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

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Basic information

Entry
Database: PDB / ID: 6mln
TitleCrystal structure of the periplasmic Lysine-, Arginine-, Ornithine-binding protein (LAO) S72A 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: 1.721 Å
AuthorsRomero-Romero, S. / Vergara, R. / Espinoza-Perez, G. / Rodriguez-Romero, A.
Funding support Mexico, 4items
OrganizationGrant numberCountry
Other privateIN208418 Mexico
Other private221169 Mexico
Other private254514 Mexico
Other privateIN220516 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 9, 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)26,7969
Polymers26,0421
Non-polymers7548
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-5 kcal/mol
Surface area10460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.804, 59.050, 115.370
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: 26042.314 Da / Num. of mol.: 1 / Mutation: S72A
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-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2
#3: Chemical ChemComp-ACT / ACETATE ION


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


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


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.41 Å3/Da / Density % sol: 49 %
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 16, 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: 1.72→50 Å / Num. obs: 54116 / % possible obs: 100 % / Redundancy: 9.5 % / Biso Wilson estimate: 13.5 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 44.1
Reflection shellResolution: 1.72→1.75 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.385 / Mean I/σ(I) obs: 6 / Num. unique obs: 2679 / CC1/2: 0.91 / % possible all: 99.8

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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: 1.721→32.225 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1747 2000 7.25 %
Rwork0.144 --
obs0.1462 51410 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.721→32.225 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1762 0 50 266 2078
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061836
X-RAY DIFFRACTIONf_angle_d0.9992472
X-RAY DIFFRACTIONf_dihedral_angle_d12.459652
X-RAY DIFFRACTIONf_chiral_restr0.04273
X-RAY DIFFRACTIONf_plane_restr0.004322
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7212-1.7430.24271350.19351744X-RAY DIFFRACTION96
1.743-1.76590.24561380.18671715X-RAY DIFFRACTION99
1.7659-1.79010.21861390.16811778X-RAY DIFFRACTION100
1.7901-1.81570.18461390.16911768X-RAY DIFFRACTION100
1.8157-1.84280.20251390.15591802X-RAY DIFFRACTION100
1.8428-1.87160.18821370.14551716X-RAY DIFFRACTION100
1.8716-1.90230.1531450.15011786X-RAY DIFFRACTION100
1.9023-1.93510.18791440.13931786X-RAY DIFFRACTION100
1.9351-1.97030.18181370.14871739X-RAY DIFFRACTION100
1.9703-2.00820.20441370.16021761X-RAY DIFFRACTION100
2.0082-2.04910.19341430.14221802X-RAY DIFFRACTION100
2.0491-2.09370.22161360.13591746X-RAY DIFFRACTION100
2.0937-2.14240.15831360.13811757X-RAY DIFFRACTION100
2.1424-2.19590.14121360.13431773X-RAY DIFFRACTION100
2.1959-2.25530.18171330.13411783X-RAY DIFFRACTION100
2.2553-2.32160.20081410.14211778X-RAY DIFFRACTION100
2.3216-2.39660.17211390.14421744X-RAY DIFFRACTION100
2.3966-2.48220.19481360.14171798X-RAY DIFFRACTION100
2.4822-2.58150.18011380.14221757X-RAY DIFFRACTION100
2.5815-2.6990.1561370.13521764X-RAY DIFFRACTION100
2.699-2.84120.17441350.14171780X-RAY DIFFRACTION100
2.8412-3.01910.17421360.13211764X-RAY DIFFRACTION100
3.0191-3.2520.15741380.13391767X-RAY DIFFRACTION100
3.252-3.57880.16411330.1241755X-RAY DIFFRACTION100
3.5788-4.09580.13881400.13041799X-RAY DIFFRACTION100
4.0958-5.15690.13651390.13931755X-RAY DIFFRACTION100
5.1569-32.23090.21491410.18941766X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 3.0487 Å / Origin y: -0.1307 Å / Origin z: -12.922 Å
111213212223313233
T0.0304 Å20.0032 Å20.0008 Å2-0.0512 Å2-0.0004 Å2--0.0436 Å2
L0.6236 °20.2094 °2-0.1468 °2-0.6792 °20.0902 °2--0.8974 °2
S-0.0244 Å °0.0333 Å °-0.0136 Å °0.0005 Å °0.0202 Å °-0.06 Å °0.0199 Å °-0.0242 Å °-0.0002 Å °
Refinement TLS groupSelection details: all

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