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

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Basic information

Entry
Database: PDB / ID: 3fwr
TitleCrystal Structure of the CBS domains from the Bacillus subtilis CcpN repressor complexed with ADP
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
ADENOSINE-5'-DIPHOSPHATE / Transcriptional repressor CcpN
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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 19, 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 1.2Nov 1, 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: YqzB protein
B: YqzB protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8874
Polymers36,0322
Non-polymers8542
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-49 kcal/mol
Surface area14170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.273, 103.047, 98.342
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: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 1.91 Å3/Da / Density % sol: 35.53 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 17% PEG 2000 MME, 0.1M HEPES, 8mg/ml Protein; 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: Jan 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.45→98.53 Å / Num. obs: 9555 / % possible obs: 92.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 41.041 Å2 / Rmerge(I) obs: 0.103 / Rsym value: 0.095 / Net I/σ(I): 19.5
Reflection shellResolution: 2.45→2.58 Å / Redundancy: 4 % / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 2.6 / Num. unique all: 4024 / Rsym value: 0.477 / % possible all: 92.9

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Processing

Software
NameVersionClassification
SOLVEphasing
REFMAC5.4.0062refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FV6

3fv6


Resolution: 2.45→45.64 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.882 / SU B: 23.097 / SU ML: 0.267 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.359 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28073 284 2.9 %RANDOM
Rwork0.19983 ---
obs0.20219 9437 92.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.022 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å20 Å2
2--0.24 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.45→45.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2285 0 54 47 2386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222379
X-RAY DIFFRACTIONr_angle_refined_deg1.8722.0173231
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1955293
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.81325.05493
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.23915463
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4341514
X-RAY DIFFRACTIONr_chiral_restr0.1150.2410
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211656
X-RAY DIFFRACTIONr_mcbond_it0.6021.51455
X-RAY DIFFRACTIONr_mcangle_it1.11422396
X-RAY DIFFRACTIONr_scbond_it1.9173924
X-RAY DIFFRACTIONr_scangle_it3.1354.5833
LS refinement shellResolution: 2.45→2.514 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 12 -
Rwork0.284 477 -
obs--65.64 %
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)
14.8866-1.70290.25352.2302-0.30731.3440.08210.0136-0.2644-0.097-0.05270.20440.0795-0.188-0.02950.0458-0.0413-0.01170.01450.0074-0.0279-1.383834.595639.0414
23.0717-2.26440.20024.084-0.26561.014-0.0340.0390.1411-0.01680.0189-0.1472-0.0130.0980.015-0.037-0.0157-0.0019-0.01740.0011-0.057815.722648.505235.2207
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 149
2X-RAY DIFFRACTION2B1 - 146

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