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- PDB-8dhd: Neutron crystal structure of maltotetraose bound tmMBP -

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Basic information

Entry
Database: PDB / ID: 8dhd
TitleNeutron crystal structure of maltotetraose bound tmMBP
Componentsmaltose-binding protein MalE2
KeywordsSUGAR BINDING PROTEIN / neutron / maltose binding protein / periplasmic binding protein
Function / homology
Function and homology information


carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / proteasome core complex, alpha-subunit complex / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ubiquitin-dependent protein catabolic process
Similarity search - Function
Bacterial extracellular solute-binding protein / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Proteasome alpha-subunit, N-terminal domain / Proteasome subunit A N-terminal signature Add an annotation / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
alpha-maltotetraose / Maltose ABC transporter, periplasmic maltose-binding protein
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsCuneo, M.J. / Shukla, S. / Myles, D.A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Rep / Year: 2022
Title: Mapping periplasmic binding protein oligosaccharide recognition with neutron crystallography.
Authors: Shukla, S. / Myles, D.A. / Cuneo, M.J.
History
DepositionJun 27, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2022Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: maltose-binding protein MalE2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7302
Polymers42,0631
Non-polymers6671
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.915, 56.340, 90.001
Angle α, β, γ (deg.)90.000, 94.250, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein maltose-binding protein MalE2


Mass: 42063.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_1839 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q9S5Y1
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotetraose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1a_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION1

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 25 % (wt./vol.) PEG 3350, 0.2 M sodium acetate, 0.1 M BisTris pH 5.5

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
12931N
22931N
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU MICROMAX-00711.5418
SPALLATION SOURCEORNL Spallation Neutron Source MANDI22.78-4.50
Detector
TypeIDDetectorDate
DECTRIS EIGER R 4M1PIXELJan 1, 2020
MAATEL IMAGINE2IMAGE PLATEJan 1, 2020
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2LAUELneutron2
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
22.781
34.51
Reflection

Entry-ID: 8DHD / CC1/2: 0.99

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Biso Wilson estimate (Å2)Rmerge(I) obsRpim(I) allRrim(I) allDiffraction-IDNet I/σ(I)
1.7-89.753960299.9919.918.650.1240.020.12151.66
2.1-35.711517273.13.50.1440.0780.16527.4
Reflection shell

CC1/2: 0.96

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allDiffraction-ID% possible all
1.7-1.760.3789.8539610.090.4199.9
2.1-2.210.316280.1680.3472

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
CrysalisProdata reduction
LAUENORMdata scaling
PHASERphasing
Refinement

Cross valid method: THROUGHOUT / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Stereochemistry target values: ML / Solvent model: FLAT BULK SOLVENT MODEL

Method to determine structureStarting modelResolution (Å)Refine-IDBiso max (Å2)Biso mean (Å2)Biso min (Å2)Rfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection RworkNum. reflection obs% reflection Rfree (%)% reflection obs (%)SU MLσ(F)Phase error
MOLECULAR REPLACEMENT6DTS

6dts

1.7-22.142X-RAY DIFFRACTION111.1529.036210.040.17510.14140.1431193237632395644.8899.980.131.3917.26
2.106-35.816NEUTRON DIFFRACTION0.27240.24470.2461730151454.8272.370
Refinement stepCycle: final / Resolution: 1.7→22.142 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2913 0 100 483 3496
Biso mean--19.32 45.52 -
Num. residues----378
LS refinement shell

Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.106-2.26830.3662960.31942138NEUTRON DIFFRACTION54
2.2683-2.49650.29291470.28722414NEUTRON DIFFRACTION62
2.4965-2.85760.26941270.26442781NEUTRON DIFFRACTION70
2.8576-3.59970.25211570.23123360NEUTRON DIFFRACTION84
3.5997-35.8160.24932030.20243722NEUTRON DIFFRACTION92
1.7-1.74250.22921280.18022671X-RAY DIFFRACTION100
1.7425-1.78960.21251240.1682701X-RAY DIFFRACTION100
1.7896-1.84220.21111430.16172651X-RAY DIFFRACTION100
1.8422-1.90170.19811390.16312697X-RAY DIFFRACTION100
1.9017-1.96960.181470.16022656X-RAY DIFFRACTION100
1.9696-2.04840.19591510.15052634X-RAY DIFFRACTION100
2.0484-2.14150.17211560.15392685X-RAY DIFFRACTION100
2.1415-2.25440.19731260.14572701X-RAY DIFFRACTION100
2.2544-2.39540.17921470.14532681X-RAY DIFFRACTION100
2.3954-2.58010.1971430.15072667X-RAY DIFFRACTION100
2.5801-2.83930.17441140.15412707X-RAY DIFFRACTION100
2.8393-3.24910.1751270.15542717X-RAY DIFFRACTION100
3.2491-4.08920.15961340.12532719X-RAY DIFFRACTION100
4.0892-22.1420.14631530.1122745X-RAY DIFFRACTION100

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