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- PDB-1z15: Crystal structure analysis of periplasmic Leu/Ile/Val-binding pro... -

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Basic information

Entry
Database: PDB / ID: 1z15
TitleCrystal structure analysis of periplasmic Leu/Ile/Val-binding protein in superopen form
ComponentsLeu/Ile/Val-binding protein
KeywordsTRANSPORT PROTEIN / periplasmic binding proteins / alpha-beta fold / aliphatic amino acid 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 / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsTrakhanov, S.D. / Vyas, N.K. / Kristensen, D.M. / Ma, J. / Quiocho, F.A.
Citation
Journal: Biochemistry / Year: 2005
Title: Ligand-free and -bound structures of the binding protein (LivJ) of the Escherichia coli ABC leucine/isoleucine/valine transport system: trajectory and dynamics of the interdomain rotation and ligand specificity.
Authors: Trakhanov, S.D. / Vyas, N.K. / Luecke, H. / Kristensen, D.M. / Ma, J. / Quiocho, F.A.
#1: 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.
#2: 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.
History
DepositionMar 3, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999 SEQUENCE This sequence occurs with n-terminal leader sequence, which is modified post translation ... SEQUENCE This sequence occurs with n-terminal leader sequence, which is modified post translation to produce a mature protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Leu/Ile/Val-binding protein


Theoretical massNumber of molelcules
Total (without water)36,8121
Polymers36,8121
Non-polymers00
Water4,035224
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.210, 65.290, 109.610
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 Leu/Ile/Val-binding protein / LIV-BP


Mass: 36812.395 Da / Num. of mol.: 1 / Fragment: matured protein (residues 24-367) / Source method: isolated from a natural source / Details: Periplasmic / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P02917, UniProt: P0AD96*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 293 K / Method: microdialysis / pH: 7.3
Details: 12.5% PEG 6000, potassium chloride, sodium choloride, sodium azide, potassium acetate, sodium citrate, pH 7.3, MICRODIALYSIS, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: SDMS / Detector: AREA DETECTOR / Date: Jan 10, 1990
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 44773 / Num. obs: 44773 / % possible obs: 96 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 9.8
Reflection shellResolution: 1.7→1.75 Å / Redundancy: 4 % / Rmerge(I) obs: 0.277 / Mean I/σ(I) obs: 1.9 / Num. unique all: 4655 / Rsym value: 0.277 / % possible all: 89

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Processing

Software
NameVersionClassification
CNS1.1refinement
SDMSdata reduction
SDMSdata scaling
MERLOTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2LIV

2liv


Resolution: 1.7→6 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2081291.91 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.237 4319 10.1 %RANDOM
Rwork0.185 ---
all-42957 --
obs-42957 95.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 111.766 Å2 / ksol: 0.41215 e/Å3
Displacement parametersBiso mean: 26.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.48 Å20 Å20 Å2
2--2.35 Å20 Å2
3----3.83 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 1.7→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2591 0 0 224 2815
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_improper_angle_d1.46
X-RAY DIFFRACTIONc_mcbond_it1.611.5
X-RAY DIFFRACTIONc_mcangle_it2.32
X-RAY DIFFRACTIONc_scbond_it2.912
X-RAY DIFFRACTIONc_scangle_it4.312.5
LS refinement shellResolution: 1.7→1.8 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.338 662 10.1 %
Rwork0.312 5861 -
obs-4177 88.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMION.TOP

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