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

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Basic information

Entry
Database: PDB / ID: 6mld
TitleCrystal structure of the periplasmic Lysine-, Arginine-, Ornithine-binding protein (LAO) F52A 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
ACETATE ION / Lysine/arginine/ornithine-binding periplasmic protein
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.66 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)26,2185
Polymers25,9821
Non-polymers2364
Water5,693316
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area590 Å2
ΔGint0 kcal/mol
Surface area11450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.758, 76.231, 85.363
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: 25982.217 Da / Num. of mol.: 1 / Mutation: F52A
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 / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 316 / Source method: isolated from a natural source / Formula: H2O

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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: 2.18 Å3/Da / Density % sol: 43.59 %
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 2, 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: 1.66→50 Å / Num. obs: 27708 / % possible obs: 99.9 % / Redundancy: 10.6 % / Biso Wilson estimate: 13.5 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 25.7
Reflection shellResolution: 1.66→1.69 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.784 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2632 / CC1/2: 0.644 / % possible all: 99.6

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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: 2LAO

2lao


Resolution: 1.66→42.681 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.34
RfactorNum. reflection% reflection
Rfree0.2108 1994 7.24 %
Rwork0.1613 --
obs0.1647 27544 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.66→42.681 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1785 0 16 316 2117
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061829
X-RAY DIFFRACTIONf_angle_d0.9872470
X-RAY DIFFRACTIONf_dihedral_angle_d12.643652
X-RAY DIFFRACTIONf_chiral_restr0.039275
X-RAY DIFFRACTIONf_plane_restr0.005326
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.70150.29361380.25161767X-RAY DIFFRACTION100
1.7015-1.74750.28331420.22691817X-RAY DIFFRACTION100
1.7475-1.79890.28611380.21411764X-RAY DIFFRACTION100
1.7989-1.8570.25861400.18631800X-RAY DIFFRACTION100
1.857-1.92340.1881410.17611806X-RAY DIFFRACTION100
1.9234-2.00040.21321420.15731805X-RAY DIFFRACTION100
2.0004-2.09140.21581400.15891807X-RAY DIFFRACTION100
2.0914-2.20170.19841420.15071821X-RAY DIFFRACTION100
2.2017-2.33960.19671420.16141814X-RAY DIFFRACTION100
2.3396-2.52020.22191410.16181814X-RAY DIFFRACTION100
2.5202-2.77380.24091430.16391833X-RAY DIFFRACTION100
2.7738-3.17510.2061450.15681862X-RAY DIFFRACTION100
3.1751-3.99980.16221460.1311868X-RAY DIFFRACTION100
3.9998-42.69560.19661540.15171972X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 4.7598 Å / Origin y: -57.9783 Å / Origin z: 107.3088 Å
111213212223313233
T0.035 Å2-0.0014 Å20.0015 Å2-0.029 Å2-0.0151 Å2--0.0308 Å2
L0.341 °2-0.0313 °2-0.0147 °2-0.3023 °2-0.0765 °2--0.2106 °2
S0.0127 Å °0.0288 Å °-0.0137 Å °-0.0474 Å °0.0022 Å °-0.0181 Å °0.0249 Å °-0.0154 Å °0.0003 Å °
Refinement TLS groupSelection details: all

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