[English] 日本語
Yorodumi
- PDB-2iww: Structure of the monomeric outer membrane porin OmpG in the open ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2iww
TitleStructure of the monomeric outer membrane porin OmpG in the open and closed conformation
ComponentsOUTER MEMBRANE PROTEIN G
KeywordsION CHANNEL / TRANSMEMBRANE / OUTER MEMBRANE / PORIN / MEMBRANE / TRANSPORT / ION TRANSPORT
Function / homology
Function and homology information


carbohydrate transmembrane transport / oligosaccharide transporting porin activity / maltose transporting porin activity / porin activity / pore complex / monoatomic ion transport / cell outer membrane
Similarity search - Function
Outer membrane porin G / Outer membrane protein G (OmpG) / monomeric porin ompg / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
beta-D-glucopyranose / Outer membrane porin G
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.7 Å
AuthorsYildiz, O. / Vinothkumar, K.R. / Goswami, P. / Kuehlbrandt, W.
CitationJournal: Embo J. / Year: 2006
Title: Structure of the Monomeric Outer-Membrane Porin Ompg in the Open and Closed Conformation.
Authors: Yildiz, O. / Vinothkumar, K.R. / Goswami, P. / Kuhlbrandt, W.
History
DepositionJul 5, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4May 8, 2024Group: 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 16-STRANDED BARREL THIS IS REPRESENTED BY A 17-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 14-STRANDED BARREL THIS IS REPRESENTED BY A 15-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: OUTER MEMBRANE PROTEIN G
B: OUTER MEMBRANE PROTEIN G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,33219
Polymers65,8732
Non-polymers4,45817
Water66737
1
A: OUTER MEMBRANE PROTEIN G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,68511
Polymers32,9371
Non-polymers2,74910
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: OUTER MEMBRANE PROTEIN G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6468
Polymers32,9371
Non-polymers1,7107
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)70.380, 71.140, 191.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNPROPROAA4 - 545 - 55
21ASNASNPROPROBB4 - 545 - 55
12THRTHRASNASNAA64 - 17865 - 179
22THRTHRASNASNBB64 - 17865 - 179
13GLUGLUASPASPAA187 - 215188 - 216
23GLUGLUASPASPBB187 - 215188 - 216
14ARGARGGLNGLNAA235 - 259236 - 260
24ARGARGGLNGLNBB235 - 259236 - 260
15ASPASPPHEPHEAA267 - 280268 - 281
25ASPASPPHEPHEBB267 - 280268 - 281

-
Components

#1: Protein OUTER MEMBRANE PROTEIN G / / OMPG


Mass: 32936.527 Da / Num. of mol.: 2 / Fragment: TRANSMEMBRANE BETA-BARREL, RESIDUES 22-301
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P76045
#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.: 4
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
#3: Chemical ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE / Lauryldimethylamine oxide


Mass: 229.402 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#4: Sugar
ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 3.4 Å3/Da / Density % sol: 64 %
Crystal growpH: 5.6 / Details: 100 MM NA-CITRATE PH 5.6 150 MM NACL 12% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9764
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 20, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9764 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 188983 / % possible obs: 92.7 % / Observed criterion σ(I): 1.75 / Redundancy: 5.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.9

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 2.7→19.87 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.841 / SU B: 11.749 / SU ML: 0.253 / Cross valid method: THROUGHOUT / ESU R: 0.624 / ESU R Free: 0.364 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.301 1342 5 %RANDOM
Rwork0.245 ---
obs0.248 25487 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.73 Å2
Baniso -1Baniso -2Baniso -3
1--2.2 Å20 Å20 Å2
2---2.04 Å20 Å2
3---4.24 Å2
Refinement stepCycle: LAST / Resolution: 2.7→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4596 0 304 37 4937
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225047
X-RAY DIFFRACTIONr_bond_other_d0.0060.023439
X-RAY DIFFRACTIONr_angle_refined_deg1.8361.9796837
X-RAY DIFFRACTIONr_angle_other_deg0.9563.017840
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.8935552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.51524.161298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.38915680
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5371530
X-RAY DIFFRACTIONr_chiral_restr0.0980.2690
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025534
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021140
X-RAY DIFFRACTIONr_nbd_refined0.2360.21119
X-RAY DIFFRACTIONr_nbd_other0.2180.23529
X-RAY DIFFRACTIONr_nbtor_refined0.2120.22173
X-RAY DIFFRACTIONr_nbtor_other0.1010.22907
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2163
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.220.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2710.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.89633440
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.71854354
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.38462838
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.45572483
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3254 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.030.05
tight thermal0.090.5
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.362 97
Rwork0.305 1839

+
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