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- PDB-6do0: Crystal structure of the multidrug binding transcriptional regula... -

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Basic information

Entry
Database: PDB / ID: 6do0
TitleCrystal structure of the multidrug binding transcriptional regulator LmrR in complex with Rhodium Bis-diphosphine Complex
ComponentsTranscriptional regulator, PadR-like familyTranscriptional regulation
KeywordsMETAL BINDING PROTEIN / protein scaffold / rhodium bis-diphosphine complex / CO2 hydrogenation
Function / homology
Function and homology information


Transcription regulator PadR, N-terminal / Transcriptional regulator PadR-like family / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-JY1 / Transcriptional regulator, PadR-like family
Similarity search - Component
Biological speciesLactococcus lactis subsp. cremoris (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.798 Å
AuthorsZadvornyy, O.A. / Laureanti, J.A. / Katipamula, S. / O'Hagan, M. / Peters, J.W.
Funding support United States, 2items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0012518 United States
Other governmentPNNL Laboratory Directed Research and Development 69937 United States
CitationJournal: Acs Catalysis / Year: 2019
Title: Protein Scaffold Activates Catalytic CO2 Hydrogenation by a Rhodium Bis(diphosphine) Complex
Authors: Laureanti, J.A. / Buckho, G.W. / Katipamula, S. / Su, Q. / Linehan, J.C. / Zadvornyy, O.A. / Peters, J.W. / O'Hagan, M.
History
DepositionJun 8, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jan 29, 2020Group: Non-polymer description / Structure summary / Category: chem_comp / entity
Item: _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight
Revision 2.1Sep 2, 2020Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _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_conn.ptnr2_label_seq_id
Revision 2.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator, PadR-like family
B: Transcriptional regulator, PadR-like family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8983
Polymers26,9842
Non-polymers9141
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-25 kcal/mol
Surface area13040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.645, 35.569, 71.259
Angle α, β, γ (deg.)90.00, 96.51, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Transcriptional regulator, PadR-like family / Transcriptional regulation


Mass: 13492.228 Da / Num. of mol.: 2 / Mutation: K55D, K59Q, M89C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis subsp. cremoris (strain MG1363) (lactic acid bacteria)
Strain: MG1363 / Gene: llmg_0323
Production host: Lactococcus lactis subsp. cremoris MG1363 (lactic acid bacteria)
References: UniProt: A2RI36
#2: Chemical ChemComp-JY1 / bis[diethyl(methyl)-lambda~5~-phosphanyl]{bis[{[(2-{[2-(2,5-dioxopyrrolidin-1-yl)ethyl]amino}-2-oxoethyl)amino]methyl}(diethyl)-lambda~5~-phosphanyl]}rhodium


Mass: 913.810 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H74N6O6P4Rh
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.33 Å3/Da / Density % sol: 47.22 % / Description: needles, plates
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M Ammonium acetate in 0.1 M Sodium citrate (pH 6.5), 22% w/v PEG 4000, and 1 mM sodium dithionite
PH range: 5.6-6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.95 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.8→39.07 Å / Num. obs: 6343 / % possible obs: 98.3 % / Redundancy: 3.7 % / Biso Wilson estimate: 26.77 Å2 / CC1/2: 0.982 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.034 / Χ2: 0.65 / Net I/σ(I): 12.9
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 922 / CC1/2: 0.918 / Rpim(I) all: 0.212 / Χ2: 0.29 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3f8b

3f8b


Resolution: 2.798→39.068 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 43.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3227 336 5.31 %RANDOM
Rwork0.2313 ---
obs0.2366 6333 97.72 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.798→39.068 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1694 0 53 6 1753
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111788
X-RAY DIFFRACTIONf_angle_d1.7522406
X-RAY DIFFRACTIONf_dihedral_angle_d16.1731085
X-RAY DIFFRACTIONf_chiral_restr0.076250
X-RAY DIFFRACTIONf_plane_restr0.009303
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7981-3.52490.48061640.27072970X-RAY DIFFRACTION98
3.5249-39.07230.28571720.22023027X-RAY DIFFRACTION98
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)
13.2423-0.2984-3.39472.8852-0.62676.42740.02720.2037-0.2525-0.0408-0.43670.07710.3136-0.45420.17680.5184-0.1405-0.07460.3967-0.04390.366116.4617-17.97149.992
22.29240.106-0.06630.84241.55227.1366-0.32990.1517-0.19440.0178-0.08490.2331-0.3404-1.07180.20510.90410.0286-0.1480.8747-0.08720.475110.2221-15.121431.9494
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 5:110)
2X-RAY DIFFRACTION2(chain B and resseq 0:111)

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