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- PDB-6xks: Crystal structure of domain A from the periplasmic Lysine-, Argin... -

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Entry
Database: PDB / ID: 6xks
TitleCrystal structure of domain A from the periplasmic Lysine-, Arginine-, Ornithine-binding protein (LAO) of Salmonella typhimurium
ComponentsHistidine ABC transporter substrate-binding protein HisJ
KeywordsPROTEIN BINDING / Periplasmic Binding Protein / LAO / Protein folding / Thermodynamics / Kinetics
Function / homology
Function and homology information


nitrogen compound 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
Similarity search - Domain/homology
ACETATE ION / DI(HYDROXYETHYL)ETHER / Histidine ABC transporter substrate-binding protein HisJ
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsRomero-Romero, S. / Berrocal, T. / Vergara, R. / Espinoza-Perez, G. / Rodriguez-Romero, A.
Funding support Mexico, 5items
OrganizationGrant numberCountry
Programa de Apoyo a Proyectos de Investigacion e Innovacion Tecnologica (PAPIIT)IN208418 Mexico
Consejo Nacional de Ciencia y Tecnologia (CONACYT)221169 Mexico
Consejo Nacional de Ciencia y Tecnologia (CONACYT)254514 Mexico
Programa de Apoyo a Proyectos de Investigacion e Innovacion Tecnologica (PAPIIT)IN220516 Mexico
Programa de Apoyo a Proyectos de Investigacion e Innovacion Tecnologica (PAPIIT)IN219519 Mexico
CitationJournal: Febs J. / Year: 2023
Title: Thermodynamic and kinetic analysis of the LAO binding protein and its isolated domains reveal non-additivity in stability, folding and function.
Authors: Vergara, R. / Berrocal, T. / Juarez Mejia, E.I. / Romero-Romero, S. / Velazquez-Lopez, I. / Pulido, N.O. / Lopez Sanchez, H.A. / Silva, D.A. / Costas, M. / Rodriguez-Romero, A. / Rodriguez- ...Authors: Vergara, R. / Berrocal, T. / Juarez Mejia, E.I. / Romero-Romero, S. / Velazquez-Lopez, I. / Pulido, N.O. / Lopez Sanchez, H.A. / Silva, D.A. / Costas, M. / Rodriguez-Romero, A. / Rodriguez-Sotres, R. / Sosa-Peinado, A. / Fernandez-Velasco, D.A.
History
DepositionJun 27, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2023Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histidine ABC transporter substrate-binding protein HisJ
B: Histidine ABC transporter substrate-binding protein HisJ
C: Histidine ABC transporter substrate-binding protein HisJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0788
Polymers48,6883
Non-polymers3895
Water2,684149
1
A: Histidine ABC transporter substrate-binding protein HisJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2882
Polymers16,2291
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Histidine ABC transporter substrate-binding protein HisJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5014
Polymers16,2291
Non-polymers2713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Histidine ABC transporter substrate-binding protein HisJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2882
Polymers16,2291
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.597, 87.785, 109.154
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein Histidine ABC transporter substrate-binding protein HisJ / Lysine-arginine-ornithine-binding periplasmic protein / Lysine/arginine/ornithine ABC transporter ...Lysine-arginine-ornithine-binding periplasmic protein / Lysine/arginine/ornithine ABC transporter substrate-binding protein ArgT / Lysine/arginine/ornithine transport protein / Lysine/arginine/ornithine-binding periplasmic protein


Mass: 16229.394 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: argT / Plasmid: pET12b / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): AI / References: UniProt: A0A0D6FBD8
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Sequence detailsDomain A is the discontinuous domain in LAO protein. To generate a continuous protein, all residues ...Domain A is the discontinuous domain in LAO protein. To generate a continuous protein, all residues previous to D91 (inclusive) and all residues after V185 (inclusive) were connected in the sequence for expression (numbers from LAO wt).

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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: 2.3 Å3/Da / Density % sol: 46.46 %
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 / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Apr 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 32910 / % possible obs: 99.3 % / Redundancy: 6.7 % / Biso Wilson estimate: 31.4 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.16 / Net I/σ(I): 16.6
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.826 / Mean I/σ(I) obs: 2 / Num. unique obs: 1691 / CC1/2: 0.694 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.25data extraction
CrystalCleardata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2LAO

2lao


Resolution: 2.4→42.86 Å / SU ML: 0.3496 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.3884
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.288 3273 10.01 %
Rwork0.2302 29432 -
obs0.2361 32705 96.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.36 Å2
Refinement stepCycle: LAST / Resolution: 2.4→42.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3282 0 26 152 3460
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00423360
X-RAY DIFFRACTIONf_angle_d0.67764530
X-RAY DIFFRACTIONf_chiral_restr0.0436507
X-RAY DIFFRACTIONf_plane_restr0.0041590
X-RAY DIFFRACTIONf_dihedral_angle_d6.0516469
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.440.46911290.32261135X-RAY DIFFRACTION85.12
2.44-2.480.32091420.28811262X-RAY DIFFRACTION95.97
2.48-2.520.351340.25831274X-RAY DIFFRACTION97.24
2.52-2.560.34291490.25931299X-RAY DIFFRACTION96.99
2.56-2.610.34041480.25961298X-RAY DIFFRACTION97.9
2.61-2.660.30731370.24791282X-RAY DIFFRACTION98.06
2.66-2.710.31171440.24291316X-RAY DIFFRACTION98.78
2.71-2.770.35851440.24661306X-RAY DIFFRACTION98.71
2.77-2.830.35191420.23141287X-RAY DIFFRACTION97.68
2.83-2.90.29511480.23941344X-RAY DIFFRACTION99.33
2.91-2.980.29251410.24931265X-RAY DIFFRACTION98.87
2.98-3.070.31271480.25051322X-RAY DIFFRACTION99.19
3.07-3.170.30811460.20711284X-RAY DIFFRACTION99.31
3.17-3.280.27641480.22181334X-RAY DIFFRACTION99.33
3.28-3.410.31061460.21341305X-RAY DIFFRACTION99.45
3.42-3.570.26981500.20861299X-RAY DIFFRACTION98.71
3.57-3.760.28031230.2511124X-RAY DIFFRACTION85.53
3.76-3.990.22311370.20751242X-RAY DIFFRACTION92.55
4-4.30.24031450.1881308X-RAY DIFFRACTION99.66
4.3-4.730.25491380.20121224X-RAY DIFFRACTION92.84
4.73-5.420.27331390.21861283X-RAY DIFFRACTION98.2
5.42-6.820.31131470.26151334X-RAY DIFFRACTION99.87
6.82-42.860.26731480.24221305X-RAY DIFFRACTION99.38

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