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

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Basic information

Entry
Database: PDB / ID: 6mlg
TitleCrystal structure of the periplasmic Lysine-, Arginine-, Ornithine-binding protein (LAO) R77A 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: 1.892 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.3Nov 20, 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)26,3486
Polymers25,9721
Non-polymers3755
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area530 Å2
ΔGint-8 kcal/mol
Surface area10680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.207, 57.656, 101.260
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: 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.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 2.09 Å3/Da / Density % sol: 41.28 %
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: May 4, 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: 1.91→50 Å / Num. obs: 31889 / % possible obs: 98.9 % / Redundancy: 4.8 % / Biso Wilson estimate: 20.7 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 19.9
Reflection shellResolution: 1.91→1.94 Å / Redundancy: 3 % / Rmerge(I) obs: 0.658 / Mean I/σ(I) obs: 2 / Num. unique obs: 1582 / CC1/2: 0.572 / % possible all: 97.1

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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: 1.892→34.924 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2116 1737 10.07 %
Rwork0.1594 --
obs0.1647 31889 94.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.892→34.924 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1787 0 25 203 2015
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071840
X-RAY DIFFRACTIONf_angle_d0.9392487
X-RAY DIFFRACTIONf_dihedral_angle_d12.951653
X-RAY DIFFRACTIONf_chiral_restr0.037277
X-RAY DIFFRACTIONf_plane_restr0.004329
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.892-1.92020.35731050.2737914X-RAY DIFFRACTION69
1.9202-1.95020.30951350.26741169X-RAY DIFFRACTION89
1.9502-1.98220.27671350.23541190X-RAY DIFFRACTION91
1.9822-2.01640.3081280.22781199X-RAY DIFFRACTION92
2.0164-2.0530.2921330.21461228X-RAY DIFFRACTION92
2.053-2.09250.24481290.20571197X-RAY DIFFRACTION92
2.0925-2.13520.27491380.20041267X-RAY DIFFRACTION94
2.1352-2.18160.22521350.19371229X-RAY DIFFRACTION95
2.1816-2.23240.26491370.17781226X-RAY DIFFRACTION95
2.2324-2.28820.27541450.18061275X-RAY DIFFRACTION95
2.2882-2.350.26251390.17661261X-RAY DIFFRACTION96
2.35-2.41920.25061360.17911245X-RAY DIFFRACTION97
2.4192-2.49720.24951490.17831294X-RAY DIFFRACTION98
2.4972-2.58650.25091360.16941281X-RAY DIFFRACTION98
2.5865-2.690.26921480.15741281X-RAY DIFFRACTION98
2.69-2.81240.1951460.15331299X-RAY DIFFRACTION98
2.8124-2.96060.19491470.15781271X-RAY DIFFRACTION99
2.9606-3.1460.2111550.13641332X-RAY DIFFRACTION99
3.146-3.38870.19051470.14021296X-RAY DIFFRACTION99
3.3887-3.72930.14241430.13061298X-RAY DIFFRACTION100
3.7293-4.26820.14691470.11651301X-RAY DIFFRACTION99
4.2682-5.37430.17491500.11771315X-RAY DIFFRACTION100
5.3743-34.930.17961490.1631309X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -10.617 Å / Origin y: -0.3912 Å / Origin z: 12.7605 Å
111213212223313233
T0.0688 Å20.0047 Å2-0.0047 Å2-0.0793 Å20.0033 Å2--0.0658 Å2
L0.6156 °2-0.0341 °20.1611 °2-0.309 °20.0104 °2--0.4955 °2
S-0.0265 Å °-0.0706 Å °0.0169 Å °-0.005 Å °0.0218 Å °-0.0255 Å °0.0066 Å °-0.0055 Å °-0 Å °
Refinement TLS groupSelection details: all

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