[English] 日本語
Yorodumi
- PDB-3zoj: High-resolution structure of Pichia Pastoris aquaporin Aqy1 at 0.88 A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3zoj
TitleHigh-resolution structure of Pichia Pastoris aquaporin Aqy1 at 0.88 A
ComponentsAQUAPORIN
KeywordsMEMBRANE PROTEIN / CHANNEL
Function / homology
Function and homology information


water channel activity / metal ion binding / 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 speciesKOMAGATAELLA PASTORIS (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.88 Å
AuthorsKosinska-Eriksson, U. / Fischer, G. / Friemann, R. / Enkavi, G. / Tajkhorshid, E. / Neutze, R.
Citation
Journal: Science / Year: 2013
Title: Subangstrom Resolution X-Ray Structure Details Aquaporin-Water Interactions
Authors: Kosinska-Eriksson, U. / Fischer, G. / Friemann, R. / Enkavi, G. / Tajkhorshid, E. / Neutze, R.
#1: Journal: Plos Biol. / Year: 2009
Title: Crystal Structure of a Yeast Aquaporin at 1.15 Angstrom Reveals a Novel Gating Mechanism.
Authors: Fischer, G. / Kosinska-Eriksson, U. / Aponte-Santamaria, C. / Palmgren, M. / Geijer, C. / Hedfalk, K. / Hohmann, S. / De Groot, B.L. / Neutze, R. / Lindkvist-Petersson, K.
History
DepositionFeb 21, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Derived calculations
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: 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 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: AQUAPORIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9167
Polymers29,9321
Non-polymers9836
Water3,819212
1
A: AQUAPORIN
hetero molecules

A: AQUAPORIN
hetero molecules

A: AQUAPORIN
hetero molecules

A: AQUAPORIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,66428
Polymers119,7304
Non-polymers3,93424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area26590 Å2
ΔGint-205.6 kcal/mol
Surface area32990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.763, 90.763, 80.311
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11A-1277-

CL

-
Components

#1: Protein AQUAPORIN / AQUAPORIN PIP2-7 7


Mass: 29932.436 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) KOMAGATAELLA PASTORIS (fungus) / Strain: X33 / Production host: KOMAGATAELLA PASTORIS (fungus) / Strain (production host): X33 / References: UniProt: F2QVG4
#2: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsCHLORIDE ION (CL): ASSIGNED BASED ON DIFFERENCE DENSITY AND CHEMICAL SANITY B-OCTYLGLUCOSIDE (BOG): ...CHLORIDE ION (CL): ASSIGNED BASED ON DIFFERENCE DENSITY AND CHEMICAL SANITY B-OCTYLGLUCOSIDE (BOG): ONLY ASSIGNED WHEN HEADGROUP WAS UNAMBIGUOUSLY VISIBLE IN THE DENSITY.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.6 %
Description: 2 LOW-, 2 MEDIUM- AND 3 HIGH-RESOLUTION DATASETS WERE COLLECTED FROM A SINGLE CRYSTAL.
Crystal growpH: 8 / Details: 26% PEG600, 100 MM TRIS (PH=8.0), 200 MM CACL2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.65
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 16, 2010 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.65 Å / Relative weight: 1
ReflectionResolution: 0.88→64 Å / Num. obs: 252057 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 13.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 26.2
Reflection shellResolution: 0.88→0.93 Å / Redundancy: 11 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 2.8 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2W2E

2w2e


Resolution: 0.88→60.15 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.98 / SU B: 0.206 / SU ML: 0.006 / Cross valid method: THROUGHOUT / ESU R: 0.009 / ESU R Free: 0.009 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. POLAR HYDROGENS WERE SET TO OCCUPANCY 0 UNLESS THEY WERE OBSERVED IN THE DIFFERENCE DENSITY. HYDROGEN ATOMS FOR WATERS IN THE CHANNEL CAN ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. POLAR HYDROGENS WERE SET TO OCCUPANCY 0 UNLESS THEY WERE OBSERVED IN THE DIFFERENCE DENSITY. HYDROGEN ATOMS FOR WATERS IN THE CHANNEL CAN BE OBSERVED THROUGH THE DIFFERENCE DENSITY BUT HAVE NOT BEEN MODELLED.
RfactorNum. reflection% reflectionSelection details
Rfree0.10739 2381 0.9 %RANDOM
Rwork0.10325 ---
obs0.10329 249442 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.806 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2---0.04 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 0.88→60.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2001 0 63 212 2276
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0192243
X-RAY DIFFRACTIONr_bond_other_d0.0010.022150
X-RAY DIFFRACTIONr_angle_refined_deg1.6911.9533073
X-RAY DIFFRACTIONr_angle_other_deg0.8723.0014902
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9215286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.0821.88285
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.48515305
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0841512
X-RAY DIFFRACTIONr_chiral_restr0.0960.2336
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212560
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02568
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
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_it0.9010.8661105
X-RAY DIFFRACTIONr_mcbond_other0.8730.8641104
X-RAY DIFFRACTIONr_mcangle_it1.0551.3031398
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6921.1211138
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr5.42334393
X-RAY DIFFRACTIONr_sphericity_free16.2650.552
X-RAY DIFFRACTIONr_sphericity_bonded8.0060.54475
LS refinement shellResolution: 0.8846→0.908 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 53 -
Rwork0.248 18437 -
obs--99.44 %

+
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