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- PDB-3r6s: Crystal structure of GlxR transcription factor from Corynebacteri... -

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Basic information

Entry
Database: PDB / ID: 3r6s
TitleCrystal structure of GlxR transcription factor from Corynebacterium glutamicum with cAMP
Componentstranscription regulatorTranscriptional regulation
KeywordsTRANSCRIPTION / N-terminal cAMP-binding domain / C-terminal HTH-motif / Transcription factor / Homodimer
Function / homology
Function and homology information


regulation of glyoxylate cycle / DNA-binding transcription repressor activity / DNA-binding transcription activator activity / cAMP binding / protein-DNA complex / kinase activity / transcription cis-regulatory region binding / phosphorylation / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
helix_turn_helix, cAMP Regulatory protein / Crp-type HTH domain profile. / Crp-like helix-turn-helix domain / Crp-type HTH domain / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Jelly Rolls ...helix_turn_helix, cAMP Regulatory protein / Crp-type HTH domain profile. / Crp-like helix-turn-helix domain / Crp-type HTH domain / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Jelly Rolls / Winged helix-like DNA-binding domain superfamily / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / HEXANE-1,6-DIOL / CRP-like cAMP-activated global transcriptional regulator
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsJungwirth, B. / Pojer, F.
CitationJournal: To be Published
Title: Crystal structure of GlxR transcription factor from Corynebacterium glutamicum with cAMP
Authors: Jungwirth, B. / Pojer, F.
History
DepositionMar 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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

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Assembly

Deposited unit
A: transcription regulator
B: transcription regulator
C: transcription regulator
D: transcription regulator
E: transcription regulator
F: transcription regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,48115
Polymers163,1526
Non-polymers2,3309
Water2,900161
1
A: transcription regulator
C: transcription regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1605
Polymers54,3842
Non-polymers7773
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-23 kcal/mol
Surface area19910 Å2
MethodPISA
2
B: transcription regulator
hetero molecules

B: transcription regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0424
Polymers54,3842
Non-polymers6582
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area5420 Å2
ΔGint-21 kcal/mol
Surface area20010 Å2
MethodPISA
3
D: transcription regulator
E: transcription regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1605
Polymers54,3842
Non-polymers7773
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-19 kcal/mol
Surface area20550 Å2
MethodPISA
4
F: transcription regulator
hetero molecules

F: transcription regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2796
Polymers54,3842
Non-polymers8954
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area4090 Å2
ΔGint-20 kcal/mol
Surface area20760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.248, 111.248, 186.951
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein
transcription regulator / Transcriptional regulation / TRANSCRIPTIONAL REGULATOR / CRP/FNR FAMILY / cAMP-binding domains-Catabolite gene activator and ...TRANSCRIPTIONAL REGULATOR / CRP/FNR FAMILY / cAMP-binding domains-Catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases


Mass: 27191.928 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: Novagen / Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Strain: ATCC13032 / Gene: cg0350, cg0350 (glxR), Cgl0291 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): JM109(DE3) / References: UniProt: Q79VI7
#2: Chemical
ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP / Cyclic adenosine monophosphate


Mass: 329.206 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H12N5O6P
#3: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL / 1,6-Hexanediol


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.05 Å3/Da / Density % sol: 39.91 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Morpheus buffer 3 (Tris; Bicine), 30% Morpheus GOL_P4K (Glycerol, PEG4K), Morpheus Alcohols Mix at 0.12 M, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 29, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.38→67.09 Å / Num. obs: 53828 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 %
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2.38-2.535.12.5515910194.8
2.53-2.75.53.65156591100
2.7-2.925.75.89146811100
2.92-3.25.910.26134681100
3.2-3.575.917.87121711100
3.57-4.125.929.77107031100
4.12-5.055.841.8991071100

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3I54

3i54


Resolution: 2.38→67.09 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.893 / SU B: 10.109 / SU ML: 0.243 / Cross valid method: THROUGHOUT / ESU R Free: 0.321 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28786 2742 5.1 %RANDOM
Rwork0.21015 ---
obs0.21415 51087 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.563 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.38→67.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10387 0 156 161 10704
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02210767
X-RAY DIFFRACTIONr_angle_refined_deg1.7191.97614614
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.61951350
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.71522.655501
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.128151816
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.52115132
X-RAY DIFFRACTIONr_chiral_restr0.1070.21700
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218106
X-RAY DIFFRACTIONr_mcbond_it0.8121.56688
X-RAY DIFFRACTIONr_mcangle_it1.515210757
X-RAY DIFFRACTIONr_scbond_it2.41234079
X-RAY DIFFRACTIONr_scangle_it3.9214.53851
LS refinement shellResolution: 2.383→2.444 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 168 -
Rwork0.229 3410 -
obs--91.39 %

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