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- PDB-2liv: PERIPLASMIC BINDING PROTEIN STRUCTURE AND FUNCTION. REFINED X-RAY... -

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Entry
Database: PDB / ID: 2liv
TitlePERIPLASMIC BINDING PROTEIN STRUCTURE AND FUNCTION. REFINED X-RAY STRUCTURES OF THE LEUCINE/ISOLEUCINE/VALINE-BINDING PROTEIN AND ITS COMPLEX WITH LEUCINE
ComponentsLEUCINE
KeywordsPERIPLASMIC BINDING PROTEIN
Function / homology
Function and homology information


branched-chain amino acid transport / isoleucine transport / valine transport / L-leucine transport / amino acid transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / outer membrane-bounded periplasmic space / 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
Leu/Ile/Val-binding protein / Leu/Ile/Val-binding protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsSack, J.S. / Saper, M.A. / Quiocho, F.A.
Citation
Journal: J.Mol.Biol. / Year: 1989
Title: Periplasmic binding protein structure and function. Refined X-ray structures of the leucine/isoleucine/valine-binding protein and its complex with leucine.
Authors: Sack, J.S. / Saper, M.A. / Quiocho, F.A.
#1: Journal: J.Mol.Biol. / Year: 1989
Title: 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
Authors: Sack, J.S. / Trakhanov, S.D. / Tsigannik, I.H. / Quiocho, F.A.
#2: Journal: J.Biol.Chem. / Year: 1983
Title: Leucine, Isoleucine, Valine-Binding Protein from Escherichia Coli
Authors: Saper, M.A. / Quiocho, F.A.
History
DepositionApr 10, 1989Processing site: BNL
Revision 1.0Jul 12, 1989Provider: repository / Type: Initial release
Revision 1.1Mar 3, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
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


Theoretical massNumber of molelcules
Total (without water)36,7841
Polymers36,7841
Non-polymers00
Water2,180121
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.880, 70.990, 115.630
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


Mass: 36784.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P02917, UniProt: P0AD96*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.22 Å3/Da / Density % sol: 44.69 %
Crystal grow
*PLUS
pH: 7.6 / Method: other
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
250 mM1dropNaCl
30.02 %1dropNaN3
410 mMsodium citrate1drop
510 mMTris-HCl1drop
620 %PEG60001drop
718 %PEG60001reservoir
80.02 %1reservoirNaN3
910 mMsodium citrate1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.4 Å / Num. obs: 12004 / Num. measured all: 41179 / Rmerge(I) obs: 0.021

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.4→10 Å /
RfactorNum. reflection
obs0.179 11817
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2589 0 0 121 2710
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.02
X-RAY DIFFRACTIONp_angle_d0.0460.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0630.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.7641
X-RAY DIFFRACTIONp_mcangle_it1.2951.5
X-RAY DIFFRACTIONp_scbond_it1.3471.5
X-RAY DIFFRACTIONp_scangle_it2.1112
X-RAY DIFFRACTIONp_plane_restr0.0160.02
X-RAY DIFFRACTIONp_chiral_restr0.2120.15
X-RAY DIFFRACTIONp_singtor_nbd0.2160.5
X-RAY DIFFRACTIONp_multtor_nbd0.3190.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2590.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor4.93
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 all: 11817 / Rfactor all: 0.179
Solvent computation
*PLUS
Displacement parameters
*PLUS

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