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- PDB-8f23: The crystal structure of a rationally designed zinc sensor based ... -

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Basic information

Entry
Database: PDB / ID: 8f23
TitleThe crystal structure of a rationally designed zinc sensor based on maltose binding protein - Apo conformation
ComponentsZinc Sensor protein
KeywordsMETAL BINDING PROTEIN / zinc / sensing / Xe NMR
Function / homology
Function and homology information


carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / outer membrane-bounded periplasmic space
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
Similarity search - Domain/homology
Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsZhao, Z. / Zhou, M. / Zemerov, S.d. / Marmorstein, R. / Dmochowski, I.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R35GM131907-02 United States
CitationJournal: Chem Sci / Year: 2023
Title: Rational design of a genetically encoded NMR zinc sensor.
Authors: Zhao, Z. / Zhou, M. / Zemerov, S.D. / Marmorstein, R. / Dmochowski, I.J.
History
DepositionNov 6, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._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_author.identifier_ORCID / _citation_author.name
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Zinc Sensor protein


Theoretical massNumber of molelcules
Total (without water)40,2221
Polymers40,2221
Non-polymers00
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.050, 68.431, 57.676
Angle α, β, γ (deg.)90.000, 101.000, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Zinc Sensor protein / Maltose/maltodextrin-binding periplasmic protein / MMBP / Maltodextrin-binding protein / Maltose- ...Maltose/maltodextrin-binding periplasmic protein / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP


Mass: 40222.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: malE, Z5632, ECs5017 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AEY0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O

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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: 2.12 Å3/Da / Density % sol: 42.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2M sodium formate, pH 7.0, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.92→68.43 Å / Num. obs: 25254 / % possible obs: 98.1 % / Redundancy: 6.8 % / Biso Wilson estimate: 42.9 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.041 / Rrim(I) all: 0.108 / Net I/σ(I): 10.4
Reflection shellResolution: 1.92→1.97 Å / Redundancy: 5.9 % / Num. unique obs: 1328 / CC1/2: 0.497 / % possible all: 77.3

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1omp

1omp


Resolution: 1.93→56.62 Å / SU ML: 0.2993 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.1192
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.229 1997 8.06 %
Rwork0.1886 22767 -
obs0.192 24764 98.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.49 Å2
Refinement stepCycle: LAST / Resolution: 1.93→56.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2832 0 0 72 2904
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092917
X-RAY DIFFRACTIONf_angle_d1.06983964
X-RAY DIFFRACTIONf_chiral_restr0.0661430
X-RAY DIFFRACTIONf_plane_restr0.0077517
X-RAY DIFFRACTIONf_dihedral_angle_d15.99341067
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.980.43461280.38881462X-RAY DIFFRACTION89.28
1.98-2.040.32421430.31521618X-RAY DIFFRACTION98.6
2.04-2.10.34571390.29861609X-RAY DIFFRACTION97.98
2.1-2.160.32541430.2531610X-RAY DIFFRACTION98.82
2.16-2.240.27631430.24831637X-RAY DIFFRACTION98.89
2.24-2.330.32761440.24371636X-RAY DIFFRACTION98.83
2.33-2.440.3011440.22851646X-RAY DIFFRACTION99.33
2.44-2.570.28291440.22321636X-RAY DIFFRACTION99.44
2.57-2.730.27291450.19961650X-RAY DIFFRACTION99.56
2.73-2.940.28851430.20321640X-RAY DIFFRACTION99.55
2.94-3.230.21951440.19331641X-RAY DIFFRACTION99.44
3.23-3.70.21991450.17661650X-RAY DIFFRACTION99.01
3.7-4.660.18631440.14521655X-RAY DIFFRACTION99.5
4.66-56.620.18541480.171677X-RAY DIFFRACTION98.17

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