhang, Q. / Yu, E.W.
History
DepositionFeb 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 29, 2012Group: Database references
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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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)25,6072
Polymers25,0921
Non-polymers5161
Water97354
1
A: CmeR
hetero molecules

A: CmeR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2154
Polymers50,1842
Non-polymers1,0312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area5840 Å2
ΔGint-34 kcal/mol
Surface area19850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.992, 37.774, 57.642
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein CmeR / Transcriptional repressor


Mass: 25091.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: cmeR, CmeR / Production host: Escherichia coli (E. coli) / References: UniProt: Q7B8P6
#2: Chemical ChemComp-TCH / TAUROCHOLIC ACID


Mass: 515.703 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H45NO7S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 39.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8
Details: 30 % PEG3350, 0.1 M Tris, and 0.16 M MgCl2, pH 8.0, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 2, 2010
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 11011 / Num. obs: 10812 / % possible obs: 98.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 16
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.2-2.284.80.255199.8
2.28-2.374.80.189199.4
2.37-2.484.80.146199.2
2.48-2.614.80.109199.3
2.61-2.774.80.08199.1
2.77-2.994.70.062199
2.99-3.294.70.053198.4
3.29-3.764.60.052197.9
3.76-4.744.40.037197.3
4.74-504.50.021193.4

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→31.594 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.4 / σ(F): 0.21 / Phase error: 28.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2841 505 4.83 %
Rwork0.2218 --
obs0.2248 10457 95 %
all-11011 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.419 Å2 / ksol: 0.348 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.146 Å20 Å2-0 Å2
2--3.5022 Å20 Å2
3----1.3562 Å2
Refinement stepCycle: LAST / Resolution: 2.2→31.594 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1635 0 35 54 1724
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061708
X-RAY DIFFRACTIONf_angle_d1.0692305
X-RAY DIFFRACTIONf_dihedral_angle_d19.405640
X-RAY DIFFRACTIONf_chiral_restr0.069257
X-RAY DIFFRACTIONf_plane_restr0.003285
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.196-2.4170.34891170.25242321X-RAY DIFFRACTION91
2.417-2.76650.31031260.24292468X-RAY DIFFRACTION96
2.7665-3.48480.31571280.23042522X-RAY DIFFRACTION97
3.4848-31.59760.25131340.20492641X-RAY DIFFRACTION96

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