[English] 日本語
Yorodumi
- PDB-2nop: An unusual twin-His arrangement in the pore of ammonia channels i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2nop
TitleAn unusual twin-His arrangement in the pore of ammonia channels is essential for substrate conductance
ComponentsAmmonia channel
KeywordsTRANSPORT PROTEIN / Membrane Protein / Ammonia Transport / wild-type AmtB
Function / homology
Function and homology information


ammonium transmembrane transport / ammonium channel activity / carbon dioxide transport / identical protein binding / plasma membrane
Similarity search - Function
Ammonium transporter, conserved site / Ammonium transporters signature. / Ammonium transporter / Ammonium transporter fold / Ammonium transporter AmtB like domains / Ammonium transporter AmtB-like domain / Ammonium Transporter Family / Ammonium/urea transporter / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / IMIDAZOLE / Ammonium transporter AmtB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLupo, D. / Winkler, F.K.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: An unusual twin-his arrangement in the pore of ammonia channels is essential for substrate conductance
Authors: Javelle, A. / Lupo, D. / Zheng, L. / Li, X.-D. / Winkler, F.K. / Merrick, M.
History
DepositionOct 26, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ammonia channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7685
Polymers44,4521
Non-polymers3164
Water1,35175
1
A: Ammonia channel
hetero molecules

A: Ammonia channel
hetero molecules

A: Ammonia channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,30415
Polymers133,3553
Non-polymers94912
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area12850 Å2
ΔGint-166 kcal/mol
Surface area32670 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)109.879, 109.879, 84.170
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Ammonia channel / Ammonia transporter


Mass: 44451.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: amtB / Plasmid: pET22b-AmtBLH / Production host: Escherichia coli (E. coli) / Strain (production host): C43 (DE3) / References: UniProt: P69681

-
Non-polymers , 5 types, 79 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 75 / 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: 3.3 Å3/Da / Density % sol: 62.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 30% PEG 400, 0.1M SODIUM ACETATE, 0.2M AMMONIUM SULFATE, PH 4.6, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K, pH 4.60

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.901031 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 13, 2005
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.901031 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 36385 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rsym value: 0.068 / Net I/σ(I): 21.57
Reflection shellResolution: 2→2.1 Å / Mean I/σ(I) obs: 5.55 / Rsym value: 0.428 / % possible all: 100

-
Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.2.0019refinement
MAR345data collection
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XQF

1xqf


Resolution: 2→15 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.96 / SU B: 4.68 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.114 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17815 1856 5.1 %RANDOM
Rwork0.15989 ---
all0.16082 38983 --
obs0.16082 34486 93.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.252 Å2
Baniso -1Baniso -2Baniso -3
1-1.27 Å20.63 Å20 Å2
2--1.27 Å20 Å2
3----1.9 Å2
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2639 0 20 75 2734
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222718
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2751.9433702
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.8215360
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.30322.96381
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.49615386
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.204155
X-RAY DIFFRACTIONr_chiral_restr0.1020.2445
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022327
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1950.21491
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21968
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2103
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.272
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0710.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.08121813
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.70532810
X-RAY DIFFRACTIONr_scbond_it2.6564.51062
X-RAY DIFFRACTIONr_scangle_it3.7356892
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 138 -
Rwork0.188 2686 -
obs--100 %

+
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