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- PDB-7mq7: Tetragonal Maltose Binding Protein -

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Basic information

Entry
Database: PDB / ID: 7mq7
TitleTetragonal Maltose Binding Protein
ComponentsMaltodextrin-binding protein
KeywordsSUGAR BINDING PROTEIN / Maltose Binding Protein
Function / homologybeta-maltose / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsThaker, A. / Sirajudeen, L. / Simmons, C.R. / Nannenga, B.L.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Defense (DOD, United States) United States
CitationJournal: Biotechnol.Bioeng. / Year: 2021
Title: Structure-guided identification of a peptide for bio-enabled gold nanoparticle synthesis.
Authors: Thaker, A. / Sirajudeen, L. / Simmons, C.R. / Nannenga, B.L.
History
DepositionMay 5, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 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: Maltodextrin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7867
Polymers41,0851
Non-polymers7016
Water6,521362
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-35 kcal/mol
Surface area15540 Å2
Unit cell
Length a, b, c (Å)69.070, 69.070, 211.803
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Maltodextrin-binding protein


Mass: 41084.586 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: malE, GF950_09430 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A778V697
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2122h-1a_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / Source method: isolated from a natural source / Formula: H2O
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: 3.07 Å3/Da / Density % sol: 59.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 2.4 M ammonium sulfate, 0.1 M sodium acetate pH 4.5

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.08724 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08724 Å / Relative weight: 1
ReflectionResolution: 1.95→32.001 Å / Num. obs: 35971 / % possible obs: 95 % / Redundancy: 8.3 % / Biso Wilson estimate: 29.08 Å2 / CC1/2: 0.992 / Net I/σ(I): 16
Reflection shellResolution: 1.95→2.01 Å / Num. unique obs: 3070 / CC1/2: 0.948

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1anf

1anf


Resolution: 1.95→32.001 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2347 1690 4.7 %
Rwork0.1951 34281 -
obs0.197 35971 93.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.36 Å2 / Biso mean: 40.7854 Å2 / Biso min: 26.28 Å2
Refinement stepCycle: final / Resolution: 1.95→32.001 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2891 0 40 362 3293
Biso mean--64.85 49.12 -
Num. residues----373
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.95-2.00740.28951470.2559292398
2.0074-2.07220.29921450.2418294198
2.0722-2.14620.2321420.213298099
2.1462-2.23210.23721480.1946297599
2.2321-2.33370.26851460.196296799
2.3337-2.45670.24561490.1881300099
2.4567-2.61050.25381460.1932296599
2.6105-2.8120.25421500.1936301999
2.812-3.09470.26771490.2003302299
3.0947-3.54210.20161410.1899286293
3.5421-4.46070.20721140.1723231474
4.4607-32.0010.21661130.197231370
Refinement TLS params.Method: refined / Origin x: 22.6173 Å / Origin y: 63.1743 Å / Origin z: 0.4661 Å
111213212223313233
T0.3216 Å2-0.0583 Å20.011 Å2-0.3252 Å2-0.021 Å2--0.3307 Å2
L0.249 °2-0.2415 °2-0.0763 °2-0.5502 °20.3885 °2--1.1451 °2
S0.013 Å °-0.032 Å °0.0193 Å °-0.0158 Å °-0.0268 Å °0.0048 Å °0.135 Å °-0.0357 Å °-0.0001 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 373
2X-RAY DIFFRACTION1allA374 - 375
3X-RAY DIFFRACTION1allS1 - 417
4X-RAY DIFFRACTION1allB3 - 5
5X-RAY DIFFRACTION1allC1 - 2

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