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

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Basic information

Entry
Database: PDB / ID: 6mlo
TitleCrystal structure of the periplasmic Lysine-, Arginine-, Ornithine-binding protein (LAO) Y14A mutant from Salmonella typhimurium complexed with arginine
ComponentsLysine/arginine/ornithine-binding periplasmic protein
KeywordsPROTEIN BINDING / Periplasmic Binding Protein / LAO / Thermodynamics / Protein Ligand Complex
Function / homology
Function and homology information


amino acid binding / 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 / ARGININE / Lysine/arginine/ornithine-binding periplasmic protein
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.717 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 1.3Oct 23, 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)26,2934
Polymers25,9661
Non-polymers3263
Water5,134285
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area430 Å2
ΔGint-1 kcal/mol
Surface area11050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.168, 58.653, 115.463
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: 25966.219 Da / Num. of mol.: 1 / Mutation: Y14A
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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2 / Feature type: SUBJECT OF INVESTIGATION
#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.: 285 / 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: 49.34 %
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: Apr 12, 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: 1.717→50 Å / Num. obs: 51155 / % possible obs: 99.2 % / Redundancy: 7.9 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 29.6
Reflection shellResolution: 1.72→1.78 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.669 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3103 / CC1/2: 0.676 / % possible all: 94.3

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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: 1LAF

1laf


Resolution: 1.717→32.178 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.74
RfactorNum. reflection% reflection
Rfree0.2192 1996 7.22 %
Rwork0.1755 --
obs0.1786 51155 98.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.717→32.178 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1815 0 22 285 2122
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071883
X-RAY DIFFRACTIONf_angle_d1.0212540
X-RAY DIFFRACTIONf_dihedral_angle_d12.868697
X-RAY DIFFRACTIONf_chiral_restr0.04280
X-RAY DIFFRACTIONf_plane_restr0.005333
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7169-1.73950.37111180.31631563X-RAY DIFFRACTION84
1.7395-1.76330.33431340.29331730X-RAY DIFFRACTION93
1.7633-1.78850.30011410.27541730X-RAY DIFFRACTION94
1.7885-1.81520.28311370.24841775X-RAY DIFFRACTION96
1.8152-1.84360.30131380.24151822X-RAY DIFFRACTION96
1.8436-1.87380.30341400.22521798X-RAY DIFFRACTION96
1.8738-1.90610.23071370.21131772X-RAY DIFFRACTION98
1.9061-1.94070.25661490.22061868X-RAY DIFFRACTION99
1.9407-1.97810.30751440.21471828X-RAY DIFFRACTION99
1.9781-2.01840.26341480.20831849X-RAY DIFFRACTION100
2.0184-2.06230.23731450.20471878X-RAY DIFFRACTION100
2.0623-2.11030.22551440.19511847X-RAY DIFFRACTION100
2.1103-2.1630.24721520.18771878X-RAY DIFFRACTION100
2.163-2.22150.23611440.17711821X-RAY DIFFRACTION100
2.2215-2.28690.22481430.18171865X-RAY DIFFRACTION100
2.2869-2.36070.28481430.17461850X-RAY DIFFRACTION100
2.3607-2.4450.23891470.16871866X-RAY DIFFRACTION100
2.445-2.54280.21261400.17221854X-RAY DIFFRACTION100
2.5428-2.65850.21161470.17151882X-RAY DIFFRACTION100
2.6585-2.79860.21181350.1811845X-RAY DIFFRACTION100
2.7986-2.97380.20231440.17061831X-RAY DIFFRACTION100
2.9738-3.20330.2251390.16331867X-RAY DIFFRACTION100
3.2033-3.52530.19461440.15331863X-RAY DIFFRACTION100
3.5253-4.03450.16011430.14481875X-RAY DIFFRACTION100
4.0345-5.07990.15761440.12071844X-RAY DIFFRACTION100
5.0799-32.1840.17241520.14921862X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 3.3013 Å / Origin y: 0.7879 Å / Origin z: -13.1009 Å
111213212223313233
T0.0061 Å2-0.0079 Å2-0.0063 Å2--0.005 Å2-0.0425 Å2---0.004 Å2
L0.0015 °20.001 °20.001 °2-0.0035 °20.0056 °2--0.0147 °2
S-0.0119 Å °0.0188 Å °0.003 Å °-0.0022 Å °-0.0033 Å °-0.0046 Å °0.0177 Å °-0.0025 Å °-0.0064 Å °
Refinement TLS groupSelection details: all

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