[English] 日本語
Yorodumi
- PDB-2fvy: High Resolution Glucose Bound Crystal Structure of GGBP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2fvy
TitleHigh Resolution Glucose Bound Crystal Structure of GGBP
ComponentsD-galactose-binding periplasmic protein
KeywordsTRANSPORT PROTEIN / PERIPLASMIC BINDING PROTEIN / HINGE / CHEMOTAXIS / TRANSPORT
Function / homology
Function and homology information


methylgalactoside transport / galactose transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / chemotaxis / outer membrane-bounded periplasmic space / carbohydrate binding / calcium ion binding / membrane
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
ACETATE ION / beta-D-glucopyranose / CARBON DIOXIDE / D-galactose/methyl-galactoside binding periplasmic protein MglB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.92 Å
AuthorsBorrok, M.J. / Kiessling, L.L. / Forest, K.T.
CitationJournal: Protein Sci. / Year: 2007
Title: Conformational changes of glucose/galactose-binding protein illuminated by open, unliganded, and ultra-high-resolution ligand-bound structures.
Authors: Borrok, M.J. / Kiessling, L.L. / Forest, K.T.
History
DepositionJan 31, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name / _struct_conn.pdbx_leaving_atom_flag
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 / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 2, 2020Group: Structure summary / Category: chem_comp / struct_keywords / Item: _chem_comp.pdbx_synonyms / _struct_keywords.text
Revision 2.2Oct 21, 2020Group: Derived calculations / Category: struct_conn / struct_conn_type
Revision 2.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: D-galactose-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8236
Polymers33,4081
Non-polymers4155
Water7,530418
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.989, 36.238, 80.101
Angle α, β, γ (deg.)90.00, 124.50, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-792-

HOH

-
Components

-
Protein / Sugars , 2 types, 2 molecules A

#1: Protein D-galactose-binding periplasmic protein / GBP / D-galactose/ D-glucose-binding protein / GGBP


Mass: 33407.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mglB / Plasmid: pVB2 / Production host: Escherichia coli (E. coli) / Strain (production host): HB929 / References: UniProt: P0AEE5
#2: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / 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 , 5 types, 422 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-CO2 / CARBON DIOXIDE / Carbon dioxide


Mass: 44.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 418 / 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: 2.12 Å3/Da / Density % sol: 42.72 %
Description: Residues 1, 307-309 not found in refinement and left out
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 25% PEG 4000, 5% Glycerol, 0.1M HEPES PH 7.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.83 / Wavelength: 0.83 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 12, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.83 Å / Relative weight: 1
ReflectionResolution: 0.92→9 Å / Num. all: 196667 / Num. obs: 187424 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 8.9 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.027 / Net I/σ(I): 36.8
Reflection shellResolution: 0.92→0.95 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.247 / Mean I/σ(I) obs: 2.7 / Num. unique all: 14655 / % possible all: 74.7

-
Processing

Software
NameVersionClassification
SHELXL-97refinement
SCALEPACKdata scaling
AMoREphasing
CNS1.1 & SHELXrefinement
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Salmonella Typhimuruim GGBP

Resolution: 0.92→9 Å / Num. parameters: 25511 / Num. restraintsaints: 30847 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 4.0
RfactorNum. reflection% reflectionSelection details
Rfree0.1296 9389 5.3 %RANDOM
Rwork0.11 ---
all0.1097 178035 --
obs0.1179 187424 90.6 %-
Displacement parametersBiso mean: 12.7 Å2
Refine analyzeLuzzati coordinate error obs: 0.096 Å / Num. disordered residues: 23 / Occupancy sum hydrogen: 2277 / Occupancy sum non hydrogen: 2761.75
Refinement stepCycle: LAST / Resolution: 0.92→9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2319 0 26 418 2763
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.018
X-RAY DIFFRACTIONs_angle_d0.032
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0301
X-RAY DIFFRACTIONs_zero_chiral_vol0.111
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.136
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.052
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.03
X-RAY DIFFRACTIONs_approx_iso_adps0.096
LS refinement shell
Resolution (Å)Rfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
0.92-0.950.237X-RAY DIFFRACTION1268670.82
0.95-1.20.104X-RAY DIFFRACTION8169791.25
1.2-1.50.086X-RAY DIFFRACTION4032693.3
1.5-20.09X-RAY DIFFRACTION2493694.59
2-30.115X-RAY DIFFRACTION1300395.23
3-90.16X-RAY DIFFRACTION538795.16

+
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