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

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Basic information

Entry
Database: PDB / ID: 3osr
TitleMaltose-bound maltose sensor engineered by insertion of circularly permuted green fluorescent protein into E. coli maltose binding protein at position 311
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
Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Green Fluorescent Protein / Green fluorescent protein / Bacterial extracellular solute-binding protein / Green fluorescent protein, GFP / Bacterial extracellular solute-binding protein / Green fluorescent protein-related / Green fluorescent protein ...Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Green Fluorescent Protein / Green fluorescent protein / 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: 2 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: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...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_db_accession / _struct_ref_seq.pdbx_db_accession
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / 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_ref_seq_dif / 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 / _struct_ref_seq_dif.details
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 / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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
B: Maltose-binding periplasmic protein,Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,0364
Polymers145,3522
Non-polymers6852
Water10,070559
1
A: Maltose-binding periplasmic protein,Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,0182
Polymers72,6761
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Maltose-binding periplasmic protein,Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,0182
Polymers72,6761
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.825, 74.813, 171.504
Angle α, β, γ (deg.)90.00, 97.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 72675.812 Da / Num. of mol.: 2
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.: 2
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 559 / 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: 2.49 Å3/Da / Density % sol: 50.53 %
Crystal growTemperature: 296 K / Method: vapor diffusion / pH: 4.6
Details: 0.1 M Sodium acetate pH 4.6, 8% w/v polyethylene glycol 4000, VAPOR DIFFUSION, 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 2, 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: 2→34.24 Å / Num. obs: 96467 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 19.5 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 11.4
Reflection shellResolution: 2→2.11 Å / % possible all: 100

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Processing

Software
NameVersionClassification
specdata collection
PHASERphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 3EK4, 1ANF
Resolution: 2→34.24 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.919 / SU B: 8.508 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.153 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22573 4826 5 %RANDOM
Rwork0.18269 ---
obs0.18488 91629 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.638 Å2
Baniso -1Baniso -2Baniso -3
1-1 Å20 Å2-0.95 Å2
2---0.52 Å20 Å2
3----0.72 Å2
Refinement stepCycle: LAST / Resolution: 2→34.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9479 0 46 559 10084
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0229781
X-RAY DIFFRACTIONr_bond_other_d0.0010.026611
X-RAY DIFFRACTIONr_angle_refined_deg1.8681.96913268
X-RAY DIFFRACTIONr_angle_other_deg1.005316208
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.29851205
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.92825.516446
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.088151649
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1571526
X-RAY DIFFRACTIONr_chiral_restr0.1230.21434
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02110885
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021881
X-RAY DIFFRACTIONr_mcbond_it1.0671.55986
X-RAY DIFFRACTIONr_mcbond_other0.3091.52453
X-RAY DIFFRACTIONr_mcangle_it1.89729629
X-RAY DIFFRACTIONr_scbond_it3.04733793
X-RAY DIFFRACTIONr_scangle_it4.7944.53635
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 371 -
Rwork0.223 6696 -
obs--99.99 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.45610.09050.30.10360.07010.49640.02010.0182-0.01640.01360.0191-0.0347-0.0035-0.0073-0.03920.07250.02180.0010.0446-0.01020.046610.13449.27126.468
20.46620.288-0.37450.74420.26771.5681-0.02450.04560.03120.08120.099-0.02670.2950.0677-0.07450.14460.0073-0.03160.0295-0.01170.021212.54614.36516.257
30.39270.20540.05580.2788-0.02570.6474-0.00230.05060.0235-0.0454-0.0011-0.0586-0.04920.05050.00340.07180.01160.00570.04190.00080.0538.27154.70614.554
40.14330.13740.16240.34460.25440.90230.0314-0.0201-0.042-0.05030.013-0.0897-0.0445-0.0114-0.04440.09940.0011-0.01460.02660.00180.040429.14817.07461.389
52.45350.14471.12030.43280.44960.8772-0.00710.2628-0.04260.04630.0719-0.061-0.00330.1696-0.06490.11230.0228-0.04440.0506-0.03540.045839.03251.88265.748
60.11810.19530.33350.3560.62981.19450.07030.0623-0.09240.04830.1319-0.15670.06880.2106-0.20220.08480.0121-0.03090.0464-0.03970.124238.43211.9469.063
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-3 - 312
2X-RAY DIFFRACTION2A313 - 559
3X-RAY DIFFRACTION3A560 - 619
4X-RAY DIFFRACTION4B-3 - 312
5X-RAY DIFFRACTION5B313 - 559
6X-RAY DIFFRACTION6B560 - 619

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