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- PDB-6mli: Crystal structure of the periplasmic Lysine-, Arginine-, Ornithin... -

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Basic information

Entry
Database: PDB / ID: 6mli
TitleCrystal structure of the periplasmic Lysine-, Arginine-, Ornithine-binding protein (LAO) R77A mutant from Salmonella typhimurium complexed with histidine
ComponentsLysine/arginine/ornithine-binding periplasmic protein
KeywordsPROTEIN BINDING / Periplasmic Binding Protein / LAO / Thermodynamics / Protein Ligand Complex
Function / homology
Function and homology information


amino acid transport / outer membrane-bounded periplasmic space
Similarity search - Function
Specific amino acids and opine-binding periplasmic protein, ABC transporter / Solute-binding protein family 3, conserved site / Bacterial extracellular solute-binding proteins, family 3 signature. / Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / HISTIDINE / Lysine/arginine/ornithine-binding periplasmic protein
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.883 Å
AuthorsRomero-Romero, S. / Vergara, R. / Espinoza-Perez, G. / Rodriguez-Romero, A.
Funding support Mexico, 4items
OrganizationGrant numberCountry
Other governmentIN208418 Mexico
Other government221169 Mexico
Other government254514 Mexico
Other governmentIN220516 Mexico
CitationJournal: Febs J. / Year: 2020
Title: The interplay of protein-ligand and water-mediated interactions shape affinity and selectivity in the LAO binding protein.
Authors: Vergara, R. / Romero-Romero, S. / Velazquez-Lopez, I. / Espinoza-Perez, G. / Rodriguez-Hernandez, A. / Pulido, N.O. / Sosa-Peinado, A. / Rodriguez-Romero, A. / Fernandez-Velasco, D.A.
History
DepositionSep 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: Lysine/arginine/ornithine-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5759
Polymers25,9721
Non-polymers6038
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-2 kcal/mol
Surface area10960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.199, 58.850, 115.282
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Lysine/arginine/ornithine-binding periplasmic protein / LAO-binding protein


Mass: 25972.197 Da / Num. of mol.: 1 / Mutation: R77A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: argT, STM2355 / Plasmid: pET12b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-AI / References: UniProt: P02911
#2: Chemical ChemComp-HIS / HISTIDINE


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10N3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.43 Å3/Da / Density % sol: 49.46 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M Sodium acetate trihydrate. 0.1 M Sodium cacodylate trihydrate pH 6.5 30% w/v Polyethylene glycol 8,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: May 18, 2018 / Details: Osmic VariMax Cu-HF
RadiationMonochromator: VariMax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. obs: 40663 / % possible obs: 99.4 % / Redundancy: 6.5 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 26.9
Reflection shellResolution: 1.88→1.91 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2011 / CC1/2: 0.667 / % possible all: 94.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIX1.9_1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LAG

1lag


Resolution: 1.883→41.179 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.94
RfactorNum. reflection% reflection
Rfree0.2134 1971 9.48 %
Rwork0.1636 --
obs0.1683 38630 97.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.883→41.179 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1809 0 41 214 2064
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071890
X-RAY DIFFRACTIONf_angle_d0.9832550
X-RAY DIFFRACTIONf_dihedral_angle_d13.433682
X-RAY DIFFRACTIONf_chiral_restr0.04280
X-RAY DIFFRACTIONf_plane_restr0.005338
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8833-1.90810.34461140.32371122X-RAY DIFFRACTION84
1.9081-1.93420.30511440.24471363X-RAY DIFFRACTION95
1.9342-1.96180.28591430.25331318X-RAY DIFFRACTION96
1.9618-1.99110.26861380.2161319X-RAY DIFFRACTION96
1.9911-2.02220.24291380.19641290X-RAY DIFFRACTION96
2.0222-2.05540.25171450.20011364X-RAY DIFFRACTION97
2.0554-2.09080.23011380.19381301X-RAY DIFFRACTION97
2.0908-2.12880.22661440.1921337X-RAY DIFFRACTION97
2.1288-2.16980.21681420.18361387X-RAY DIFFRACTION97
2.1698-2.21410.26651390.17631311X-RAY DIFFRACTION97
2.2141-2.26220.22761430.1831350X-RAY DIFFRACTION98
2.2622-2.31480.23811390.17411385X-RAY DIFFRACTION98
2.3148-2.37270.25761420.17771332X-RAY DIFFRACTION99
2.3727-2.43690.24491400.16881362X-RAY DIFFRACTION99
2.4369-2.50860.22471410.17621366X-RAY DIFFRACTION99
2.5086-2.58950.24591400.1641348X-RAY DIFFRACTION98
2.5895-2.6820.26491450.16131385X-RAY DIFFRACTION99
2.682-2.78940.21131380.15681348X-RAY DIFFRACTION99
2.7894-2.91630.21441410.15911372X-RAY DIFFRACTION99
2.9163-3.070.20061450.15371374X-RAY DIFFRACTION99
3.07-3.26230.20721400.14281356X-RAY DIFFRACTION100
3.2623-3.51410.18371430.13571377X-RAY DIFFRACTION99
3.5141-3.86750.14591490.13141365X-RAY DIFFRACTION100
3.8675-4.42650.17721420.12621377X-RAY DIFFRACTION100
4.4265-5.57480.18171420.14111378X-RAY DIFFRACTION100
5.5748-41.1890.21051480.18011380X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 15.7552 Å / Origin y: -0.0599 Å / Origin z: -12.7411 Å
111213212223313233
T0.0737 Å20.0023 Å2-0.0023 Å2-0.095 Å2-0.0026 Å2--0.0848 Å2
L0.5398 °20.1584 °20.1268 °2-0.6138 °2-0.0468 °2--0.7895 °2
S-0.0246 Å °0.0215 Å °0.0143 Å °-0.0084 Å °0.0096 Å °0.0596 Å °-0.0367 Å °0.0258 Å °-0.0002 Å °
Refinement TLS groupSelection details: all

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