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- PDB-1usi: L-leucine-binding protein with phenylalanine bound -

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Basic information

Entry
Database: PDB / ID: 1usi
TitleL-leucine-binding protein with phenylalanine bound
ComponentsLEUCINE-SPECIFIC BINDING PROTEIN
KeywordsTRANSPORT PROTEIN / LEUCINE-BINDING PROTEIN / PROTEIN STRUCTURE / ABC TRANSPORT SYSTEMS
Function / homology
Function and homology information


branched-chain amino acid transport / L-leucine binding / phenylalanine transport / isoleucine transport / valine transport / L-leucine transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / outer membrane-bounded periplasmic space / membrane
Similarity search - Function
Leu/Ile/Val-binding protein / Leucine-binding protein domain / Periplasmic binding protein / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHENYLALANINE / Leucine-specific-binding protein
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMagnusson, U. / Salopek-Sondi, B. / Luck, L.A. / Mowbray, S.L.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: X-Ray Structures of the Leucine-Binding Protein Illustrate Conformational Changes and the Basis of Ligand Specificity
Authors: Magnusson, U. / Salopek-Sondi, B. / Luck, L.A. / Mowbray, S.L.
History
DepositionNov 24, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LEUCINE-SPECIFIC BINDING PROTEIN
C: LEUCINE-SPECIFIC BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4904
Polymers74,1592
Non-polymers3302
Water5,386299
1
A: LEUCINE-SPECIFIC BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2452
Polymers37,0801
Non-polymers1651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: LEUCINE-SPECIFIC BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2452
Polymers37,0801
Non-polymers1651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)68.236, 78.143, 70.183
Angle α, β, γ (deg.)90.00, 102.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein LEUCINE-SPECIFIC BINDING PROTEIN / L-LEUCINE-BINDING PROTEIN / LS-BP / L-BP


Mass: 37079.699 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PKSTY / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P04816
#2: Chemical ChemComp-PHE / PHENYLALANINE


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / Source method: isolated from a natural source / Formula: H2O
Compound detailsA COMPONENT OF THE LEUCINE-SPECIFIC TRANSPORT SYSTEM, WHICH IS ONE OF TWO PERIPLASMIC BINDING ...A COMPONENT OF THE LEUCINE-SPECIFIC TRANSPORT SYSTEM, WHICH IS ONE OF TWO PERIPLASMIC BINDING PROTEIN-DEPENDENT TRANSPORT SYSTEMS OF THE HIGH-AFFINITY TRANSPORT OF THE BRANCHED-CHAIN AMINO ACIDS IN E.COLI.
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: 2.5 Å3/Da / Density % sol: 51 %
Crystal growpH: 6.5 / Details: pH 6.50
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
16 mg/mlprotein1drop
220 mMTris-HCl1droppH8.0
320 %PEG50001reservoir
4100 mMsodium acetate1reservoirpH4.6
50.2 Mammonium sulfate1reservoir
610 mM1reservoirCoCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.98
DetectorDate: Mar 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→35 Å / Num. obs: 60887 / % possible obs: 96.2 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 10.6
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 1.5 / % possible all: 74
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 35 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.095
Reflection shell
*PLUS
% possible obs: 74 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1USG

1usg


Resolution: 1.8→35 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.849 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.222 3242 5.1 %RANDOM
Rwork0.189 ---
obs0.191 60887 96.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.63 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å20 Å2-0.17 Å2
2--0.36 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.8→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5192 0 24 299 5515
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0225314
X-RAY DIFFRACTIONr_bond_other_d0.0020.024744
X-RAY DIFFRACTIONr_angle_refined_deg1.871.9577186
X-RAY DIFFRACTIONr_angle_other_deg0.928311100
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9825688
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1220.2780
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.026042
X-RAY DIFFRACTIONr_gen_planes_other0.0120.02998
X-RAY DIFFRACTIONr_nbd_refined0.2170.21086
X-RAY DIFFRACTIONr_nbd_other0.2510.25563
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0920.23050
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2255
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2570.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2120.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2180.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1141.53414
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.88425430
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.32931900
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.2384.51756
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.349 193
Rwork0.276 3529
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.025
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.9

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