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- PDB-2lbp: STRUCTURE OF THE L-LEUCINE-BINDING PROTEIN REFINED AT 2.4 ANGSTRO... -

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Basic information

Entry
Database: PDB / ID: 2lbp
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
ComponentsLEUCINE-BINDING PROTEIN
KeywordsPERIPLASMIC BINDING PROTEIN
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
Leucine-specific-binding protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsSack, J.S. / Trakhanov, S.D. / Tsigannik, I.H. / Quiocho, F.A.
Citation
Journal: J.Mol.Biol. / Year: 1989
Title: Structure of the L-leucine-binding protein refined at 2.4 A resolution and comparison with the Leu/Ile/Val-binding protein structure.
Authors: Sack, J.S. / Trakhanov, S.D. / Tsigannik, I.H. / Quiocho, F.A.
#1: Journal: J.Mol.Biol. / Year: 1989
Title: Periplasmic Binding Protein Structure and Function. Refined X-Ray Structures of the Leucine(Slash)Isoleucine(Slash)Valine-Binding Protein and its Complex with Leucine
Authors: Sack, J.S. / Saper, M.A. / Quiocho, F.A.
History
DepositionApr 10, 1989Processing site: BNL
Revision 1.0Jul 12, 1989Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LEUCINE-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)37,0071
Polymers37,0071
Non-polymers00
Water1,63991
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.800, 69.340, 74.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein LEUCINE-BINDING PROTEIN


Mass: 37006.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain (production host): K12 / References: UniProt: P04816
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.6 %
Crystal grow
*PLUS
pH: 4.3 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 %(v/v)MPD11
220 mMsodium acetate11

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Data collection

Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 20 Å / Num. obs: 13797 / % possible obs: 95.6 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.1057

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.4→10 Å /
RfactorNum. reflection
obs0.213 13797
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2600 0 0 91 2691
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0190.02
X-RAY DIFFRACTIONp_angle_d0.0450.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0670.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.6621
X-RAY DIFFRACTIONp_mcangle_it1.1521.5
X-RAY DIFFRACTIONp_scbond_it1.2031.5
X-RAY DIFFRACTIONp_scangle_it1.8962
X-RAY DIFFRACTIONp_plane_restr0.0140.02
X-RAY DIFFRACTIONp_chiral_restr0.2350.15
X-RAY DIFFRACTIONp_singtor_nbd0.230.5
X-RAY DIFFRACTIONp_multtor_nbd0.3260.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2890.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor9.23
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 10 Å / Num. reflection obs: 13797 / Rfactor obs: 0.213
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: p_mcbond_it / Dev ideal: 0.662

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