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- PDB-4z7e: Soluble binding domain of Lmo1422 ABC-transporter -

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Basic information

Entry
Database: PDB / ID: 4z7e
TitleSoluble binding domain of Lmo1422 ABC-transporter
ComponentsLmo1422 protein
KeywordsTRANSPORT PROTEIN / ABC-transporter / SBD
Function / homology
Function and homology information


glycine betaine transport / SOS response / transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex
Similarity search - Function
Osmoprotection protein (prox); domain 2 / ABC-type glycine betaine transport system, substrate-binding domain / Substrate binding domain of ABC-type glycine betaine transport system / ABC transporter type 1, transmembrane domain MetI-like / MetI-like superfamily / Binding-protein-dependent transport system inner membrane component / ABC transporter integral membrane type-1 domain profile. / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / PROPANOIC ACID / Lmo1422 protein
Similarity search - Component
Biological speciesListeria monocytogenes EGD-e (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsRuiz, S.J. / Guskov, A. / Poolman, B.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
NWO Netherlands
CitationJournal: Crystals / Year: 2016
Title: Crystal Structure of the Substrate-Binding Domain from Listeria monocytogenes Bile-Resistance Determinant BilE
Authors: Ruiz, S.J. / Schuurman-Wolters, G.K. / Poolman, B.
History
DepositionApr 7, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2017Group: Source and taxonomy
Revision 1.2May 17, 2017Group: Database references
Revision 1.3Jan 10, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lmo1422 protein
B: Lmo1422 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,90110
Polymers66,9162
Non-polymers9858
Water8,467470
1
A: Lmo1422 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0256
Polymers33,4581
Non-polymers5675
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lmo1422 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8764
Polymers33,4581
Non-polymers4183
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.960, 62.870, 97.020
Angle α, β, γ (deg.)90.00, 91.71, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lmo1422 protein


Mass: 33457.949 Da / Num. of mol.: 2 / Fragment: UNP residues 231-504
Source method: isolated from a genetically manipulated source
Details: soluble binding domain of Lmo1422 transporter
Source: (gene. exp.) Listeria monocytogenes EGD-e (bacteria)
Gene: lmo1422 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8Y775
#2: Chemical
ChemComp-PPI / PROPANOIC ACID / Propionic acid


Mass: 74.079 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H6O2
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 470 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.25 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / Details: 25% PEG1500, 0.1 M PCTP / PH range: 4.25

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97734 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 14, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97734 Å / Relative weight: 1
ReflectionResolution: 1.5→48.5 Å / Num. obs: 166913 / % possible obs: 96 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.025 / Net I/σ(I): 13
Reflection shellResolution: 1.5→1.54 Å / Rmerge(I) obs: 0.8 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SW5

1sw5


Resolution: 1.5→48.488 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1982 8333 4.99 %Random
Rwork0.1527 ---
obs0.155 166898 95.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→48.488 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4298 0 66 470 4834
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014544
X-RAY DIFFRACTIONf_angle_d1.2426119
X-RAY DIFFRACTIONf_dihedral_angle_d16.0491773
X-RAY DIFFRACTIONf_chiral_restr0.071668
X-RAY DIFFRACTIONf_plane_restr0.006795
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.5170.32722800.30075303X-RAY DIFFRACTION97
1.517-1.53490.30452900.28825437X-RAY DIFFRACTION97
1.594-1.61580.26912750.23235278X-RAY DIFFRACTION97
1.8898-1.93380.21362740.15285313X-RAY DIFFRACTION96
3.6987-4.65940.14392680.1245184X-RAY DIFFRACTION94

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