[English] 日本語
Yorodumi
- PDB-5aez: Crystal structure of Candida albicans Mep2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5aez
TitleCrystal structure of Candida albicans Mep2
ComponentsMEP2
KeywordsMEMBRANE PROTEIN / AMMONIUM TRANSPORTER
Function / homology
Function and homology information


filamentous growth of a population of unicellular organisms in response to starvation / ammonium transmembrane transport / ammonium channel activity / filamentous growth / cellular response to nitrogen starvation / cellular response to starvation / 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
Ammonium transporter
Similarity search - Component
Biological speciesCANDIDA ALBICANS (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsRutherford, J.C. / Chembath, A. / van den Berg, B.
CitationJournal: Nat.Commun. / Year: 2016
Title: Structural Basis for Mep2 Ammonium Transceptor Activation by Phosphorylation.
Authors: Van Den Berg, B. / Chembath, A. / Jefferies, D. / Basle, A. / Khalid, S. / Rutherford, J.
History
DepositionJan 12, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 1.2May 11, 2016Group: Database references
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / 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_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Jan 10, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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: MEP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3216
Polymers52,7891
Non-polymers1,5325
Water4,936274
1
A: MEP2
hetero molecules

A: MEP2
hetero molecules

A: MEP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,96418
Polymers158,3683
Non-polymers4,59615
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area20410 Å2
ΔGint-123.8 kcal/mol
Surface area40420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.880, 104.880, 160.650
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-2065-

HOH

-
Components

#1: Protein MEP2


Mass: 52789.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CANDIDA ALBICANS (yeast) / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain (production host): W303 DELTA PEP4 / References: UniProt: Q59UP8
#2: Sugar
ChemComp-BNG / nonyl beta-D-glucopyranoside / Beta-NONYLGLUCOSIDE / nonyl beta-D-glucoside / nonyl D-glucoside / nonyl glucoside


Type: D-saccharide / Mass: 306.395 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C15H30O6 / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 63 % / Description: NONE
Crystal growpH: 8 / Details: 0.04 M TRIS PH 8.0 0.04 M NACL 27% PEG350 MME

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.47→43.7 Å / Num. obs: 112103 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 17.78 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.5
Reflection shellResolution: 1.47→1.5 Å / Redundancy: 5 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.9 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5AEX

5aex


Resolution: 1.47→43.702 Å / SU ML: 0.13 / σ(F): 1.98 / Phase error: 14.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1499 5601 5 %
Rwork0.137 --
obs0.1376 111840 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.5 Å2
Refinement stepCycle: LAST / Resolution: 1.47→43.702 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3484 0 80 274 3838
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073730
X-RAY DIFFRACTIONf_angle_d1.0815090
X-RAY DIFFRACTIONf_dihedral_angle_d12.2141271
X-RAY DIFFRACTIONf_chiral_restr0.073563
X-RAY DIFFRACTIONf_plane_restr0.005620
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.47-1.48670.26331790.22833479X-RAY DIFFRACTION100
1.4867-1.50420.21371870.21543529X-RAY DIFFRACTION99
1.5042-1.52260.19931990.1973607X-RAY DIFFRACTION100
1.5226-1.54180.19581900.1883459X-RAY DIFFRACTION100
1.5418-1.56210.19241820.17673539X-RAY DIFFRACTION100
1.5621-1.58350.18572060.17183562X-RAY DIFFRACTION100
1.5835-1.60610.1841670.16113511X-RAY DIFFRACTION100
1.6061-1.63010.16591820.15373541X-RAY DIFFRACTION100
1.6301-1.65560.16551730.14653574X-RAY DIFFRACTION100
1.6556-1.68270.16151650.14633629X-RAY DIFFRACTION100
1.6827-1.71180.14752010.14763504X-RAY DIFFRACTION100
1.7118-1.74290.14161710.14363544X-RAY DIFFRACTION100
1.7429-1.77640.15771960.13823510X-RAY DIFFRACTION100
1.7764-1.81270.14981840.1333575X-RAY DIFFRACTION100
1.8127-1.85210.14111780.12853533X-RAY DIFFRACTION100
1.8521-1.89520.13671710.12733579X-RAY DIFFRACTION100
1.8952-1.94260.15271930.13323551X-RAY DIFFRACTION100
1.9426-1.99510.1641920.13193523X-RAY DIFFRACTION100
1.9951-2.05380.14271770.13323576X-RAY DIFFRACTION100
2.0538-2.12010.15482020.13363547X-RAY DIFFRACTION100
2.1201-2.19580.14812060.13333531X-RAY DIFFRACTION100
2.1958-2.28380.15521930.12693529X-RAY DIFFRACTION100
2.2838-2.38770.13611780.13123582X-RAY DIFFRACTION100
2.3877-2.51360.14511980.13653492X-RAY DIFFRACTION100
2.5136-2.6710.15691850.13343553X-RAY DIFFRACTION100
2.671-2.87720.13571840.12923560X-RAY DIFFRACTION100
2.8772-3.16670.1382030.12693511X-RAY DIFFRACTION100
3.1667-3.62470.13561840.12583556X-RAY DIFFRACTION100
3.6247-4.5660.12921790.12773543X-RAY DIFFRACTION99
4.566-43.7210.16731960.14723510X-RAY DIFFRACTION100
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)
10.5758-0.90860.29352.2615-0.56790.2574-0.01890.21760.1598-0.314-0.0218-0.1406-0.18360.06280.04280.287-0.01590.02470.20970.05780.2054-48.702848.6898-45.7946
20.65080.07360.24370.53070.0070.5913-0.00150.01290.1087-0.00860.0046-0.0836-0.15090.1601-0.00460.149-0.03180.00770.1586-0.00390.1864-38.107344.3747-20.9229
30.59330.39740.0880.91360.15540.71820.0188-0.15370.03310.1773-0.0018-0.1493-0.03090.21360.01030.1607-0.0298-0.04780.2739-0.01820.2064-27.759837.0738-2.3118
40.54140.08580.07220.65120.09560.76590.0167-0.0194-0.03990.03810.0106-0.16320.04250.2575-0.02650.10870.008-0.00960.2049-0.00950.1919-29.563728.0128-18.3418
51.82710.55130.13670.44270.09311.01860.2853-0.97720.20850.3801-0.1856-0.021-0.2311-0.0469-0.09240.427-0.1024-0.01950.5203-0.140.3353-40.364852.24467.5437
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 1 THROUGH 24 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 25 THROUGH 183 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 184 THROUGH 221 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 222 THROUGH 407 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 408 THROUGH 455 )

+
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