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- PDB-3fv6: Crystal Structure of the CBS domains from the Bacillus subtilis C... -

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Basic information

Entry
Database: PDB / ID: 3fv6
TitleCrystal Structure of the CBS domains from the Bacillus subtilis CcpN repressor
ComponentsYqzB protein
KeywordsTRANSCRIPTION / CBS DOMAIN DIMER / Metabolism regulator / Central glycolytic gene regulator
Function / homology
Function and homology information


carbon catabolite repression of transcription / DNA binding
Similarity search - Function
Protein of unknown function UCP026546, HtH-CBS / : / Helix-turn-helix, type 11 / HTH domain / CBS-domain / CBS-domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain ...Protein of unknown function UCP026546, HtH-CBS / : / Helix-turn-helix, type 11 / HTH domain / CBS-domain / CBS-domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Transcriptional repressor CcpN
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsChaix, D. / Arold, S. / Hoh, F. / Declerck, N.
CitationJournal: To be Published
Title: Ligand recognition by the energy sensor domain of the CcpN repressor
Authors: Chaix, D. / de Guillen, K. / Coq, D.L. / Hoh, F. / Roumestand, C. / Aymerich, S. / Arold, S.T. / Declerck, N.
History
DepositionJan 15, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YqzB protein
B: YqzB protein


Theoretical massNumber of molelcules
Total (without water)36,0322
Polymers36,0322
Non-polymers00
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-31 kcal/mol
Surface area14730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.751, 104.052, 99.523
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein YqzB protein / Central glycolytic gene regulator


Mass: 18016.092 Da / Num. of mol.: 2
Fragment: CBS domain, regulatory domain of the transcription factor CcpN, UNP residues 63-212
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: yqzB / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: O34994
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 1.97 Å3/Da / Density % sol: 37.47 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 17% PEG 2000 MME, 0.1M HEPES, Protein 8mg/ml; Drops 1+1 microliter, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 78 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 15, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.95→52.058 Å / Num. obs: 19404 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 24.432 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.074 / Net I/σ(I): 15.1
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.191 / Mean I/σ(I) obs: 5.9 / Num. unique all: 2992 / Rsym value: 0.162 / % possible all: 99.5

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Processing

Software
NameVersionClassification
SOLVEphasing
REFMAC5.4.0062refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.95→43.56 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.91 / SU B: 8.409 / SU ML: 0.127 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.21 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2718 642 3.3 %RANDOM
Rwork0.19967 ---
all0.20203 ---
obs0.20193 19395 91.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.221 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2--0.07 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.95→43.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2285 0 0 140 2425
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0222309
X-RAY DIFFRACTIONr_angle_refined_deg2.11.9863121
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.2655289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.79524.94591
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.41615461
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0171514
X-RAY DIFFRACTIONr_chiral_restr0.1740.2396
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211618
X-RAY DIFFRACTIONr_mcbond_it1.1781.51449
X-RAY DIFFRACTIONr_mcangle_it1.95322384
X-RAY DIFFRACTIONr_scbond_it3.2483860
X-RAY DIFFRACTIONr_scangle_it5.1714.5737
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 50 -
Rwork0.222 1448 -
obs--99.01 %
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)
14.2453-1.45520.2371.627-0.01941.23250.11510.1465-0.5448-0.1897-0.01710.31840.2417-0.3137-0.0981-0.0485-0.0664-0.05-0.07220.0408-0.0707-2.181635.720239.834
23.2975-2.2692-0.11882.9037-0.12131.24130.06740.00340.2287-0.0635-0.0421-0.19090.00860.1246-0.0253-0.1452-0.021-0.0115-0.12010.0042-0.177915.023850.482335.247
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 149
2X-RAY DIFFRACTION2B8 - 149

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