[English] 日本語
Yorodumi
- PDB-2vql: Crystal structure of PorB from Corynebacterium glutamicum (crysta... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2vql
TitleCrystal structure of PorB from Corynebacterium glutamicum (crystal form III)
ComponentsUNCHARACTERIZED PROTEIN CGL0972
KeywordsMEMBRANE PROTEIN / TRANSMEMBRANE / PORIN / MEMBRANE / TRANSPORT / ION TRANSPORT
Function / homology
Function and homology information


Alpha-helical porin B/porin C / Porin PorB/PorC / Alpha-helical PorB/PorC / Alpha helical Porin B / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CACODYLATE ION / PorB
Similarity search - Component
Biological speciesCORYNEBACTERIUM GLUTAMICUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.16 Å
AuthorsZiegler, K. / Benz, R. / Schulz, G.E.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: A Putative Alpha-Helical Porin from Corynebacterium Glutamicum.
Authors: Ziegler, K. / Benz, R. / Schulz, G.E.
History
DepositionMar 17, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 20, 2008Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UNCHARACTERIZED PROTEIN CGL0972
B: UNCHARACTERIZED PROTEIN CGL0972
C: UNCHARACTERIZED PROTEIN CGL0972
D: UNCHARACTERIZED PROTEIN CGL0972
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,90720
Polymers42,5744
Non-polymers1,33316
Water0
1
A: UNCHARACTERIZED PROTEIN CGL0972
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1797
Polymers10,6441
Non-polymers5366
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: UNCHARACTERIZED PROTEIN CGL0972
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1797
Polymers10,6441
Non-polymers5366
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: UNCHARACTERIZED PROTEIN CGL0972
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7743
Polymers10,6441
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: UNCHARACTERIZED PROTEIN CGL0972
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7743
Polymers10,6441
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)78.392, 78.392, 191.859
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein
UNCHARACTERIZED PROTEIN CGL0972 / PORB / ANION-SPECIFIC PORIN / ANION-SPECIFIC PORIN PRECURSOR


Mass: 10643.550 Da / Num. of mol.: 4 / Fragment: RESIDUES 28-126
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CORYNEBACTERIUM GLUTAMICUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q8NRS3
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6AsO2

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.37 Å3/Da / Density % sol: 63.57 % / Description: NONE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Type: SLS / Wavelength: 0.98
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.16→60.75 Å / Num. obs: 10828 / % possible obs: 99.4 % / Observed criterion σ(I): 3 / Redundancy: 8.4 % / Rsym value: 0.06 / Net I/σ(I): 23.9
Reflection shellRedundancy: 8.8 % / Mean I/σ(I) obs: 6.5 / Rsym value: 0.36 / % possible all: 100

-
Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.16→60.75 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.87 / SU B: 39.254 / SU ML: 0.392 / Cross valid method: THROUGHOUT / ESU R: 1.225 / ESU R Free: 0.463 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.307 542 5 %RANDOM
Rwork0.281 ---
obs0.282 10285 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 109.56 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2---0.07 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 3.16→60.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2230 0 32 0 2262
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222292
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9111.9343116
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0355292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.34826.174115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.8315343
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.594158
X-RAY DIFFRACTIONr_chiral_restr0.0740.2329
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021788
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.21047
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2910.21584
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1050.265
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.272
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it01.51446
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it022253
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it03846
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it04.5863
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
LS refinement shellResolution: 3.16→3.24 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.395 40
Rwork0.316 749
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)
13.87080.9688-4.57665.8009-1.322114.28070.08860.8017-0.24760.4091-0.2803-0.2866-0.2092-0.40070.1917-0.5491-0.0902-0.0068-0.1232-0.0767-0.3023-20.990316.9964-18.7186
24.2511-3.39853.03169.8985-6.39948.08210.1040.2159-0.1365-0.3678-0.00080.07830.4133-0.4321-0.1032-0.5541-0.07920.09670.0679-0.12-0.319-37.97878.4539-21.6758
34.9431.167-0.72243.6763-2.381518.3917-0.12470.22080.06560.60540.24590.242-1.068-0.0451-0.12120.2784-0.0694-0.1319-0.5251-0.0178-0.1738-21.607120.40398.6464
412.3819-2.6337-3.21518.94891.493410.86660.2402-0.3489-0.43720.5877-0.59491.1669-0.3821-0.76580.3548-0.4402-0.10920.04610.1077-0.0137-0.0819-39.9212-13.9882-10.5649
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 88
2X-RAY DIFFRACTION2B16 - 88
3X-RAY DIFFRACTION3C13 - 88
4X-RAY DIFFRACTION4D17 - 87

+
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