[English] 日本語
Yorodumi
- PDB-2f2b: Crystal structure of integral membrane protein Aquaporin AqpM at ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2f2b
TitleCrystal structure of integral membrane protein Aquaporin AqpM at 1.68A resolution
ComponentsAquaporin aqpM
KeywordsMEMBRANE PROTEIN / protein / integral membrane protein / channel / Structural Genomics / PSI-2 / Protein Structure Initiative / Center for Structures of Membrane Proteins / CSMP
Function / homology
Function and homology information


water channel activity / plasma membrane
Similarity search - Function
Glycerol uptake facilitator protein / Glycerol uptake facilitator protein. / Aquaporin transporter / Major intrinsic protein, conserved site / MIP family signature. / Major intrinsic protein / Major intrinsic protein / Aquaporin-like / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMethanothermobacter marburgensis str. Marburg (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsLee, J.K. / Kozono, D. / Remis, J. / Kitagawa, Y. / Agre, P. / Stroud, R.M. / Center for Structures of Membrane Proteins (CSMP)
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: Structural basis for conductance by the archaeal aquaporin AqpM at 1.68 A.
Authors: Lee, J.K. / Kozono, D. / Remis, J. / Kitagawa, Y. / Agre, P. / Stroud, R.M.
History
DepositionNov 15, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 23, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Aquaporin aqpM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4492
Polymers25,3571
Non-polymers921
Water2,324129
1
A: Aquaporin aqpM
hetero molecules

A: Aquaporin aqpM
hetero molecules

A: Aquaporin aqpM
hetero molecules

A: Aquaporin aqpM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,7958
Polymers101,4274
Non-polymers3684
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area15360 Å2
ΔGint-152 kcal/mol
Surface area27590 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)88.513, 88.513, 79.947
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
DetailsThe biological assembly is a tetramer generated from the monomer in the asymmetric unit

-
Components

#1: Protein Aquaporin aqpM


Mass: 25356.643 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter marburgensis str. Marburg (archaea)
Species: Methanothermobacter marburgensis / Strain: Marburg / DSM 2133 / Gene: aqpM / Plasmid: pTRCa / Production host: Escherichia coli (E. coli) / Strain (production host): bl21(DE3)RIL / References: UniProt: Q9C4Z5
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 129 / 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: 3.09 Å3/Da / Density % sol: 60.15 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG4000 23%, 200 mM MgCl2, 10% glycerol, TRIS pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 15, 2005 / Details: KOHZU: Double Crystal Si(111)
RadiationMonochromator: KOHZU: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.68→40 Å / Num. all: 35162 / Num. obs: 34031 / % possible obs: 96.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 9.1 % / Biso Wilson estimate: 19.3 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 18.8
Reflection shellResolution: 1.68→1.79 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 3.3 / Num. unique all: 4576 / % possible all: 83.7

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
CNS1.1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2evu

2evu


Resolution: 1.68→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.193 1665 -random
Rwork0.184 ---
all0.184 35162 --
obs0.193 34031 96.8 %-
Refine analyze
FreeObs
Luzzati coordinate error0.019 Å0.018 Å
Luzzati d res low-5 Å
Luzzati sigma a0.019 Å0.018 Å
Refinement stepCycle: LAST / Resolution: 1.68→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1780 0 6 129 1915
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d0.008
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d19.6
X-RAY DIFFRACTIONc_improper_angle_d0.81
LS refinement shellResolution: 1.68→1.79 Å / Rfactor Rfree error: 0.018
RfactorNum. reflection% reflection
Rfree0.302 275 -
Rwork0.3 --
obs-4576 0.832 %

+
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