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- PDB-1nmu: MBP-L30 -

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Basic information

Entry
Database: PDB / ID: 1nmu
TitleMBP-L30
Components
  • 60S ribosomal protein L30
  • maltose-binding periplasmic protein
KeywordsSUGAR BINDING PROTEIN/RIBOSOME / structural flexibility / ribosomal protein L30 / MBP-L30 fusion protein / SUGAR BINDING PROTEIN-RIBOSOME COMPLEX
Function / homology
Function and homology information


pre-mRNA 5'-splice site binding / detection of maltose stimulus / maltose transport complex / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / negative regulation of mRNA splicing, via spliceosome / carbohydrate transport / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits ...pre-mRNA 5'-splice site binding / detection of maltose stimulus / maltose transport complex / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / negative regulation of mRNA splicing, via spliceosome / carbohydrate transport / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / L13a-mediated translational silencing of Ceruloplasmin expression / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / rRNA processing / outer membrane-bounded periplasmic space / cytosolic large ribosomal subunit / cytoplasmic translation / periplasmic space / structural constituent of ribosome / DNA damage response / RNA binding / membrane / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L30/S12 / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / 60s Ribosomal Protein L30; Chain: A; / Bacterial extracellular solute-binding protein / Ribosomal protein L30e signature 1. / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / Bacterial extracellular solute-binding protein ...Ribosomal protein L30/S12 / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / 60s Ribosomal Protein L30; Chain: A; / Bacterial extracellular solute-binding protein / Ribosomal protein L30e signature 1. / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / Bacterial extracellular solute-binding protein / Ribosomal protein L30/YlxQ / Periplasmic binding protein-like II / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / D-Maltodextrin-Binding Protein; domain 2 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-maltotetraose / Maltose/maltodextrin-binding periplasmic protein / Maltose/maltodextrin-binding periplasmic protein / Large ribosomal subunit protein eL30
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsChao, J.A. / Prasad, G.S. / White, S.A. / Stout, C.D. / Williamson, J.R.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Inherent Protein Structural Flexibility at the RNA-binding Interface of L30e
Authors: Chao, J.A. / Prasad, G.S. / White, S.A. / Stout, C.D. / Williamson, J.R.
History
DepositionJan 10, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_validate_close_contact / 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 / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _entity.src_method / _entity.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 21, 2022Group: 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 2.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: maltose-binding periplasmic protein
B: 60S ribosomal protein L30
C: maltose-binding periplasmic protein
D: 60S ribosomal protein L30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,6146
Polymers106,2814
Non-polymers1,3332
Water4,179232
1
A: maltose-binding periplasmic protein
B: 60S ribosomal protein L30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8073
Polymers53,1402
Non-polymers6671
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: maltose-binding periplasmic protein
D: 60S ribosomal protein L30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8073
Polymers53,1402
Non-polymers6671
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.650, 118.390, 153.780
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 / Maltodextrin-binding protein / MBP


Mass: 41841.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P02928, UniProt: P0AEX9*PLUS
#2: Protein 60S ribosomal protein L30 / YL32 / RP73


Mass: 11299.168 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P14120
#3: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotetraose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 666.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotetraose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1a_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 3.41 Å3/Da / Density % sol: 63.92 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Sodium Citrate, Tris, Sodium Chloride, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 6.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15 mg/mlprotein1drop
210 mMsodium citrate1droppH6.2
31 mMmaltose1drop
40.02 %(w/v)sodium azide1drop
550 %satsodium citrate1reservoir
60.1 MTris1reservoirpH7.0

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 16, 2000 / Details: double crystal monochromater
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.31→18 Å / Num. all: 65857 / Num. obs: 65330 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.31→2.38 Å / % possible all: 99.8
Reflection
*PLUS
Lowest resolution: 18 Å / Num. measured all: 708695 / Rmerge(I) obs: 0.086
Reflection shell
*PLUS
% possible obs: 99.8 % / Rmerge(I) obs: 0.359

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.31→18 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.254 3235 random
Rwork0.214 --
obs0.223 64644 -
all-65330 -
Refinement stepCycle: LAST / Resolution: 2.31→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7273 0 90 232 7595
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.426
X-RAY DIFFRACTIONc_bond_d0.0066
X-RAY DIFFRACTIONc_dihedral_angle_d22.0177
X-RAY DIFFRACTIONc_improper_angle_d1.124
Refinement
*PLUS
Lowest resolution: 18 Å / Rfactor Rfree: 0.2544 / Rfactor Rwork: 0.2225
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.0177
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.124

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