[English] 日本語
Yorodumi
- PDB-5kws: Crystal Structure of Galactose Binding Protein from Yersinia pest... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5kws
TitleCrystal Structure of Galactose Binding Protein from Yersinia pestis in the Complex with beta D Glucose
ComponentsGalactose-binding protein
KeywordsOXIDOREDUCTASE / alpha-beta structure / solute-binding protein fold (SBP) / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


outer membrane-bounded periplasmic space / carbohydrate binding / metal ion binding
Similarity search - Function
D-galactose-binding periplasmic protein MglB-like, PBP domain / : / Periplasmic binding protein / Periplasmic binding protein domain / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / beta-D-glucopyranose / D-galactose/methyl-galactoside binding periplasmic protein MglB
Similarity search - Component
Biological speciesYersinia pestis CO92 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.316 Å
AuthorsKim, Y. / Maltseva, N. / Mulligan, R. / Grimshaw, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Crystal Structure of Galactose Binding Protein from Yersinia pestis in the Complex with beta D Glucose
Authors: Kim, Y. / Maltseva, N. / Mulligan, R. / Grimshaw, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJul 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2017Group: Database references / Structure summary
Revision 1.2Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Oct 4, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Galactose-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5978
Polymers34,0481
Non-polymers5507
Water5,531307
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.236, 56.753, 69.129
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-754-

HOH

-
Components

-
Protein / Sugars , 2 types, 2 molecules A

#1: Protein Galactose-binding protein / Periplasmic D-galactose-binding ABC transport protein


Mass: 34047.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis CO92 (bacteria) / Gene: mglB, y2662, YP_1397 / Plasmid: pMCSG53
Details (production host): cleavable N-terminal 6 Histidine tag
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Gold / References: UniProt: Q8D072
#2: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 6 types, 313 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 2.71 Å3/Da / Density % sol: 54.69 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.085M Tris:HCl pH 8.5, 25.5% (w/v) PEG 4000, 15% (v/v) Glycerol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.316→50 Å / Num. obs: 86602 / % possible obs: 98.1 % / Redundancy: 4.7 % / Biso Wilson estimate: 18.81 Å2 / Rsym value: 0.077 / Net I/σ(I): 24.6
Reflection shellResolution: 1.32→1.34 Å / Redundancy: 3 % / Rmerge(I) obs: 0.516 / Mean I/σ(I) obs: 1 / CC1/2: 0.741 / % possible all: 80.3

-
Processing

Software
NameVersionClassification
PHENIX(dev_2411: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBID 3GAS

3gas


Resolution: 1.316→36.252 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1603 4349 5.03 %random
Rwork0.144 ---
obs0.1448 86540 97.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.316→36.252 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2350 0 34 307 2691
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072563
X-RAY DIFFRACTIONf_angle_d0.9783487
X-RAY DIFFRACTIONf_dihedral_angle_d18.1973
X-RAY DIFFRACTIONf_chiral_restr0.088392
X-RAY DIFFRACTIONf_plane_restr0.005463
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3159-1.33080.29561050.24521953X-RAY DIFFRACTION71
1.3308-1.34650.25771230.23232388X-RAY DIFFRACTION86
1.3465-1.36290.26411570.22222527X-RAY DIFFRACTION93
1.3629-1.38020.25291510.20992691X-RAY DIFFRACTION96
1.3802-1.39830.26181540.20072677X-RAY DIFFRACTION98
1.3983-1.41750.22631420.1892751X-RAY DIFFRACTION99
1.4175-1.43770.21931330.17512758X-RAY DIFFRACTION99
1.4377-1.45920.21391430.16252786X-RAY DIFFRACTION100
1.4592-1.4820.22031400.14512738X-RAY DIFFRACTION99
1.482-1.50630.161460.13472782X-RAY DIFFRACTION100
1.5063-1.53230.16041500.1252775X-RAY DIFFRACTION100
1.5323-1.56010.14391510.1232739X-RAY DIFFRACTION100
1.5601-1.59010.17351370.11312778X-RAY DIFFRACTION99
1.5901-1.62260.1391340.11442817X-RAY DIFFRACTION100
1.6226-1.65790.14631430.11632759X-RAY DIFFRACTION100
1.6579-1.69640.1761480.1162757X-RAY DIFFRACTION100
1.6964-1.73890.13881270.11442784X-RAY DIFFRACTION99
1.7389-1.78590.15121590.11992774X-RAY DIFFRACTION100
1.7859-1.83840.1771440.12022799X-RAY DIFFRACTION100
1.8384-1.89780.13851260.1212818X-RAY DIFFRACTION100
1.8978-1.96560.15341620.122787X-RAY DIFFRACTION100
1.9656-2.04430.14541700.12492767X-RAY DIFFRACTION100
2.0443-2.13730.15291270.13032803X-RAY DIFFRACTION100
2.1373-2.250.1691570.1292787X-RAY DIFFRACTION99
2.25-2.39090.15131500.13832816X-RAY DIFFRACTION100
2.3909-2.57550.16061410.14822826X-RAY DIFFRACTION100
2.5755-2.83460.17541590.16022828X-RAY DIFFRACTION100
2.8346-3.24450.19331440.16462849X-RAY DIFFRACTION99
3.2445-4.08680.14371570.14972898X-RAY DIFFRACTION100
4.0868-36.26610.13591690.14912979X-RAY DIFFRACTION99

+
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