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- PDB-3osq: Maltose-bound maltose sensor engineered by insertion of circularl... -

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Basic information

Entry
Database: PDB / ID: 3osq
TitleMaltose-bound maltose sensor engineered by insertion of circularly permuted green fluorescent protein into E. coli maltose binding protein at position 175
ComponentsMaltose-binding periplasmic protein,Green fluorescent protein
KeywordsFLUORESCENT PROTEIN / Transport Protein / Engineered Protein / Sensor Protein / MBP / GFP / Maltose Sensor
Function / homology
Function and homology information


carbohydrate transmembrane transporter activity / bioluminescence / generation of precursor metabolites and energy / outer membrane-bounded periplasmic space
Similarity search - Function
Green Fluorescent Protein / Green fluorescent protein / 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 / Green fluorescent protein, GFP / Bacterial extracellular solute-binding protein / Green fluorescent protein-related / Green fluorescent protein ...Green Fluorescent Protein / Green fluorescent protein / 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 / Green fluorescent protein, GFP / Bacterial extracellular solute-binding protein / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / Maltose/maltodextrin-binding periplasmic protein / Green fluorescent protein
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
Aequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsEchevarria, I.M. / Marvin, J.S. / Looger, L.L. / Schreiter, E.R.
CitationJournal: Proteins / Year: 2011
Title: A genetically encoded, high-signal-to-noise maltose sensor.
Authors: Marvin, J.S. / Schreiter, E.R. / Echevarria, I.M. / Looger, L.L.
History
DepositionSep 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2013Group: Database references
Revision 1.2Jun 21, 2017Group: Advisory / Database references ...Advisory / Database references / Source and taxonomy / Structure summary
Category: database_PDB_caveat / entity ...database_PDB_caveat / entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_name_com.name ..._entity.pdbx_description / _entity_name_com.name / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Dec 6, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0Jul 10, 2024Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity / struct_conn
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight / _struct_conn.pdbx_leaving_atom_flag
Revision 3.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltose-binding periplasmic protein,Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,2394
Polymers73,7051
Non-polymers5343
Water5,296294
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.262, 88.686, 119.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Maltose-binding periplasmic protein,Green fluorescent protein / MBP / MMBP / Maltodextrin-binding protein


Mass: 73705.000 Da / Num. of mol.: 1
Fragment: GFP P42212 residues 2-146, 147-238, MBP P0AEX9 residues 27-199, 201-396
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria), (gene. exp.) Aequorea victoria (jellyfish)
Gene: malE, Z5632, ECs5017, GFP / Plasmid: pRSET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AEY0, UniProt: P42212
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


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


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H2O
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: 2.92 Å3/Da / Density % sol: 57.84 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.5 M Ammonium sulfate, 0.1M Sodium citrate tribasic dihydrate pH 5.6, 1.0 M Lithium sulfate monohydrate, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 21, 2010
RadiationMonochromator: Diamond (111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.9→31.41 Å / Num. obs: 68612 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.1 % / Biso Wilson estimate: 26.6 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 14.4
Reflection shellResolution: 1.9→2 Å / % possible all: 100

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Processing

Software
NameVersionClassification
specdata collection
PHASERphasing
REFMAC5.5.0088refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 3EK4, 1ANF

3ek4

1anf


Resolution: 1.9→29.06 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.044 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.108 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19921 3486 5.1 %RANDOM
Rwork0.16489 ---
obs0.16663 65035 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.188 Å2
Baniso -1Baniso -2Baniso -3
1--0.88 Å20 Å2-0 Å2
2--0.91 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4783 0 33 294 5110
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0224953
X-RAY DIFFRACTIONr_bond_other_d0.0010.023326
X-RAY DIFFRACTIONr_angle_refined_deg2.0191.9736719
X-RAY DIFFRACTIONr_angle_other_deg1.25838168
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1935612
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.78525.619226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.99815840
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9481512
X-RAY DIFFRACTIONr_chiral_restr0.1590.2731
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0215488
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02943
X-RAY DIFFRACTIONr_mcbond_it1.2741.53022
X-RAY DIFFRACTIONr_mcbond_other0.4361.51238
X-RAY DIFFRACTIONr_mcangle_it2.22624864
X-RAY DIFFRACTIONr_scbond_it3.57831930
X-RAY DIFFRACTIONr_scangle_it5.6674.51851
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 285 -
Rwork0.217 4702 -
obs--100 %
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)
10.5276-0.25510.32430.9581-0.44410.7297-0.0621-0.13080.04860.09360.02260.0187-0.0729-0.02930.03950.03660.009-0.0020.1304-0.01130.0764-19.66619.20916.083
21.2108-0.0558-0.36760.4212-0.08991.0569-0.0257-0.1766-0.0599-0.00410.0248-0.02380.1280.1340.00090.04490.0318-0.01510.1243-0.02370.063419.2423.40826.857
30.7181-0.31120.50290.8532-0.44380.8379-0.0948-0.14460.14320.09090.03270.0206-0.1397-0.05960.06210.03290.013-0.00720.1023-0.02360.0807-20.72924.84411.533
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 175
2X-RAY DIFFRACTION2A176 - 423
3X-RAY DIFFRACTION3A424 - 617

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