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- PDB-6fuu: Transcriptional regulator LmrR with bound heme -

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Basic information

Entry
Database: PDB / ID: 6fuu
TitleTranscriptional regulator LmrR with bound heme
ComponentsTranscriptional regulator PadR family
KeywordsDNA BINDING PROTEIN / Artificial enzyme / Complex / Heme-based catalysis / Transcriptional regulator / Multi-drug resistance
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
PROTOPORPHYRIN IX CONTAINING FE / Transcriptional regulator, Acidobacterial, PadR-family
Similarity search - Component
Biological speciesLactococcus lactis subsp. cremoris (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsReddem, E.R. / Thunnissen, A.M.W.H.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
NWO Netherlands
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2018
Title: An Artificial Heme Enzyme for Cyclopropanation Reactions.
Authors: Villarino, L. / Splan, K.E. / Reddem, E. / Alonso-Cotchico, L. / Gutierrez de Souza, C. / Lledos, A. / Marechal, J.D. / Thunnissen, A.W.H. / Roelfes, G.
History
DepositionFeb 27, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2018Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_special_symmetry
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Jan 17, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator PadR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3812
Polymers14,7651
Non-polymers6161
Water88349
1
A: Transcriptional regulator PadR family
hetero molecules

A: Transcriptional regulator PadR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7634
Polymers29,5302
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666-y+1,-x+1,-z+3/21
Buried area4580 Å2
ΔGint-63 kcal/mol
Surface area11880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.145, 35.145, 180.668
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-201-

HEM

21A-201-

HEM

31A-201-

HEM

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Components

#1: Protein Transcriptional regulator PadR family / Transcriptional regulator / Acidobacterial / PadR-family


Mass: 14764.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Residues 1-4, 70-73 and 109-126 are not included in the model due to weak/absent electron density
Source: (gene. exp.) Lactococcus lactis subsp. cremoris (lactic acid bacteria)
Gene: NCDO763_1045, VN96_2738 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0M2ZSQ6
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 1.89 Å3/Da / Density % sol: 34.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM cacodylate, 300 mM sodium acetate, 25% PEG 200 MME, 200 uM hemin

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.75→45.17 Å / Num. obs: 12313 / % possible obs: 99.6 % / Redundancy: 9.1 % / Biso Wilson estimate: 29.87 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.025 / Rrim(I) all: 0.078 / Net I/σ(I): 16.3 / Num. measured all: 112667 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.75-1.788.50.64453936310.8790.2250.6843.197.8
9.09-45.176.80.0689111340.9930.0260.07424.899

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
Aimless0.5.32data scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3F8C

3f8c


Resolution: 1.75→34.498 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2366 589 4.82 %
Rwork0.2124 11643 -
obs0.2137 12233 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.13 Å2 / Biso mean: 39.2471 Å2 / Biso min: 17.09 Å2
Refinement stepCycle: final / Resolution: 1.75→34.498 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms824 0 86 49 959
Biso mean--53.05 40.77 -
Num. residues----100
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006956
X-RAY DIFFRACTIONf_angle_d0.9761314
X-RAY DIFFRACTIONf_chiral_restr0.061127
X-RAY DIFFRACTIONf_plane_restr0.003157
X-RAY DIFFRACTIONf_dihedral_angle_d11.355565
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7502-1.92630.31371430.24232779292299
1.9263-2.2050.25511520.20352844299699
2.205-2.77790.22481280.22962907303599
2.7779-34.5050.22871660.204731133279100
Refinement TLS params.Method: refined / Origin x: 20.9142 Å / Origin y: 18.6764 Å / Origin z: 123.0833 Å
111213212223313233
T0.1737 Å20.029 Å20.0518 Å2-0.1854 Å20.0344 Å2--0.2014 Å2
L1.5793 °2-0.3667 °20.5201 °2-2.3646 °2-2.0853 °2--3.9643 °2
S-0.1191 Å °-0.1245 Å °-0.038 Å °0.0015 Å °0.0787 Å °0.1855 Å °0.0677 Å °0.0842 Å °0.0234 Å °
Refinement TLS groupSelection details: chain 'A' and (resid 5 through 108 )

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