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- PDB-7mq6: Tetragonal Maltose Binding Protein in the presence of gold -

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Basic information

Entry
Database: PDB / ID: 7mq6
TitleTetragonal Maltose Binding Protein in the presence of gold
ComponentsMaltodextrin-binding protein
KeywordsSUGAR BINDING PROTEIN / Maltose Binding Protein / gold
Function / homologybeta-maltose / : / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.372 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

Downloads & links

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Assembly

Deposited unit
A: Maltodextrin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,29215
Polymers41,0851
Non-polymers1,20714
Water81145
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-89 kcal/mol
Surface area15040 Å2
Unit cell
Length a, b, c (Å)68.327, 68.327, 210.382
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein / Sugars , 2 types, 2 molecules A

#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

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Non-polymers , 4 types, 58 molecules

#3: Chemical ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Au / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O

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Details

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 Matthews: 2.99 Å3/Da / Density % sol: 58.84 %
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: 0.92017 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: 0.92017 Å / Relative weight: 1
ReflectionResolution: 2.37→50 Å / Num. obs: 20852 / % possible obs: 98.82 % / Redundancy: 5.2 % / CC1/2: 0.99 / Net I/σ(I): 15.8
Reflection shellResolution: 2.37→2.45 Å / Num. unique obs: 2772 / CC1/2: 0.972

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1anf

1anf


Resolution: 2.372→35.581 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2487 997 4.78 %
Rwork0.2104 19855 -
obs0.2122 20852 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 133.97 Å2 / Biso mean: 63.8389 Å2 / Biso min: 43.06 Å2
Refinement stepCycle: final / Resolution: 2.372→35.581 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2829 0 52 45 2926
Biso mean--77.8 61.97 -
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 (%)
2.372-2.49670.30771340.25582772100
2.4967-2.65310.31751300.26612821100
2.6531-2.85790.2771420.26422837100
2.8579-3.14530.33741600.28082789100
3.1453-3.60010.26771320.238286299
3.6001-4.53430.21051430.1857277296
4.5343-35.5810.22381560.174300297
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2926-0.4472-0.03141.7023-0.01073.39-0.11890.0536-0.12260.16520.03540.31340.1475-0.49850.10170.6568-0.18660.06020.67990.01760.654812.268263.940616.8915
20.1089-0.44180.20733.4938-0.72910.3799-0.1530.17280.2351-0.01340.27620.2788-0.0489-0.2778-0.09440.5592-0.12050.03930.66140.02920.665714.370673.62447.8722
30.5917-0.7014-0.27160.79951.09362.98380.073-0.18510.04660.0806-0.0028-0.18450.02960.4058-0.06750.5039-0.1848-0.00040.53350.05170.511426.855359.0338-1.5368
41.4083-2.2143-0.24595.78212.56426.2413-0.0842-0.02090.0702-0.18440.386-1.0631-0.66311.8125-0.20490.725-0.33890.03620.7851-0.07090.649629.675375.7315-11.8866
51.1121-0.95860.00831.0739-1.13694.05750.165-0.0511-0.19290.20990.12650.41410.5369-0.2017-0.27230.6447-0.1374-0.03320.4936-0.02880.596320.622249.518-7.852
60.9371-0.3133-0.56841.76070.78272.6322-0.09340.0262-0.15270.22760.01830.02410.13060.09010.07560.3981-0.1373-0.01480.506-0.00650.437126.926662.123610.6758
70.39710.86160.60574.4825-0.77322.6837-0.02220.08620.1420.12250.05240.0253-0.15790.5232-0.0560.4867-0.12370.06460.6166-0.03040.552324.268964.7154-5.7318
82.10370.7617-2.59895.42361.25224.7977-0.06590.0308-0.0803-0.29030.03610.62450.2218-0.2333-0.06220.5493-0.0733-0.04760.59560.00510.618416.518371.6412-19.3133
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 47 )A1 - 47
2X-RAY DIFFRACTION2chain 'A' and (resid 48 through 74 )A48 - 74
3X-RAY DIFFRACTION3chain 'A' and (resid 75 through 164 )A75 - 164
4X-RAY DIFFRACTION4chain 'A' and (resid 165 through 186 )A165 - 186
5X-RAY DIFFRACTION5chain 'A' and (resid 187 through 246 )A187 - 246
6X-RAY DIFFRACTION6chain 'A' and (resid 247 through 315 )A247 - 315
7X-RAY DIFFRACTION7chain 'A' and (resid 316 through 353 )A316 - 353
8X-RAY DIFFRACTION8chain 'A' and (resid 354 through 373 )A354 - 373

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