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- PDB-6vwe: Crystal structure of the D100R multidrug binding transcriptional ... -

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Basic information

Entry
Database: PDB / ID: 6vwe
TitleCrystal structure of the D100R multidrug binding transcriptional regulator LmrR in complex with Rhodium Bis-diphosphine Complex
ComponentsTranscriptional regulator, PadR-like family
KeywordsMETAL BINDING PROTEIN / multidrug binding transcriptional regulator
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: 2.5 Å
AuthorsZadvornyy, O.A. / Laureanti, J.A. / Peters, J.W.
Funding support United States, 3items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-FG02-04ER151563 United States
Department of Energy (DOE, United States)DE-AC02-76SF00515 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103393 United States
CitationJournal: Organometallics / Year: 2020
Title: A Positive Charge in the Outer Coordination Sphere of an Artificial Enzyme Increases CO2 Hydrogenation
Authors: Laureanti, J.A. / Ginovska, B. / Buchko, G.W. / Schenter, G.K. / Zadvornyy, O.A. / Heberta, M. / Peters, J.W. / Shaw, W.J.
History
DepositionFeb 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Advisory / Database references / Category: database_2 / pdbx_database_PDB_obs_spr
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 4, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.3Oct 25, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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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)28,2713
Polymers27,3572
Non-polymers9141
Water181
1
A: Transcriptional regulator, PadR-like family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5922
Polymers13,6781
Non-polymers9141
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcriptional regulator, PadR-like family


Theoretical massNumber of molelcules
Total (without water)13,6781
Polymers13,6781
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-26 kcal/mol
Surface area13100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.855, 35.619, 71.651
Angle α, β, γ (deg.)90.00, 95.92, 90.00
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Transcriptional regulator, PadR-like family


Mass: 13678.463 Da / Num. of mol.: 2 / Mutation: K55D,K59Q,M89C,D100R
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: Escherichia coli BL21(DE3) (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 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.3 Å3/Da / Density % sol: 46.6 % / Description: rods and plates
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.2 / Details: 0.15 M Ammonium fluoride; 18% PEG 3350;

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.95369 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 2.5→35.63 Å / Num. obs: 8942 / % possible obs: 98.3 % / Redundancy: 4.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.021 / Rrim(I) all: 0.045 / Net I/σ(I): 16.3
Reflection shellResolution: 2.5→2.63 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.821 / Num. unique obs: 1282 / CC1/2: 0.74 / Rrim(I) all: 0.927 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX(dev_3758: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DO0

6do0


Resolution: 2.5→35.63 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 41.47
RfactorNum. reflection% reflection
Rfree0.2801 464 5.19 %
Rwork0.2094 --
obs0.213 8935 97.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→35.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1752 0 0 1 1753
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091786
X-RAY DIFFRACTIONf_angle_d1.2522403
X-RAY DIFFRACTIONf_dihedral_angle_d23.049696
X-RAY DIFFRACTIONf_chiral_restr0.056250
X-RAY DIFFRACTIONf_plane_restr0.006301
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.860.4491420.32532806X-RAY DIFFRACTION98
2.86-3.60.32161780.29092784X-RAY DIFFRACTION98
3.61-35.630.25181440.17472881X-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)
15.20470.1915-3.28636.9142-0.47078.10050.14730.16680.1317-0.0938-0.27430.6306-0.6009-1.48960.36820.4752-0.052-0.02420.8063-0.11690.646411.91962.5495.4518
24.6659-4.29990.03454.7371-1.48816.8358-0.705-0.37572.01520.8020.1457-1.3539-0.5431-0.48660.27560.5605-0.0901-0.02540.52850.01820.854222.8527.3316.0604
35.0346-1.5911-2.27069.80140.35562.0546-0.0120.6076-0.1797-0.80230.0872-1.01020.2735-0.58890.39630.5223-0.05590.07060.59050.00440.701825.5173-1.3616-2.3925
48.63782.1003-2.85281.1722-1.17492.8508-0.0331-0.9613-0.4152-0.0056-0.54840.17950.55520.1820.70790.8169-0.03740.1420.5714-0.08840.802415.2003-9.747824.66
54.9225-4.9502-2.47074.72473.89427.59380.08220.46190.78440.1288-0.3301-0.1339-0.1163-0.54660.23171.0397-0.1917-0.01540.7541-0.04240.669916.1283-0.798929.7769
69.1144-2.5392-0.97516.09355.23634.3657-0.5347-0.5525-0.19361.96580.2770.0641.6334-1.45490.0370.9519-0.04230.11871.11870.07660.697612.8807-5.055442.628
77.1192-6.42686.54145.7561-5.84995.9844-0.22090.99421.02040.50930.0771-1.0437-1.0242-1.81641.39641.3490.2575-0.05381.17010.05850.910816.31569.077539.2537
84.71461.1258-2.95574.9727-0.80246.0124-0.4619-0.4908-0.70710.03680.56410.7997-0.9817-2.30590.25931.1890.47040.11951.7541-0.49290.94395.77919.682644.4645
96.0905-6.1216-5.43856.29965.25594.9324-0.7925-0.6027-0.54380.82910.07031.02881.0428-0.48850.77490.8128-0.22860.00941.348-0.13920.87153.35490.519216.4261
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 46 )
2X-RAY DIFFRACTION2chain 'A' and (resid 47 through 59 )
3X-RAY DIFFRACTION3chain 'A' and (resid 60 through 82 )
4X-RAY DIFFRACTION4chain 'A' and (resid 83 through 109 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 23 )
6X-RAY DIFFRACTION6chain 'B' and (resid 24 through 46 )
7X-RAY DIFFRACTION7chain 'B' and (resid 47 through 59 )
8X-RAY DIFFRACTION8chain 'B' and (resid 60 through 82 )
9X-RAY DIFFRACTION9chain 'B' and (resid 83 through 110 )

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