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- PDB-3keo: Crystal Structure of a Rex-family transcriptional regulatory prot... -

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Basic information

Entry
Database: PDB / ID: 3keo
TitleCrystal Structure of a Rex-family transcriptional regulatory protein from Streptococcus agalactiae complexed with NAD+
ComponentsRedox-sensing transcriptional repressor rex
KeywordsTRANSCRIPTION / DNA binding protein / winged helix / Rossmann fold / NAD+ / Repressor / Transcription regulation / Redox sensing
Function / homology
Function and homology information


response to redox state / DNA-binding transcription factor activity / negative regulation of 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 / Winged helix DNA-binding domain superfamily ...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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Redox-sensing transcriptional repressor Rex
Similarity search - Component
Biological speciesStreptococcus agalactiae serogroup III (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsThiyagarajan, S. / Logan, D. / von Wachenfeldt, C.
CitationJournal: Plos Pathog. / Year: 2021
Title: NAD+ pool depletion as a signal for the Rex regulon involved in Streptococcus agalactiae virulence.
Authors: Franza, T. / Rogstam, A. / Thiyagarajan, S. / Sullivan, M.J. / Derre-Bobillot, A. / Bauer, M.C. / Goh, K.G.K. / Da Cunha, V. / Glaser, P. / Logan, D.T. / Ulett, G.C. / von Wachenfeldt, C. / Gaudu, P.
History
DepositionOct 26, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 16, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Sep 8, 2021Group: Advisory / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)49,23312
Polymers47,7012
Non-polymers1,53210
Water9,800544
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9780 Å2
ΔGint-121 kcal/mol
Surface area18900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.270, 92.410, 47.190
Angle α, β, γ (deg.)90.00, 91.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Redox-sensing transcriptional repressor rex


Mass: 23850.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae serogroup III (bacteria)
Strain: NEM316 / Gene: gbs1167, rex / Plasmid: pET101 / Production host: Escherichia coli (E. coli) / Strain (production host): TUNER (DE3) / References: UniProt: Q8E565
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 544 / 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: 2.11 Å3/Da / Density % sol: 41.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG 6000, 175mM magnesium chloride, 100mM HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.0379 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 5, 2009 / Details: mirrors
RadiationMonochromator: Bent Si (111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0379 Å / Relative weight: 1
ReflectionResolution: 1.5→27.1 Å / Num. all: 63360 / Num. obs: 62064 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 8.42
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 2.26 / % possible all: 93.3

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0072refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DT5

2dt5


Resolution: 1.5→27.07 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.624 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23436 3147 5.1 %RANDOM
Rwork0.17544 ---
obs0.17845 58774 97.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.49 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2--0.04 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.5→27.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3258 0 96 544 3898
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0223360
X-RAY DIFFRACTIONr_bond_other_d0.0010.022212
X-RAY DIFFRACTIONr_angle_refined_deg2.0381.9934568
X-RAY DIFFRACTIONr_angle_other_deg1.10135382
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4065416
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.29524.384146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.13715557
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.741517
X-RAY DIFFRACTIONr_chiral_restr0.1370.2531
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023698
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02681
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.191.52051
X-RAY DIFFRACTIONr_mcbond_other0.9441.5845
X-RAY DIFFRACTIONr_mcangle_it3.17623304
X-RAY DIFFRACTIONr_scbond_it4.63931309
X-RAY DIFFRACTIONr_scangle_it6.3754.51261
X-RAY DIFFRACTIONr_rigid_bond_restr2.26835572
X-RAY DIFFRACTIONr_sphericity_free10.6873552
X-RAY DIFFRACTIONr_sphericity_bonded4.26235506
LS refinement shellResolution: 1.499→1.538 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 208 -
Rwork0.248 3920 -
obs--88.22 %
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)
10.4768-0.1853-0.0710.86820.42070.7917-0.01460.0276-0.0708-0.05360.02740.03550.0913-0.0779-0.01280.0495-0.0241-0.00750.01820.00270.055226.655429.772826.4765
20.66040.2118-0.31470.8317-0.69131.0697-0.0126-0.0593-0.07050.02580.0099-0.0180.0650.0590.00270.04390.0194-0.00340.01470.00170.039344.952329.214746.233
31.80410.3583-0.00740.67680.53431.1502-0.0291-0.25040.2289-0.0512-0.06460.0458-0.0498-0.09760.09370.02040.0132-0.00180.0497-0.04640.061225.353253.241944.5917
41.0535-0.0895-0.3090.6742-0.09921.58140.02420.11320.1184-0.0205-0.0337-0.0418-0.0327-0.00050.00950.0126-0.00060.00520.01620.02160.052446.883753.590526.7065
51.8102-0.9837-0.78920.78580.00951.7764-0.0445-0.01460.02310.00030.0098-0.03610.03970.0930.03470.037-0.01320.01010.0209-0.00880.065447.797838.294632.5138
63.28971.9954-2.07452.1938-0.7973.1421-0.0361-0.01910.0168-0.01960.02280.07210.0464-0.10280.01330.01680.00580.010.01540.01010.051123.774338.657439.4772
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 85
2X-RAY DIFFRACTION2B6 - 85
3X-RAY DIFFRACTION3A95 - 190
4X-RAY DIFFRACTION4B95 - 190
5X-RAY DIFFRACTION5A196 - 212
6X-RAY DIFFRACTION6B196 - 212

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