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1usg

L-leucine-binding protein, apo form

Method: X-RAY DIFFRACTION Dmax: 76.4 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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 24–369 Not recorded No other associated polymer 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

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 1USG Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1USI L-leucine-binding protein with phenylalanine bound Deposited 2003-11-24 Different oligomeric state 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 oligomeric state 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
1USK L-leucine-binding protein with leucine bound Deposited 2003-11-25 Different oligomeric state 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 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
1USK L-leucine-binding protein with leucine bound Deposited 2003-11-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 24–369（346 aa）
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
1USK L-leucine-binding protein with leucine bound Deposited 2003-11-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 24–369（346 aa）
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
1USK L-leucine-binding protein with leucine bound Deposited 2003-11-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 24–369（346 aa）
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
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 oligomeric state 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 8 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

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 1usg

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1usg
Deposition date deposition_date2003-11-24
Structure title titleL-leucine-binding protein, apo form
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_guinier23.09 Å
Radius of gyration Rg (electron density) rg_electron22.33 Å
Forward intensity I(0) i023906300.00
Molecular weight molecular_weight36901.0 kDa
Excluded volume excluded_volume45981 ų
Envelope volume envelope_volume53991 ų
Hydration-shell volume shell_volume20764 ų
Envelope diameter envelope_diameter77.8 Å
Shell Rg shell_rg28.32 Å
Envelope Rg envelope_rg22.33 Å
Shape Rg shape_rg22.30 Å
Total Rg total_rg23.15 Å
Total atoms total_atoms2596
Residues n_residues346
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 dmax76.4 Å
Rg (real space) rg_real23.12 Å
Rg uncertainty (real space) rg_real_error0.57 Å
I(0) (real space) i0_real2.3910e+07
I(0) uncertainty (real space) i0_real_error3.3090e+05
Rg (reciprocal space) rg_reciprocal23.12 Å
I(0) (reciprocal space) i0_reciprocal23910000.0000
Solution quality estimate total_estimate0.8867
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.7 Å
Skewness Skewness skewness0.370
Kurtosis Kurtosis kurtosis-0.437
Angular range angular_range— – 0.3450 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4000000.0000
Real-space data points n_real_points66
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.858; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.961; Smooth: 0.990
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1usga_
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 (2 domains)

Domain ID domain_id1usgA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
Domain ID domain_id1usgA02
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)