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- PDB-9clc: Crystal structure of maltose binding protein (Apo), mutant Trp10 ... -

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Basic information

Entry
Database: PDB / ID: 9clc
TitleCrystal structure of maltose binding protein (Apo), mutant Trp10 to 4-Cyanotryptophan
ComponentsMaltose/maltodextrin-binding periplasmic protein
KeywordsSUGAR BINDING PROTEIN / solute binding protein / non-canonical amino acid incorporation
Function / homology
Function and homology information


detection of maltose stimulus / maltose transport complex / carbohydrate transport / maltose binding / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose transport complex / carbohydrate transport / maltose binding / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / membrane
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
: / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsHabel, E. / Frkic, R.L. / Jackson, C.J. / Huber, T. / Otting, G.
Funding support Australia, 3items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP230100079 Australia
Australian Research Council (ARC)DP210100088 Australia
Australian Research Council (ARC)CE200100012 Australia
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2024
Title: Rendering Proteins Fluorescent Inconspicuously: Genetically Encoded 4-Cyanotryptophan Conserves Their Structure and Enables the Detection of Ligand Binding Sites.
Authors: Qianzhu, H. / Abdelkader, E. / Welegedara, A. / Habel, E. / Paul, N. / Frkic, R. / Jackson, C. / Huber, T. / Otting, G.
History
DepositionJul 10, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maltose/maltodextrin-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,80726
Polymers41,0751
Non-polymers1,73325
Water5,368298
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.914, 64.655, 57.732
Angle α, β, γ (deg.)90.00, 101.42, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 41074.535 Da / Num. of mol.: 1 / Mutation: T356A
Source method: isolated from a genetically manipulated source
Details: Expressed with genetic incorporation of non canonical amino acid
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: malE, b4034, JW3994 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9

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Non-polymers , 6 types, 323 molecules

#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cd
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 1.96 Å3/Da / Density % sol: 37.15 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 30% v/v PEG400, 100 mM sodium acetate (pH 4.6), 100 mM cadmium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 16, 2024
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.48→42.56 Å / Num. obs: 50774 / % possible obs: 96.4 % / Redundancy: 4 % / CC1/2: 0.995 / Net I/σ(I): 10
Reflection shellResolution: 1.48→1.51 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2463 / CC1/2: 0.464 / % possible all: 94.5

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_5058: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→42.56 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1652 2529 4.98 %
Rwork0.1527 --
obs0.1533 50774 96.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.48→42.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2866 0 91 298 3255
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_d0.995
X-RAY DIFFRACTIONf_dihedral_angle_d13.9361156
X-RAY DIFFRACTIONf_chiral_restr0.073447
X-RAY DIFFRACTIONf_plane_restr0.007540
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.510.29621360.26362617X-RAY DIFFRACTION94
1.51-1.540.21771350.22712605X-RAY DIFFRACTION95
1.54-1.570.23531510.19382660X-RAY DIFFRACTION95
1.57-1.610.19261240.1772629X-RAY DIFFRACTION95
1.61-1.650.19581510.17272613X-RAY DIFFRACTION95
1.65-1.690.19161570.15942628X-RAY DIFFRACTION95
1.69-1.740.17111280.15452674X-RAY DIFFRACTION96
1.74-1.80.1471320.13942658X-RAY DIFFRACTION96
1.8-1.860.16421470.14482663X-RAY DIFFRACTION96
1.86-1.940.18711470.14132653X-RAY DIFFRACTION96
1.94-2.030.1551570.13872659X-RAY DIFFRACTION96
2.03-2.130.1421510.13852685X-RAY DIFFRACTION96
2.13-2.270.171330.13522681X-RAY DIFFRACTION97
2.27-2.440.14341370.1332751X-RAY DIFFRACTION98
2.44-2.690.15831460.14142714X-RAY DIFFRACTION98
2.69-3.080.17521290.14922775X-RAY DIFFRACTION98
3.08-3.880.16131410.14572743X-RAY DIFFRACTION98
3.88-42.560.14991270.16732837X-RAY DIFFRACTION98

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