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- PDB-6r1l: Crystal structure of LmrR with bound copper phenanthroline -

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Basic information

Entry
Database: PDB / ID: 6r1l
TitleCrystal structure of LmrR with bound copper phenanthroline
ComponentsTranscriptional regulator, PadR-like familyTranscriptional regulation
KeywordsDNA BINDING PROTEIN / PadR family / transcriptional regulator / artificial metalloenzyme / phenanthroline
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
COPPER (II) ION / 1,10-PHENANTHROLINE / Transcriptional regulator, PadR-like family
Similarity search - Component
Biological speciesLactococcus lactis subsp. cremoris MG1363 (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.095 Å
AuthorsReddem, R. / Thunnissen, A.M.W.H.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research Netherlands
CitationJournal: Acs Catalysis / Year: 2020
Title: Cofactor Binding Dynamics Influence the Catalytic Activity and Selectivity of an Artificial Metalloenzyme.
Authors: Villarino, L. / Chordia, S. / Alonso-Cotchico, L. / Reddem, E. / Zhou, Z. / Thunnissen, A.M.W.H. / Marechal, J.D. / Roelfes, G.
History
DepositionMar 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: citation / citation_author ...citation / citation_author / database_2 / database_PDB_rev / database_PDB_rev_record / entity_src_gen / pdbx_database_proc / pdbx_struct_conn_angle / struct_conn
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 / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.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_symmetry
Revision 1.2Jan 24, 2024Group: 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: Transcriptional regulator, PadR-like family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0093
Polymers14,7651
Non-polymers2442
Water39622
1
A: Transcriptional regulator, PadR-like family
hetero molecules

A: Transcriptional regulator, PadR-like family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0176
Polymers29,5302
Non-polymers4884
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3920 Å2
ΔGint-48 kcal/mol
Surface area11940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.851, 34.851, 177.469
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-202-

CU

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Components

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


Mass: 14764.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: LmrR carrying a C-terminal strep-tag
Source: (gene. exp.) Lactococcus lactis subsp. cremoris MG1363 (lactic acid bacteria)
Gene: llmg_0323 / Production host: Escherichia coli (E. coli) / References: UniProt: A2RI36
#2: Chemical ChemComp-PHN / 1,10-PHENANTHROLINE / 1,10-Phenanthroline


Mass: 180.205 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H8N2
#3: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.3 Å3/Da / Density % sol: 46.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM cacodylate, 300 mM sodium acetate, 25% PEG 200 MME, 5 mM Cu-phenanthroline

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.09→34.85 Å / Num. obs: 7167 / % possible obs: 99.8 % / Redundancy: 9.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.032 / Rrim(I) all: 0.097 / Net I/σ(I): 14.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.09-2.169.40.9325560.8110.3120.98498.3
8.89-34.856.70.051350.9990.0190.05499.7

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Processing

Software
NameVersionClassification
PHENIX1.14rc1_3161refinement
XDSdata reduction
Aimless0.5.27data scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3F8C

3f8c


Resolution: 2.095→34.198 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 0.65 / Phase error: 25.44
RfactorNum. reflection% reflection
Rfree0.2484 1232 10.04 %
Rwork0.2012 --
obs0.2063 12273 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 95.08 Å2 / Biso mean: 45.1711 Å2 / Biso min: 20.73 Å2
Refinement stepCycle: final / Resolution: 2.095→34.198 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms824 0 15 22 861
Biso mean--70.05 43.12 -
Num. residues----100
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0952-2.17910.30681370.27021235137298
2.1791-2.27820.29551300.235612121342100
2.2782-2.39830.29361340.239812181352100
2.3983-2.54850.32071460.233912181364100
2.5485-2.74520.24681410.219312521393100
2.7452-3.02130.29281380.207712091347100
3.0213-3.45810.24151330.201712481381100
3.4581-4.35550.20681410.17312281369100
4.3555-34.20240.23061320.185812211353100

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