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- PDB-3f52: Crystal structure of the clp gene regulator ClgR from C. glutamicum -

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Basic information

Entry
Database: PDB / ID: 3f52
TitleCrystal structure of the clp gene regulator ClgR from C. glutamicum
Componentsclp gene regulator (ClgR)
KeywordsTRANSCRIPTION ACTIVATOR / gene regulator / helix-turn-helix motif / transcriptional activator / human pathogen
Function / homology
Function and homology information


DNA-binding transcription activator activity / protein-DNA complex / transcription cis-regulatory region binding / positive regulation of DNA-templated transcription / cytosol
Similarity search - Function
Helix-turn-helix domain / : / Helix-turn-helix XRE-family like proteins / lambda repressor-like DNA-binding domains / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Predicted transcriptional regulators
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsRusso, S. / Schweitzer, J.E. / Polen, T. / Bott, M. / Pohl, E.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Crystal structure of the caseinolytic protease gene regulator, a transcriptional activator in actinomycetes
Authors: Russo, S. / Schweitzer, J.E. / Polen, T. / Bott, M. / Pohl, E.
History
DepositionNov 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / 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

Downloads & links

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Assembly

Deposited unit
A: clp gene regulator (ClgR)
E: clp gene regulator (ClgR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7557
Polymers25,2952
Non-polymers4605
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-14 kcal/mol
Surface area8550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.080, 55.080, 129.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein clp gene regulator (ClgR)


Mass: 12647.396 Da / Num. of mol.: 2 / Fragment: clgr_c
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: cg2152, Cgl1962 / Plasmid: pEKEx1 / Production host: Escherichia coli (E. coli) / Strain (production host): BB1553 / References: UniProt: Q8NP59
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 1.94 Å3/Da / Density % sol: 36.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.085 M HEPES, 8.5% PEG 8000, 15% glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.0685 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 16, 2008
RadiationMonochromator: sagitally focused Si(111), bending mirror for vertical focusing, spot size 20x50um
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0685 Å / Relative weight: 1
ReflectionResolution: 1.75→42 Å / Num. all: 20944 / Num. obs: 20938 / % possible obs: 100 % / Observed criterion σ(F): 1.7 / Observed criterion σ(I): 3 / Redundancy: 10 % / Rsym value: 0.057 / Net I/σ(I): 24.56
Reflection shellResolution: 1.75→1.85 Å / Redundancy: 8.5 % / Mean I/σ(I) obs: 2.56 / Num. unique all: 3143 / Rsym value: 0.799 / % possible all: 100

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Processing

Software
NameVersionClassification
gclientdata collection
PHASERphasing
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3F51

3f51


Resolution: 1.75→41.96 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.957 / SU B: 4.273 / SU ML: 0.069 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1.7 / σ(I): 3 / ESU R: 0.098 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21254 1047 5 %RANDOM
Rwork0.18307 ---
obs0.18449 19890 100 %-
all-19890 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.788 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å20 Å20 Å2
2--0.82 Å20 Å2
3----1.64 Å2
Refinement stepCycle: LAST / Resolution: 1.75→41.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1132 0 30 156 1318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211168
X-RAY DIFFRACTIONr_angle_refined_deg1.3612.0321566
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.555153
X-RAY DIFFRACTIONr_dihedral_angle_2_deg20.7722.09343
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.73315200
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0121514
X-RAY DIFFRACTIONr_chiral_restr0.0870.2184
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02844
X-RAY DIFFRACTIONr_nbd_refined0.2110.2567
X-RAY DIFFRACTIONr_nbtor_refined0.2960.2825
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1070.291
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.217
X-RAY DIFFRACTIONr_mcbond_it0.8731.5787
X-RAY DIFFRACTIONr_mcangle_it1.57821205
X-RAY DIFFRACTIONr_scbond_it2.5933408
X-RAY DIFFRACTIONr_scangle_it4.0144.5361
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 75 -
Rwork0.254 1433 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4243-1.18910.2662.8726-0.72862.0341-0.00580.0069-0.0054-0.2490.09210.08490.0227-0.0714-0.0863-0.0291-0.0156-0.004-0.1570.0073-0.1285-12.5779-12.8237-14.4298
22.2243-1.61690.65423.0331-0.46325.0714-0.0779-0.3518-0.0740.07230.21630.2446-0.2238-0.4901-0.1384-0.07770.03080.0273-0.05240.0719-0.1193-28.4638-2.4414-5.3349
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A22 - 98
2X-RAY DIFFRACTION2E20 - 96

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