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- PDB-8etb: the crystal structure of a rationally designed zinc sensor based ... -

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Basic information

Entry
Database: PDB / ID: 8etb
Titlethe crystal structure of a rationally designed zinc sensor based on maltose binding protein - Zn binding conformation
ComponentsZinc Sensor protein
KeywordsMETAL BINDING PROTEIN / zinc / sensing / Xe NMR
Function / homologyMaltose/Cyclodextrin ABC transporter, substrate-binding protein / carbohydrate transmembrane transporter activity / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / outer membrane-bounded periplasmic space / ACETATE ION / Maltose/maltodextrin-binding periplasmic protein
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 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
DepositionOct 16, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Zinc Sensor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3473
Polymers40,2221
Non-polymers1242
Water4,432246
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)43.834, 68.501, 57.923
Angle α, β, γ (deg.)90.000, 100.790, 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: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O
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: 2.12 Å3/Da / Density % sol: 42.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.2M MgCl2 , 0.1 M Bis-Tris, pH 6.5, 25% PEG 3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 1.28215 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28215 Å / Relative weight: 1
ReflectionResolution: 1.63→29.34 Å / Num. obs: 79582 / % possible obs: 96.6 % / Redundancy: 4 % / Biso Wilson estimate: 26.24 Å2 / Rmerge(I) obs: 0.06689 / Rpim(I) all: 0.03782 / Rrim(I) all: 0.07721 / Net I/σ(I): 9.49
Reflection shellResolution: 1.631→1.69 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.5248 / Mean I/σ(I) obs: 1.36 / Num. unique obs: 3782 / CC1/2: 0.855 / CC star: 0.96 / Rrim(I) all: 0.606 / % possible all: 90.8

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Processing

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

1omp


Resolution: 1.63→29.34 Å / SU ML: 0.2155 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.6212
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2341 3852 4.84 %
Rwork0.1977 75729 -
obs0.1993 79581 96.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.9 Å2
Refinement stepCycle: LAST / Resolution: 1.63→29.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2836 0 5 246 3087
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00372969
X-RAY DIFFRACTIONf_angle_d0.67084040
X-RAY DIFFRACTIONf_chiral_restr0.0481436
X-RAY DIFFRACTIONf_plane_restr0.0041530
X-RAY DIFFRACTIONf_dihedral_angle_d14.491088
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.650.3869870.32511754X-RAY DIFFRACTION64.06
1.65-1.670.37021420.36322658X-RAY DIFFRACTION94.85
1.67-1.690.33731430.34862690X-RAY DIFFRACTION95.48
1.69-1.720.3211340.32742614X-RAY DIFFRACTION95.45
1.72-1.740.34391420.31062766X-RAY DIFFRACTION96.32
1.74-1.770.3231370.3092691X-RAY DIFFRACTION96.49
1.77-1.80.36391400.29562756X-RAY DIFFRACTION97.18
1.8-1.820.33871380.2982763X-RAY DIFFRACTION98.64
1.82-1.860.25631360.26422691X-RAY DIFFRACTION97.65
1.86-1.890.2931370.24452756X-RAY DIFFRACTION98
1.89-1.930.32671410.24172764X-RAY DIFFRACTION98.08
1.93-1.970.2881360.22472718X-RAY DIFFRACTION97.94
1.97-2.010.25211400.22172767X-RAY DIFFRACTION98.81
2.01-2.060.25531400.22622767X-RAY DIFFRACTION98.54
2.06-2.110.22791400.23212759X-RAY DIFFRACTION98.07
2.11-2.160.24941390.21552710X-RAY DIFFRACTION98.68
2.16-2.230.25511410.2232827X-RAY DIFFRACTION99.3
2.23-2.30.2281370.20812749X-RAY DIFFRACTION98.7
2.3-2.380.25321420.2082771X-RAY DIFFRACTION98.85
2.38-2.480.24661370.20332783X-RAY DIFFRACTION98.65
2.48-2.590.26371400.21142760X-RAY DIFFRACTION98.87
2.59-2.730.2181410.20472779X-RAY DIFFRACTION98.52
2.73-2.90.22531420.21162769X-RAY DIFFRACTION98.25
2.9-3.120.25141420.19572707X-RAY DIFFRACTION97.2
3.12-3.430.24121350.18682665X-RAY DIFFRACTION95.4
3.43-3.930.17261410.15672722X-RAY DIFFRACTION97.55
3.93-4.950.17271410.14262810X-RAY DIFFRACTION99.8
4.95-29.340.22871410.16942763X-RAY DIFFRACTION99.01
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)
15.16967985774-1.087707109090.8897075409292.50027208764-0.1771200423583.1807816512-0.1334259669090.1345546114430.5609213429920.005512296390560.09324895098230.0656503314531-0.139974355043-0.109541811418-0.01490792940810.161526502233-0.0539013461957-0.01148117099060.2082778664150.02579045311060.24682498539431.89990996464.755858488790.0637876073675
22.351476961210.405812609733-0.5488019929961.37064946615-1.028199702126.937980579450.248316408099-0.4841281558240.0984733386330.333018543152-0.195141181533-0.0206450653356-0.07434560101590.559407263674-0.044991770910.297664702735-0.03218601577760.01951873779350.316663332745-0.01763266836560.21856803313848.3533851071-1.1642700924125.659130282
33.65067429823-0.3679423108081.602336311790.923777569593-0.6551123018664.57865133287-0.05448858545680.3406418238410.129674805957-0.06494633493220.031438846569-0.01511878445650.2908261521360.2643133781330.0196519016490.1786233166-0.012353124070.01310876978790.188437837283-0.008466117450330.18829876891843.9269441686-0.10804400864.7801846694
44.622133159340.3738383834673.300639811042.22459795219-0.06644949122672.513458715380.3720748660860.07873320708220.1472097228370.327276128807-0.1052756451380.2896575799590.755643584483-1.11137406095-0.330398782610.547435628276-0.1530239659620.1048754171040.6513247987730.00709744433330.34972878490232.2623458135-6.0142716272931.7542984774
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 105 )1 - 1051 - 105
22chain 'A' and (resid 106 through 245 )106 - 245106 - 245
33chain 'A' and (resid 246 through 333 )246 - 333246 - 333
44chain 'A' and (resid 334 through 366 )334 - 366334 - 366

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