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- PDB-3dm0: Maltose Binding Protein fusion with RACK1 from A. thaliana -

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Basic information

Entry
Database: PDB / ID: 3dm0
TitleMaltose Binding Protein fusion with RACK1 from A. thaliana
ComponentsMaltose-binding periplasmic protein fused with RACK1
KeywordsSugar Binding Protein / Signaling Protein / MBP RACK1A / Receptor for activiated protein C-kinase 1 / beta-propeller WD40 repeat / Sugar transport / Transport / WD repeat
Function / homology
Function and homology information


gibberellin mediated signaling pathway / cellular response to abscisic acid stimulus / response to gibberellin / vegetative to reproductive phase transition of meristem / seed germination / positive regulation of signal transduction / MAP-kinase scaffold activity / detection of maltose stimulus / maltose transport complex / carbohydrate transport ...gibberellin mediated signaling pathway / cellular response to abscisic acid stimulus / response to gibberellin / vegetative to reproductive phase transition of meristem / seed germination / positive regulation of signal transduction / MAP-kinase scaffold activity / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / response to glucose / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / translation regulator activity / cytosolic ribosome / ATP-binding cassette (ABC) transporter complex / chloroplast / cell chemotaxis / ribosome biogenesis / regulation of translation / ribosome binding / outer membrane-bounded periplasmic space / molecular adaptor activity / periplasmic space / structural constituent of ribosome / ribonucleoprotein complex / mRNA binding / DNA damage response / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Small (40S) ribosomal subunit Asc1/RACK1 / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Periplasmic binding protein-like II ...Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Small (40S) ribosomal subunit Asc1/RACK1 / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / Small ribosomal subunit protein RACK1z / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Arabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsUllah, H. / Scappini, E.L. / Moon, A.F. / Williams, L.V. / Armstrong, D.L. / Pedersen, L.C.
CitationJournal: Protein Sci. / Year: 2008
Title: Structure of a signal transduction regulator, RACK1, from Arabidopsis thaliana.
Authors: Ullah, H. / Scappini, E.L. / Moon, A.F. / Williams, L.V. / Armstrong, D.L. / Pedersen, L.C.
History
DepositionJun 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 26, 2015Group: Source and taxonomy
Revision 1.3Jul 26, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / 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 / pdbx_struct_assembly_gen / struct_asym / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maltose-binding periplasmic protein fused with RACK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,1083
Polymers75,7041
Non-polymers4042
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.777, 63.263, 70.056
Angle α, β, γ (deg.)70.40, 88.38, 73.82
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Maltose-binding periplasmic protein fused with RACK1


Mass: 75703.656 Da / Num. of mol.: 1
Fragment: Fusion protein of MBP (UNP residues 27 to 387 ) and RACK1 (UNP residues 4 to 327)
Mutation: D82A, K83A, K239A, E359A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Arabidopsis thaliana (thale cress)
Gene: malE, b4034, JW3994,ARCA, At1g18080, T10F20.9, T10O22.6
Plasmid: modified pMAL-c2x / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPlusRIL / References: UniProt: P0AEX9, UniProt: O24456
#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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFUSION PROTEIN OF MUTATED MBP AND RACK1A WITH LINKER REGION AAAQTNAAA.

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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: 3.05 Å3/Da / Density % sol: 59.7 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100mM HEPES pH 7.5 20% w/v PEG 10,000, VAPOR DIFFUSION, SITTING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Aug 30, 2007 / Details: varimax HF mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 34464 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 30.7 Å2 / Rsym value: 0.08 / Net I/σ(I): 21.4
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 3325 / Rsym value: 0.452 / % possible all: 95.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
StructureStudiodata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HSJ

1hsj


Resolution: 2.4→30.27 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 355153.19 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1488 4.8 %RANDOM
Rwork0.21 ---
all0.212 ---
obs0.21 30910 88.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.4973 Å2 / ksol: 0.316935 e/Å3
Displacement parametersBiso mean: 50.1 Å2
Baniso -1Baniso -2Baniso -3
1--4.99 Å2-12.75 Å211.44 Å2
2--1.53 Å2-13.62 Å2
3---3.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.4→30.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5122 0 27 273 5422
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_mcbond_it1.291.5
X-RAY DIFFRACTIONc_mcangle_it2.152
X-RAY DIFFRACTIONc_scbond_it6.992
X-RAY DIFFRACTIONc_scangle_it8.392.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.343 171 4.1 %
Rwork0.337 4034 -
obs--72.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4edo.paredo.top

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