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

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Basic information

Entry
Database: PDB / ID: 6mkx
TitleCrystal structure of the periplasmic Lysine-, Arginine-, Ornithine-binding protein (LAO) R77A mutant from Salmonella typhimurium
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
Lysine/arginine/ornithine-binding periplasmic protein
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.284 Å
AuthorsRomero-Romero, S. / Vergara, R. / Espinoza-Perez, G. / Rodriguez-Romero, A.
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 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
A: Lysine/arginine/ornithine-binding periplasmic protein


Theoretical massNumber of molelcules
Total (without water)25,9721
Polymers25,9721
Non-polymers00
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.001, 76.750, 86.162
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.23 Å3/Da / Density % sol: 44.89 %
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 / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jun 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: 2.284→50 Å / Num. obs: 11886 / % possible obs: 99.6 % / Redundancy: 7.2 % / Biso Wilson estimate: 24.9 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 24.8
Reflection shellResolution: 2.284→2.33 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.294 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 1009 / CC1/2: 0.848 / % possible all: 91.4

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIX1.9_1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2LAO

2lao


Resolution: 2.284→43.081 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.17
RfactorNum. reflection% reflection
Rfree0.251 1000 9.05 %
Rwork0.191 --
obs0.1962 11054 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.284→43.081 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1788 0 0 120 1908
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011851
X-RAY DIFFRACTIONf_angle_d1.0612518
X-RAY DIFFRACTIONf_dihedral_angle_d5.7661503
X-RAY DIFFRACTIONf_chiral_restr0.057283
X-RAY DIFFRACTIONf_plane_restr0.007331
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2841-2.40450.29851380.23991391X-RAY DIFFRACTION99
2.4045-2.55510.36051410.22271412X-RAY DIFFRACTION100
2.5551-2.75240.26971400.22171406X-RAY DIFFRACTION100
2.7524-3.02930.26851400.22561417X-RAY DIFFRACTION100
3.0293-3.46750.26511440.18371443X-RAY DIFFRACTION100
3.4675-4.3680.21531440.15631448X-RAY DIFFRACTION100
4.368-43.08860.20871530.17571537X-RAY DIFFRACTION100

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