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- PDB-8art: ABC transporter binding protein MalE from Streptomyces scabiei in... -

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Basic information

Entry
Database: PDB / ID: 8art
TitleABC transporter binding protein MalE from Streptomyces scabiei in complex with maltose
ComponentsPutative secreted maltose-binding protein
KeywordsPROTEIN BINDING / ABC Transporter / maltose binding protein
Function / homologySolute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / transmembrane transport / Prokaryotic membrane lipoprotein lipid attachment site profile. / Putative secreted maltose-binding protein
Function and homology information
Biological speciesStreptomyces scabiei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.17 Å
AuthorsJadot, C. / Kerff, F. / Rigali, S.
Funding support Belgium, 2items
OrganizationGrant numberCountry
Fonds de la Recherche Scientifique (FNRS)CDR/OL J.0158.21 Belgium
Fonds de la Recherche Scientifique (FNRS)PDR 40008487 Belgium
CitationJournal: To Be Published
Title: Structure of ligand binding protein of ABC transporter from Streptomyces scabiei at 3.17 Angstroms resolution.
Authors: Jadot, C. / Kerff, F. / Rigali, S.
History
DepositionAug 17, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative secreted maltose-binding protein
B: Putative secreted maltose-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,0544
Polymers91,3702
Non-polymers6852
Water00
1
A: Putative secreted maltose-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0272
Polymers45,6851
Non-polymers3421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative secreted maltose-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0272
Polymers45,6851
Non-polymers3421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.310, 68.310, 260.550
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Putative secreted maltose-binding protein


Mass: 45684.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces scabiei (bacteria) / Gene: malE, SCAB_66581 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C9ZHD5
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
Has ligand of interestY

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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 % sol: 37.12 %
Crystal growTemperature: 293 K / Method: evaporation
Details: 200mM ammonium acetate, 100mM sodium acetate pH 4.6 and 30% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.17→48.8932 Å / Num. obs: 12628 / % possible obs: 99.4 % / Redundancy: 19 % / CC1/2: 0.999 / Rmerge(I) obs: 0.175 / Net I/σ(I): 12.63
Reflection shellResolution: 3.17→3.36 Å / Rmerge(I) obs: 2.724 / Num. unique obs: 1917 / CC1/2: 0.379

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Alphafold model

Resolution: 3.17→48.89 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.893 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.615
RfactorNum. reflection% reflectionSelection details
Rfree0.284 631 5 %RANDOM
Rwork0.26 ---
obs0.262 12624 99.4 %-
Displacement parametersBiso max: 171.17 Å2 / Biso mean: 125.03 Å2 / Biso min: 31.98 Å2
Baniso -1Baniso -2Baniso -3
1-0.854 Å20 Å20 Å2
2--0.854 Å20 Å2
3----1.7079 Å2
Refine analyzeLuzzati coordinate error obs: 0.68 Å
Refinement stepCycle: final / Resolution: 3.17→48.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5947 0 86 0 6033
Biso mean--96.95 --
Num. residues----785
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2586SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1861HARMONIC5
X-RAY DIFFRACTIONt_it12016HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion829SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact12161SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d12016HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg21772HARMONIC20.79
X-RAY DIFFRACTIONt_omega_torsion2.17
X-RAY DIFFRACTIONt_other_torsion16.35
LS refinement shellResolution: 3.17→3.48 Å / Rfactor Rfree error: 0 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2242 145 5.01 %
Rwork0.2461 2749 -
all0.245 2894 -
obs--97.51 %

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