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- PDB-8r3e: Huntingtin, 1-17, MBP-N -

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Basic information

Entry
Database: PDB / ID: 8r3e
TitleHuntingtin, 1-17, MBP-N
ComponentsMaltodextrin-binding protein
KeywordsUNKNOWN FUNCTION / HUNTINGTIN / N17 / MALTOSE-BINDING PROTEIN FUSION
Function / homology
Function and homology information


cell envelope / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / periplasmic space / metal ion binding
Similarity search - Function
Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain
Similarity search - Domain/homology
Maltodextrin-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å
AuthorsSteinbacher, S. / Toledo-Sherman, L. / Dominguez, C.
Funding support United States, 1items
OrganizationGrant numberCountry
CHDI Foundation United States
CitationJournal: To Be Published
Title: Post-translational modifications in the first 17 amino acids of huntingtin influence self-association and interaction with membranes
Authors: Gallo, M. / Ingenito, R. / Finotto, M. / Di Marino, S. / Cicero, D.O. / Bianchi, E. / Steinbacher, S. / Neudegger, T. / Blaesse, M. / Toledo-Sherman, L. / Lee, M.R. / Dominguez, C. / ...Authors: Gallo, M. / Ingenito, R. / Finotto, M. / Di Marino, S. / Cicero, D.O. / Bianchi, E. / Steinbacher, S. / Neudegger, T. / Blaesse, M. / Toledo-Sherman, L. / Lee, M.R. / Dominguez, C. / Monteagudo, E. / Doherty, E.M.
History
DepositionNov 8, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltodextrin-binding protein
B: Maltodextrin-binding protein
C: Maltodextrin-binding protein
D: Maltodextrin-binding protein
E: Maltodextrin-binding protein
F: Maltodextrin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)262,2337
Polymers262,1676
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Monomer in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13040 Å2
ΔGint-135 kcal/mol
Surface area95660 Å2
Unit cell
Length a, b, c (Å)96.043, 96.113, 97.673
Angle α, β, γ (deg.)76.40, 80.72, 63.19
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
77
88
99
1010
1111
1212
1313
1414
1515

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Maltodextrin-binding protein


Mass: 43694.570 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: malE, JW3994 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4P1LXE0
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN

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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: 2.98 Å3/Da / Density % sol: 58.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20% (w/v) PEG 6K, 0.24 M Na2 malonate, 10mM ZnCl2 and 0.1 M MES-NaOH, pH6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.91→45.79 Å / Num. obs: 31781 / % possible obs: 71.1 % / Redundancy: 2 % / CC1/2: 0.987 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.087 / Net I/σ(I): 6.5
Reflection shellResolution: 2.91→3.13 Å / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1590 / CC1/2: 0.385 / Rpim(I) all: 0.469

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Processing

Software
NameVersionClassification
autoPROCdata reduction
XDS(VERSION Jan 31data reduction
autoPROC(Version 1.1.7)data scaling
Aimlessdata scaling
REFMAC5.8.0267refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.91→45.79 Å / Cor.coef. Fo:Fc: 0.848 / Cor.coef. Fo:Fc free: 0.751 / SU B: 37.492 / Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32916 1602 5 %RANDOM
Rwork0.25201 ---
obs0.25592 30179 48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.156 Å2
Baniso -1Baniso -2Baniso -3
1--1.34 Å20.73 Å2-0.63 Å2
2---1.35 Å2-1.02 Å2
3---3.26 Å2
Refinement stepCycle: LAST / Resolution: 2.91→45.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18254 0 1 0 18255
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01318687
X-RAY DIFFRACTIONr_bond_other_d0.0020.01717782
X-RAY DIFFRACTIONr_angle_refined_deg1.5741.6425353
X-RAY DIFFRACTIONr_angle_other_deg1.0971.58341139
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.24152357
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.03625.389835
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.278153140
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4771530
X-RAY DIFFRACTIONr_chiral_restr0.0640.22429
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0221288
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024000
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8384.9899446
X-RAY DIFFRACTIONr_mcbond_other2.8384.9899445
X-RAY DIFFRACTIONr_mcangle_it4.8687.47611797
X-RAY DIFFRACTIONr_mcangle_other4.8687.47611798
X-RAY DIFFRACTIONr_scbond_it2.1425.1069241
X-RAY DIFFRACTIONr_scbond_other2.1425.1069242
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8637.5913557
X-RAY DIFFRACTIONr_long_range_B_refined7.47457.8720287
X-RAY DIFFRACTIONr_long_range_B_other7.47357.87220288
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A45140.05
12B45140.05
21A44920.05
22C44920.05
31A46070.05
32D46070.05
41A45280.05
42E45280.05
51A44600.05
52F44600.05
61B44990.05
62C44990.05
71B44970.05
72D44970.05
81B46060.04
82E46060.04
91B44980.05
92F44980.05
101C45310.05
102D45310.05
111C45160.05
112E45160.05
121C45630.05
122F45630.05
131D45180.05
132E45180.05
141D44580.06
142F44580.06
151E44730.05
152F44730.05
LS refinement shellResolution: 2.912→2.987 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 17 -
Rwork0.389 371 -
obs--7.9 %

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