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- PDB-2vt3: Structure and functional properties of the Bacillus subtilis tran... -

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Basic information

Entry
Database: PDB / ID: 2vt3
TitleStructure and functional properties of the Bacillus subtilis transcriptional repressor Rex
ComponentsREDOX-SENSING TRANSCRIPTIONAL REPRESSOR REX
KeywordsTRANSCRIPTION / TRANSCRIPTIONAL REGULATION / REDOX POISE
Function / homology
Function and homology information


response to redox state / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA-templated transcription / DNA binding / cytoplasm
Similarity search - Function
: / Rex DNA-binding, C-terminal domain / Redox-sensing transcriptional repressor Rex / Putative DNA-binding protein N-terminus / CoA binding domain / CoA binding domain / CoA-binding / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / NAD(P)-binding Rossmann-like Domain ...: / Rex DNA-binding, C-terminal domain / Redox-sensing transcriptional repressor Rex / Putative DNA-binding protein N-terminus / CoA binding domain / CoA binding domain / CoA-binding / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / NAD(P)-binding Rossmann-like Domain / Winged helix DNA-binding domain superfamily / NAD(P)-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Redox-sensing transcriptional repressor Rex
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWang, E. / Bauer, M.C. / Rogstam, A. / Linse, S. / Logan, D. / von Wachenfeldt, C.
CitationJournal: Mol. Microbiol. / Year: 2008
Title: Structure and functional properties of the Bacillus subtilis transcriptional repressor Rex.
Authors: Wang, E. / Bauer, M.C. / Rogstam, A. / Linse, S. / Logan, D.T. / von Wachenfeldt, C.
History
DepositionMay 8, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 17, 2018Group: Data collection / Database references / Source and taxonomy
Category: citation / citation_author ...citation / citation_author / diffrn_source / entity_src_gen
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: REDOX-SENSING TRANSCRIPTIONAL REPRESSOR REX
B: REDOX-SENSING TRANSCRIPTIONAL REPRESSOR REX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2594
Polymers48,2452
Non-polymers1,0142
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-33.3 kcal/mol
Surface area25750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.460, 53.520, 86.240
Angle α, β, γ (deg.)90.00, 125.80, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein REDOX-SENSING TRANSCRIPTIONAL REPRESSOR REX / REX


Mass: 24122.551 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Strain: 1A1 / Plasmid: PET101 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): TUNER / References: UniProt: O05521
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.57 Å3/Da / Density % sol: 52.2 % / Description: NONE
Crystal growpH: 7.1
Details: RESERVOAR SOLUTION OF 20% W/V PEG6000, 0.2M NH4CL AND 0.1M HEPES PH 7.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: May 17, 2006 / Details: FOCUSING MIRRORS
RadiationMonochromator: OXFORD DANFYSIK DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 31994 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.8
Reflection shellResolution: 2→2.1 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.8 / % possible all: 93.4

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
MrBUMPphasing
PHASERphasing
REFMAC5.3.0037refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XCB CHAIN F, C-TERMINAL DOMAIN

1xcb


Resolution: 2→19.46 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.91 / SU B: 8.383 / SU ML: 0.127 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1605 5 %RANDOM
Rwork0.194 ---
obs0.196 30388 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å20 Å21.33 Å2
2---0.8 Å20 Å2
3---1.51 Å2
Refinement stepCycle: LAST / Resolution: 2→19.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3101 0 62 224 3387
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223237
X-RAY DIFFRACTIONr_bond_other_d0.0010.022135
X-RAY DIFFRACTIONr_angle_refined_deg1.5541.9864398
X-RAY DIFFRACTIONr_angle_other_deg0.95235208
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4695390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.37223.75144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.46115546
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.991519
X-RAY DIFFRACTIONr_chiral_restr0.0880.2508
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023523
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02666
X-RAY DIFFRACTIONr_nbd_refined0.2170.2637
X-RAY DIFFRACTIONr_nbd_other0.1930.22089
X-RAY DIFFRACTIONr_nbtor_refined0.1780.21530
X-RAY DIFFRACTIONr_nbtor_other0.0890.21680
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2190
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2740.284
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9821.52537
X-RAY DIFFRACTIONr_mcbond_other0.1841.5799
X-RAY DIFFRACTIONr_mcangle_it1.19323152
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.97331491
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7144.51246
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 109 -
Rwork0.237 2008 -
obs--89.48 %
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)
18.6716-1.06632.100612.6522-7.66468.1851-0.42340.24431.3988-0.0037-0.0252-0.1578-0.26140.13910.4485-0.1401-0.0112-0.1156-0.12210.06970.0379-7.43645.791-18.126
21.7767-0.48661.45151.376-0.30793.64180.00470.1413-0.0932-0.1394-0.02120.07440.0127-0.00050.0166-0.0856-0.0134-0.0046-0.0674-0.0507-0.076312.85420.903-27.456
33.15420.5898-0.15891.68340.02852.4909-0.0060.1270.1003-0.03480.03580.2855-0.1058-0.0586-0.0299-0.08510.0252-0.0526-0.02540.0302-0.082349.1031.691-0.113
40.6532-1.009-0.27733.40680.34731.6477-0.0451-0.0014-0.30210.11770.06830.07250.18650.0485-0.0232-0.1016-0.0162-0.0129-0.117-0.0120.052414.3017.088-13.454
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 83
2X-RAY DIFFRACTION2A87 - 209
3X-RAY DIFFRACTION3B7 - 85
4X-RAY DIFFRACTION4B86 - 214

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