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- PDB-3hgg: Crystal Structure of CmeR Bound to Cholic Acid -

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Basic information

Entry
Database: PDB / ID: 3hgg
TitleCrystal Structure of CmeR Bound to Cholic Acid
ComponentsCmeR
KeywordsTRANSCRIPTION / alpha-helical / helix-turn-helix / DNA-binding / Transcription regulation
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.57 Å
AuthorsRouth, M.D. / Yang, F.
CitationJournal: To be Published
Title: Structural basis for anionic ligand recognition by multidrug binding proteins: Crystal structures of CmeR-bile acid complexes
Authors: Routh, M.D. / Yang, F. / Su, C.-C. / Long, F. / Zhang, Q. / Yu, E.W.
History
DepositionMay 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
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)25,9472
Polymers25,5381
Non-polymers4091
Water46826
1
A: CmeR
hetero molecules

A: CmeR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8944
Polymers51,0772
Non-polymers8172
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area5890 Å2
ΔGint-26 kcal/mol
Surface area20120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.923, 37.238, 57.525
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


Mass: 25538.264 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Campylobacter jejuni (Campylobacter) / References: UniProt: Q7B8P6
#2: Chemical ChemComp-CHD / CHOLIC ACID / Cholic acid


Mass: 408.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H40O5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.07 Å3/Da / Density % sol: 40.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 22% PEG 3350, 0.1M Magnesium Chloride, 5% JM600, 20mM Sodium Acetate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 21, 2009
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.57→50 Å / Num. obs: 6861 / % possible obs: 98.2 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 4 / Redundancy: 3.8 % / Biso Wilson estimate: 42.37 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 20
Reflection shellResolution: 2.57→2.66 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.216 / Mean I/σ(I) obs: 6 / Num. unique all: 6861 / % possible all: 83.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.57→31.26 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.794 / SU ML: 0.37 / σ(F): 1.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.273 579 4.76 %RANDOM
Rwork0.215 ---
all0.218 ---
obs0.215 6730 98.49 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.761 Å2 / ksol: 0.345 e/Å3
Displacement parametersBiso max: 137.98 Å2 / Biso mean: 54.811 Å2 / Biso min: 18.98 Å2
Baniso -1Baniso -2Baniso -3
1--3.801 Å20 Å20 Å2
2--1.388 Å2-0 Å2
3---2.413 Å2
Refinement stepCycle: LAST / Resolution: 2.57→31.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1649 0 29 26 1704
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021716
X-RAY DIFFRACTIONf_angle_d0.592315
X-RAY DIFFRACTIONf_chiral_restr0.048258
X-RAY DIFFRACTIONf_plane_restr0.001287
X-RAY DIFFRACTIONf_dihedral_angle_d14.079642
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.57-2.8380.3021690.2572790295995
2.838-3.2480.3011320.23729303062100
3.248-4.090.2541270.19329443071100
4.09-31.2620.2531510.20729093060100
Refinement TLS params.Method: refined / Origin x: -13.0562 Å / Origin y: 0.3754 Å / Origin z: -12.4594 Å
111213212223313233
T0.1991 Å20.0048 Å2-0.0475 Å2-0.179 Å2-0.0061 Å2--0.2244 Å2
L0.9526 °2-0.4547 °2-0.505 °2-0.3725 °20.2429 °2--0.6863 °2
S-0.0273 Å °-0.0044 Å °-0.1068 Å °-0.1138 Å °-0.0838 Å °0.2011 Å °0.0637 Å °-0.1625 Å °0.0933 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA6 - 207
2X-RAY DIFFRACTION1allA1 - 211
3X-RAY DIFFRACTION1allA1 - 233

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