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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

Method: X-RAY DIFFRACTION Dmax: 75.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

LEUCINE-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 No other associated polymer X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.40 Å

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 2LBP 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 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
1USK L-leucine-binding protein with leucine bound Deposited 2003-11-25 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 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 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 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
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 2lbp

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2lbp
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2lbp
Deposition date deposition_date1989-04-10
Structure title titleSTRUCTURE OF THE L-LEUCINE-BINDING PROTEIN REFINED AT 2.4 ANGSTROMS RESOLUTION AND COMPARISON WITH THE LEU(SLASH)ILE(SLASH)VAL-BINDING PROTEIN STRUCTURE
Keywords keywordsPERIPLASMIC BINDING PROTEIN; PERIPLASMIC BINDING 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_guinier22.86 Å
Radius of gyration Rg (electron density) rg_electron22.08 Å
Forward intensity I(0) i023792500.00
Molecular weight molecular_weight36959.0 kDa
Excluded volume excluded_volume46143 ų
Envelope volume envelope_volume54426 ų
Hydration-shell volume shell_volume21068 ų
Envelope diameter envelope_diameter79.2 Å
Shell Rg shell_rg28.26 Å
Envelope Rg envelope_rg22.09 Å
Shape Rg shape_rg22.05 Å
Total Rg total_rg22.94 Å
Total atoms total_atoms2600
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 dmax75.9 Å
Rg (real space) rg_real22.89 Å
Rg uncertainty (real space) rg_real_error0.45 Å
I(0) (real space) i0_real2.3790e+07
I(0) uncertainty (real space) i0_real_error3.3710e+05
Rg (reciprocal space) rg_reciprocal22.88 Å
I(0) (reciprocal space) i0_reciprocal23790000.0000
Solution quality estimate total_estimate0.8854
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.7 Å
Skewness Skewness skewness0.375
Kurtosis Kurtosis kurtosis-0.375
Angular range angular_range— – 0.3450 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha3952000.0000
Real-space data points n_real_points66
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.844; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.997
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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_idd2lbpa_
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_id2lbpA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
Domain ID domain_id2lbpA02
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 (2)

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9. Files and Curves (10)