[English] 日本語
Yorodumi
- PDB-5ihj: Fusion of Maltose-binding Protein and PilA from Acinetobacter bau... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ihj
TitleFusion of Maltose-binding Protein and PilA from Acinetobacter baumannii BIDMC57
ComponentsMaltose-binding periplasmic protein,Fimbrial protein
KeywordsCELL ADHESION / adhesion / extracellular appendage / fimbriae
Function / homology
Function and homology information


protein secretion by the type II secretion system / type II protein secretion system complex / pilus / detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing ...protein secretion by the type II secretion system / type II protein secretion system complex / pilus / detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / membrane => GO:0016020 / cell adhesion / DNA damage response / membrane
Similarity search - Function
Type II secretion system protein GspH / Fimbrial protein pilin / Pilin (bacterial filament) / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / 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
Similarity search - Domain/homology
alpha-maltotriose / Fimbrial protein / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Acinetobacter baumannii 216872 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsPiepenbrink, K.H. / Sundberg, E.J.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structural Diversity in the Type IV Pili of Multidrug-resistant Acinetobacter.
Authors: Piepenbrink, K.H. / Lillehoj, E. / Harding, C.M. / Labonte, J.W. / Zuo, X. / Rapp, C.A. / Munson, R.S. / Goldblum, S.E. / Feldman, M.F. / Gray, J.J. / Sundberg, E.J.
History
DepositionFeb 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2016Group: Database references
Revision 1.2Nov 9, 2016Group: Database references
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 / citation / 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_conn_angle / pdbx_struct_oper_list / struct_asym / struct_conn / struct_conn_type / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_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.pdbx_synonyms / _chem_comp.type / _citation.journal_id_CSD / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)54,15610
Polymers53,0451
Non-polymers1,1119
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)175.070, 56.636, 49.997
Angle α, β, γ (deg.)90.000, 91.600, 90.000
Int Tables number5
Space group name H-MC121

-
Components

-
Protein / Sugars , 2 types, 2 molecules A

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


Mass: 53044.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Acinetobacter baumannii 216872 (bacteria)
Strain: K12 / Gene: malE, b4034, JW3994, tfpA, J633_2062 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P0AEX9, UniProt: A0A140QW15
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotriose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotriose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1a_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}LINUCSPDB-CARE

-
Non-polymers , 4 types, 81 molecules

#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Bicine/Trizma pH 8.0 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD 0.06M CaCl 0.06M MgCl 50 mM NaCl 3% EtOH

-
Data collection

DiffractionMean temperature: 107.1 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Feb 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. obs: 23793 / % possible obs: 71.4 % / Redundancy: 4 % / Rmerge(I) obs: 0.351 / Rpim(I) all: 0.169 / Rrim(I) all: 0.392 / Χ2: 3.498 / Net I/av σ(I): 7.056 / Net I/σ(I): 4.6 / Num. measured all: 127780
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.79-1.821.15.6712400.1874.9957.5830.54110.9
1.82-1.851.23780.1870.39316.9
1.85-1.891.31.545770.1871.4242.1030.46926.2
1.89-1.931.41.0777480.0960.9761.4591.20833.2
1.93-1.971.53.0919710.0152.7744.1670.56243.4
1.97-2.021.51.26710700.1831.0471.6520.60547.9
2.02-2.071.71.44912310.1331.2031.8920.6454.2
2.07-2.121.91.22514890.1740.9611.5660.59567.7
2.12-2.182.11.03317140.8871.3695.29175.7
2.18-2.262.31.17918820.2780.8011.4340.79385.2
2.26-2.342.61.12720600.3120.7251.3490.85291.4
2.34-2.433.11.08721310.3620.6521.2760.86395.3
2.43-2.543.71.11421010.4370.5961.2691.06993.4
2.54-2.674.81.20321850.5120.5911.3450.96297.8
2.67-2.845.61.01422020.70.4661.1191.07497.4
2.84-3.065.90.70422010.8310.3170.7741.65898.3
3.06-3.375.80.44521790.8750.2020.4912.32896.3
3.37-3.866.30.27222420.9480.1180.2973.78699.1
3.86-4.8660.18322070.9690.0820.2016.40996.8
4.86-506.20.15322900.9780.0670.16711.0597.7

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→43.93 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.244 --
Rwork0.2109 --
obs-23793 94.85 %
Displacement parametersBiso max: 105.26 Å2 / Biso mean: 28.0943 Å2 / Biso min: 11.98 Å2
Refinement stepCycle: LAST / Resolution: 2.2→43.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3640 0 69 73 3782
LS refinement shellResolution: 2.2→2.279 Å / Num. reflection obs: 2036

+
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