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1usk

L-leucine-binding protein with leucine bound

Method: X-RAY DIFFRACTION Dmax: 132.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

LEUCINE-SPECIFIC BINDING PROTEIN

ESCHERICHIA COLI

UniProt P04816

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 24–369 Not recorded LEU LEUCINE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.6；PEG 4000, SODIUM CITRATE, PH 5.6, 2-PROPANOL Resolution 2.00 Å R-free 0.252
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 24–369 Not recorded LEU LEUCINE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.6；PEG 4000, SODIUM CITRATE, PH 5.6, 2-PROPANOL Resolution 2.00 Å R-free 0.252
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain C； UniProt 24–369 Not recorded LEU LEUCINE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.6；PEG 4000, SODIUM CITRATE, PH 5.6, 2-PROPANOL Resolution 2.00 Å R-free 0.252
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain D； UniProt 24–369 Not recorded LEU LEUCINE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.6；PEG 4000, SODIUM CITRATE, PH 5.6, 2-PROPANOL Resolution 2.00 Å R-free 0.252

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 1USK Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1USG L-leucine-binding protein, apo form Deposited 2003-11-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 24–369（346 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；PEG 5000, SODIUM ACETATE PH 4.6, AMMONIUM SULPHATE, COCL2.
Resolution 1.53 Å R-free 0.216
1USI L-leucine-binding protein with phenylalanine bound Deposited 2003-11-24 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 24–369（346 aa）
Not recorded PHE PHENYLALANINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；pH 6.50
Resolution 1.80 Å R-free 0.222
1USI L-leucine-binding protein with phenylalanine bound Deposited 2003-11-24 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 24–369（346 aa）
Not recorded PHE PHENYLALANINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；pH 6.50
Resolution 1.80 Å R-free 0.222
2LBP STRUCTURE OF THE L-LEUCINE-BINDING PROTEIN REFINED AT 2.4 ANGSTROMS RESOLUTION AND COMPARISON WITH THE LEU(SLASH)ILE(SLASH)VAL-BINDING PROTEIN STRUCTURE Deposited 1989-04-10 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 24–369（346 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.40 Å
8Q52 A PBP-like protein built from fragments of different folds Deposited 2023-08-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 24–163（140 aa）
Chain A 273–351（79 aa）
Not recorded SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；30% PEG 4000, 0.1M Tris.HCl, 0.3M Li sulfate
Resolution 2.15 Å R-free 0.253

4 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LIVK_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–346； UniProt 24–369 Author chain B； PDBConstruct 1–346； UniProt 24–369 Author chain C； PDBConstruct 1–346； UniProt 24–369 Author chain D； PDBConstruct 1–346； UniProt 24–369

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 1usk

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1usk
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1usk
Deposition date deposition_date2003-11-25
Structure title titleL-leucine-binding protein with leucine bound
Keywords keywordsLEUCINE-BINDING PROTEIN, PROTEIN STRUCTURE, ABC TRANSPORT SYSTEMS, TRANSPORT PROTEIN; TRANSPORT PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier41.61 Å
Radius of gyration Rg (electron density) rg_electron41.26 Å
Forward intensity I(0) i0335411000.00
Molecular weight molecular_weight148130.0 kDa
Excluded volume excluded_volume184670 ų
Envelope volume envelope_volume250250 ų
Hydration-shell volume shell_volume51182 ų
Envelope diameter envelope_diameter132.8 Å
Shell Rg shell_rg46.05 Å
Envelope Rg envelope_rg40.26 Å
Shape Rg shape_rg41.25 Å
Total Rg total_rg41.51 Å
Total atoms total_atoms10420
Residues n_residues1384
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax132.2 Å
Rg (real space) rg_real41.52 Å
Rg uncertainty (real space) rg_real_error1.07 Å
I(0) (real space) i0_real3.3540e+08
I(0) uncertainty (real space) i0_real_error5.8610e+06
Rg (reciprocal space) rg_reciprocal41.61 Å
I(0) (reciprocal space) i0_reciprocal335400000.0000
Solution quality estimate total_estimate0.8324
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary55.7 Å
Skewness Skewness skewness0.097
Kurtosis Kurtosis kurtosis-0.771
Angular range angular_range— – 0.1900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha35270000.0000
Real-space data points n_real_points39
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.941; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1uska_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.93 — Periplasmic binding protein-like I
Superfamily Superfamily superfamilyc.93.1 — Periplasmic binding protein-like I
Family Family familyc.93.1.1 — L-arabinose binding protein-like
Domain ID domain_idd1uskb_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.93 — Periplasmic binding protein-like I
Superfamily Superfamily superfamilyc.93.1 — Periplasmic binding protein-like I
Family Family familyc.93.1.1 — L-arabinose binding protein-like
Domain ID domain_idd1uskc_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.93 — Periplasmic binding protein-like I
Superfamily Superfamily superfamilyc.93.1 — Periplasmic binding protein-like I
Family Family familyc.93.1.1 — L-arabinose binding protein-like
Domain ID domain_idd1uskd_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.93 — Periplasmic binding protein-like I
Superfamily Superfamily superfamilyc.93.1 — Periplasmic binding protein-like I
Family Family familyc.93.1.1 — L-arabinose binding protein-like

CATH v4.4 (8 domains)

Domain ID domain_id1uskA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
Domain ID domain_id1uskA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
Domain ID domain_id1uskB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
Domain ID domain_id1uskB02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
Domain ID domain_id1uskC01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
Domain ID domain_id1uskC02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
Domain ID domain_id1uskD01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
Domain ID domain_id1uskD02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
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8. Citations (1)

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9. Files and Curves (10)