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- PDB-5hev: Crystal Structure of the beryllofluoride-activated LiaR from Ente... -

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Basic information

Entry
Database: PDB / ID: 5hev
TitleCrystal Structure of the beryllofluoride-activated LiaR from Enterococcus faecium
ComponentsResponse regulator protein VraR
KeywordsTRANSCRIPTION / Enterococcus faecium / LiaR / response regulator
Function / homology
Function and homology information


phosphorelay signal transduction system / regulation of DNA-templated transcription / DNA binding / metal ion binding
Similarity search - Function
LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily
Similarity search - Domain/homology
BERYLLIUM TRIFLUORIDE ION / Response regulator protein VraR
Similarity search - Component
Biological speciesEnterococcus faecium SD3B-2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.192 Å
AuthorsDavlieva, M. / Shamoo, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI080714 United States
CitationJournal: J.Mol.Biol. / Year: 2016
Title: An Adaptive Mutation in Enterococcus faecium LiaR Associated with Antimicrobial Peptide Resistance Mimics Phosphorylation and Stabilizes LiaR in an Activated State.
Authors: Davlieva, M. / Tovar-Yanez, A. / DeBruler, K. / Leonard, P.G. / Zianni, M.R. / Arias, C.A. / Shamoo, Y.
History
DepositionJan 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Response regulator protein VraR
F: Response regulator protein VraR
B: Response regulator protein VraR
C: Response regulator protein VraR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,09812
Polymers94,7374
Non-polymers3618
Water0
1
A: Response regulator protein VraR
F: Response regulator protein VraR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5496
Polymers47,3692
Non-polymers1814
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-28 kcal/mol
Surface area22090 Å2
MethodPISA
2
B: Response regulator protein VraR
C: Response regulator protein VraR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5496
Polymers47,3692
Non-polymers1814
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-28 kcal/mol
Surface area22270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.032, 68.032, 276.949
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
Response regulator protein VraR /


Mass: 23684.312 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecium SD3B-2 (bacteria) / Gene: D357_01142 / Production host: Escherichia coli (E. coli) / References: UniProt: S4FAU8
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: BeF3

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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: 3.91 Å3/Da / Density % sol: 68.51 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.1 M magnesium formate dehydrate, 15 % w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionRedundancy: 3.5 % / Number: 82921 / Rmerge(I) obs: 0.115 / Χ2: 0.82 / D res high: 3.2 Å / D res low: 50 Å / Num. obs: 23488 / % possible obs: 98.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
8.675010.0271.0133.8
6.898.6710.0370.7653.9
6.026.8910.0920.7233.9
5.476.0210.1230.8213.8
5.085.4710.1170.8343.8
4.785.0810.1040.8653.8
4.544.7810.0980.7953.7
4.344.5410.0930.7663.7
4.184.3410.1070.8033.6
4.034.1810.1470.9173.6
3.914.0310.1790.8223.5
3.793.9110.2450.7713.5
3.693.7910.2560.793.4
3.63.6910.2980.8413.4
3.523.610.3940.8283.4
3.453.5210.4470.8123.4
3.383.4510.5880.8383.3
3.313.3810.6140.8393.3
3.263.3110.7280.8233.1
3.23.2610.8310.7922.9
Reflection twinOperator: -h,-k,l / Fraction: 0.48
ReflectionResolution: 3.2→50 Å / Num. obs: 23488 / % possible obs: 98.3 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.065 / Rrim(I) all: 0.128 / Χ2: 0.823 / Net I/av σ(I): 10.071 / Net I/σ(I): 5.9 / Num. measured all: 82921
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allΧ2% possible allRrim(I) all
3.2-3.262.90.83111890.5490.5580.79297.9
3.26-3.313.10.72811250.6470.470.82398.30.871
3.31-3.383.30.61412160.650.3830.83998.60.727
3.38-3.453.30.58811490.7120.3680.83898.10.697
3.45-3.523.40.44711590.8510.2740.81298.50.527
3.52-3.63.40.39412470.820.2390.82898.90.463
3.6-3.693.40.29811100.8740.180.84198.50.35
3.69-3.793.40.25612280.8770.1530.7998.60.299
3.79-3.913.50.24511290.8380.1430.77198.20.285
3.91-4.033.50.17912210.9170.1030.82298.50.208
4.03-4.183.60.14711360.9440.0830.91798.40.169
4.18-4.343.60.10711650.9410.060.80397.80.123
4.34-4.543.70.09312180.9610.0510.76698.20.107
4.54-4.783.70.09811330.9650.0520.79598.50.111
4.78-5.083.80.10411700.9260.0550.86598.80.119
5.08-5.473.80.11711970.960.060.834990.132
5.47-6.023.80.12311880.9580.0630.821990.139
6.02-6.893.90.09211870.9730.0470.72398.60.104
6.89-8.673.90.03711710.9940.0190.765980.042
8.67-503.80.02711500.980.0131.01395.60.03

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(dev_2474: ???)refinement
HKL-2000data reduction
PHASERphasing
PDB_EXTRACT3.15data extraction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IF4

4if4


Resolution: 3.192→34.016 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 0.3 / Phase error: 29.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2704 1865 8.83 %
Rwork0.2186 --
obs0.2233 21126 88.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.192→34.016 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6591 0 20 0 6611
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036679
X-RAY DIFFRACTIONf_angle_d0.5698996
X-RAY DIFFRACTIONf_dihedral_angle_d2.3324170
X-RAY DIFFRACTIONf_chiral_restr0.0421068
X-RAY DIFFRACTIONf_plane_restr0.0031145
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1919-3.27810.3933910.313857X-RAY DIFFRACTION50
3.2781-3.37450.36061120.30291217X-RAY DIFFRACTION74
3.3745-3.48330.35081260.29361341X-RAY DIFFRACTION82
3.4833-3.60770.34111440.26131487X-RAY DIFFRACTION88
3.6077-3.7520.30711460.24851567X-RAY DIFFRACTION91
3.752-3.92250.3221520.24041508X-RAY DIFFRACTION93
3.9225-4.1290.29131560.21621583X-RAY DIFFRACTION95
4.129-4.38710.23351590.17981605X-RAY DIFFRACTION96
4.3871-4.72510.24731540.191614X-RAY DIFFRACTION96
4.7251-5.19910.25311580.2031644X-RAY DIFFRACTION98
5.1991-5.94790.30431560.23561597X-RAY DIFFRACTION97
5.9479-7.48060.24931630.23761638X-RAY DIFFRACTION97
7.4806-34.01790.18381480.16071603X-RAY DIFFRACTION96

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