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- PDB-7kd3: Structure of an HxlR/DUF24 family transcription regulator, CdTR_3... -

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Basic information

Entry
Database: PDB / ID: 7kd3
TitleStructure of an HxlR/DUF24 family transcription regulator, CdTR_3200 from hypervirulent Clostridioides difficile R20291
Components(Putative transcriptional regulator) x 2
KeywordsDNA BINDING PROTEIN / HxlR / Helix turn helix motifs / transcription regulator / Clostridioides difficile / Clostridium difficile
Function / homologyHelix-turn-helix, HxlR type / HxlR-like helix-turn-helix / HxlR-type HTH domain profile. / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Putative transcriptional regulator
Function and homology information
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMenon, S.K. / Isom, C.E. / Karr, E.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: To Be Published
Title: Crystal structure of an HxlR/DUF24 family transcription regulator, CdTR_3200 from hypervirulent Clostridioides difficile R20291
Authors: Menon, S.K. / Isom, C.E. / West, A.H. / Richter-Addo, G.B. / Karr, E.A.
History
DepositionOct 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative transcriptional regulator
B: Putative transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)26,4132
Polymers26,4132
Non-polymers00
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, SEC-MALS used to confirm that TR3200 exists as a dimer in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-32 kcal/mol
Surface area11190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.019, 55.001, 72.317
Angle α, β, γ (deg.)90.000, 96.060, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Putative transcriptional regulator


Mass: 13222.558 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (strain R20291) (bacteria)
Strain: R20291 / Gene: CDR20291_3200 / Plasmid: pQE80L (Qiagen)
Details (production host): modified pQE80L to add N-6xHis tag
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: C9YRI3
#2: Protein Putative transcriptional regulator


Mass: 13190.558 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (strain R20291) (bacteria)
Strain: R20291 / Gene: CDR20291_3200 / Plasmid: pQE80L (Qiagen)
Details (production host): modified pQE80L to add N-6xHis tag
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: C9YRI3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.5 Å3/Da / Density % sol: 50.83 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.2 M di-ammonium citrate pH 5.0, 20% PEG 3350 / PH range: 4.5-5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→29.5 Å / Num. obs: 10495 / % possible obs: 96.44 % / Redundancy: 2 % / Biso Wilson estimate: 45.36 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.016 / Rpim(I) all: 0.016 / Rrim(I) all: 0.023 / Net I/σ(I): 17.3
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 1.99 % / Rmerge(I) obs: 0.121 / Mean I/σ(I) obs: 4 / Num. unique obs: 1063 / CC1/2: 0.984 / Rpim(I) all: 0.121 / Rrim(I) all: 0.171 / % possible all: 97.34

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HZT

2hzt


Resolution: 2.3→29.5 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 29.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2578 1048 10.01 %random
Rwork0.2004 9420 --
obs0.2062 10468 96.19 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 181.9 Å2 / Biso mean: 72.36 Å2 / Biso min: 31.97 Å2
Refinement stepCycle: final / Resolution: 2.3→29.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1579 0 0 8 1587
Biso mean---55.29 -
Num. residues----197
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.420.30931470.25941338148597
2.42-2.570.30151520.23561347149997
2.57-2.770.25651490.22981338148796
2.77-3.050.3641470.24691323147096
3.05-3.490.28941520.23251368152097
3.49-4.390.24791470.18761324147195
4.4-29.50.20781540.16331382153696
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)
17.29290.7514-0.53926.2306-2.42425.69760.08960.34760.64870.1730.05850.0474-0.28230.2611-0.00050.2738-0.006-0.04840.4267-0.0470.407817.738125.13245.6794
25.06383.37490.50748.605-0.54673.52950.21040.17930.01490.1836-0.1904-0.01680.20020.1174-0.0050.32140.01410.01770.48310.01230.407525.040622.520741.12
32.6156-3.65441.32385.4714-2.63422.4126-0.5237-1.05731.31580.1639-0.8184-1.3353-0.7990.43720.81560.5595-0.0868-0.23280.8693-0.01650.680920.363530.714656.3015
47.1108-1.36124.78939.63640.24453.3756-0.4420.1299-1.093-0.53160.18870.26320.17680.26560.19180.58-0.09740.05510.70080.130.543815.156814.368459.568
53.3595-2.65143.36317.5868-1.84517.2621-0.0263-0.8061-1.65590.1496-0.1640.52011.5636-0.5372-0.11771.0079-0.0513-0.00830.95340.42510.927914.26596.476864.9061
61.6668-0.2754-2.36936.87012.0333.78250.1669-1.9262-0.67620.2033-0.2693-1.15550.17520.69651.30880.71570.0593-0.16921.26850.42830.783623.044814.539166.4529
70.5641.4389-0.89394.6565-1.57821.95660.33220.67610.53970.8712-0.193-0.9274-0.4716-1.37830.77070.6395-0.0242-0.0441.3790.57151.233219.04426.458678.4411
82.1425-1.19912.50562.542-3.03836.26720.0774-0.9483-0.32480.4008-0.13130.5520.4539-0.5042-0.0140.355-0.03490.03830.85750.06770.5067.61518.67759.0341
98.14983.8659-4.1145.9107-0.37613.4902-0.05540.96810.0677-0.35-0.0722-0.4027-0.7665-0.71790.43870.4157-0.0092-0.02540.60020.16050.492618.742230.11431.3934
108.50213.77983.02554.04152.14294.5488-0.132-0.55080.70270.13-0.09560.0253-0.7871-0.08250.78150.37580.0971-0.05190.4752-0.13830.490812.524830.931955.8944
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 44 )A7 - 44
2X-RAY DIFFRACTION2chain 'A' and (resid 45 through 62 )A45 - 62
3X-RAY DIFFRACTION3chain 'B' and (resid 7 through 19 )B7 - 19
4X-RAY DIFFRACTION4chain 'B' and (resid 20 through 30 )B20 - 30
5X-RAY DIFFRACTION5chain 'B' and (resid 31 through 49 )B31 - 49
6X-RAY DIFFRACTION6chain 'B' and (resid 50 through 67 )B50 - 67
7X-RAY DIFFRACTION7chain 'B' and (resid 68 through 77 )B68 - 77
8X-RAY DIFFRACTION8chain 'B' and (resid 78 through 107 )B78 - 107
9X-RAY DIFFRACTION9chain 'A' and (resid 63 through 83 )A63 - 83
10X-RAY DIFFRACTION10chain 'A' and (resid 84 through 107 )A84 - 107

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