[English] 日本語
Yorodumi
- PDB-3osr: Maltose-bound maltose sensor engineered by insertion of circularl... -

+
Open data


ID or keywords:

Loading...

-
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 / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / 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 / Bacterial extracellular solute-binding protein / Green fluorescent protein, GFP / 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 / Bacterial extracellular solute-binding protein / Green fluorescent protein, GFP / 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
Revision 3.0Jul 10, 2024Group: Data collection / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity
Item: _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight
Revision 3.1Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)146,0684
Polymers145,3842
Non-polymers6852
Water10,070559
1
A: Maltose-binding periplasmic protein,Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,0342
Polymers72,6921
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)73,0342
Polymers72,6921
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

-
Components

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


Mass: 72691.812 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


Mass: 18.015 Da / Num. of mol.: 559 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

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

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)
10.45610.09050.30.10360.07010.49640.02010.0182-0.01640.01360.0191-0.0347-0.0035-0.0073-0.03920.07250.02180.0010.0446-0.01020.046610.13449.27126.468
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more