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

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Basic information

Entry
Database: PDB / ID: 6mku
TitleCrystal structure of the periplasmic Lysine-, Arginine-, Ornithine-binding protein (LAO) D11A 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: 1.727 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 26, 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 30, 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)26,3414
Polymers26,0141
Non-polymers3263
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area340 Å2
ΔGint-2 kcal/mol
Surface area10590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.161, 58.611, 115.284
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: 26014.305 Da / Num. of mol.: 1 / Mutation: D11A
Source method: isolated from a genetically manipulated source
Details: Complexed with arginine
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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / 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.: 270 / 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: 2.42 Å3/Da / Density % sol: 49.1 %
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 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 / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Aug 3, 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: 1.727→50 Å / Num. obs: 51080 / % possible obs: 99.2 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 18.1
Reflection shellResolution: 1.727→1.76 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.587 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1055 / % possible all: 96

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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: 1.727→41.097 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.2
RfactorNum. reflection% reflection
Rfree0.2359 1992 7.4 %
Rwork0.1944 --
obs0.1975 48526 94.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.727→41.097 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1796 0 22 270 2088
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061848
X-RAY DIFFRACTIONf_angle_d0.9512497
X-RAY DIFFRACTIONf_dihedral_angle_d13.258662
X-RAY DIFFRACTIONf_chiral_restr0.039277
X-RAY DIFFRACTIONf_plane_restr0.005329
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7266-1.74940.28781090.29081473X-RAY DIFFRACTION80
1.7494-1.77330.33831310.28281666X-RAY DIFFRACTION89
1.7733-1.79870.30061230.2631593X-RAY DIFFRACTION89
1.7987-1.82550.28791340.26931646X-RAY DIFFRACTION90
1.8255-1.8540.31531310.2621673X-RAY DIFFRACTION91
1.854-1.88440.30971310.25981649X-RAY DIFFRACTION92
1.8844-1.91690.27581370.25021671X-RAY DIFFRACTION93
1.9169-1.95180.32211390.23841715X-RAY DIFFRACTION93
1.9518-1.98930.27451390.23391694X-RAY DIFFRACTION94
1.9893-2.02990.26721440.21771725X-RAY DIFFRACTION95
2.0299-2.07410.28341360.21111732X-RAY DIFFRACTION95
2.0741-2.12230.24911370.1991706X-RAY DIFFRACTION95
2.1223-2.17540.24511440.20021758X-RAY DIFFRACTION95
2.1754-2.23420.24951300.19321717X-RAY DIFFRACTION96
2.2342-2.29990.26471460.20051744X-RAY DIFFRACTION96
2.2999-2.37420.25481380.19061789X-RAY DIFFRACTION97
2.3742-2.4590.22221330.19271762X-RAY DIFFRACTION97
2.459-2.55740.23511430.19251771X-RAY DIFFRACTION98
2.5574-2.67380.28171380.19661806X-RAY DIFFRACTION98
2.6738-2.81470.20581440.18731783X-RAY DIFFRACTION99
2.8147-2.99110.22991520.18781799X-RAY DIFFRACTION99
2.9911-3.22190.21831450.18031802X-RAY DIFFRACTION100
3.2219-3.5460.19781420.16561819X-RAY DIFFRACTION100
3.546-4.05870.19881500.15671818X-RAY DIFFRACTION100
4.0587-5.1120.16111420.14251806X-RAY DIFFRACTION100
5.112-41.1090.19411520.17261819X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 3.0008 Å / Origin y: 0.4015 Å / Origin z: -12.9741 Å
111213212223313233
T0.0107 Å2-0.0023 Å20.0079 Å2-0.0049 Å2-0.0175 Å2--0.0138 Å2
L0.0137 °20.0035 °20.0034 °2-0.0129 °20.0056 °2--0.0393 °2
S-0.0205 Å °0.0446 Å °-0.0042 Å °-0.0048 Å °-0.0015 Å °-0.0227 Å °0.0308 Å °0.0108 Å °-0.0168 Å °
Refinement TLS groupSelection details: all

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