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- PDB-5aid: Crystal structure of the Mep2 mutant delta442 from Candida albicans -

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Basic information

Entry
Database: PDB / ID: 5aid
TitleCrystal structure of the Mep2 mutant delta442 from Candida albicans
ComponentsMEP2
KeywordsMEMBRANE PROTEIN / AMMONIUM TRANSPORTER / MEP2
Function / homology
Function and homology information


filamentous growth of a population of unicellular organisms in response to starvation / nitrogen utilization / 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: 3.4 Å
Authorsvan den Berg, B. / Chembath, A. / Rutherford, J.
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
DepositionFeb 12, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 1.2May 11, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MEP2


Theoretical massNumber of molelcules
Total (without water)48,8091
Polymers48,8091
Non-polymers00
Water00
1
A: MEP2

A: MEP2

A: MEP2


Theoretical massNumber of molelcules
Total (without water)146,4283
Polymers146,4283
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area11120 Å2
ΔGint-153.9 kcal/mol
Surface area36970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.733, 114.733, 289.964
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein MEP2


Mass: 48809.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CANDIDA ALBICANS (yeast) / Plasmid: 83NU / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain (production host): W303 DELTA PEP4 / References: UniProt: Q59UP8
Sequence detailsCONTAINS MUTATIONS R452D S453D

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.76 Å3/Da / Density % sol: 67 % / Description: NONE
Crystal growpH: 6
Details: 24% PEG400, 0.05 M SODIUM ACETATE, 0.05 M MAGNESIUM ACETATE PH 6.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: DEXTRIS / Detector: PIXEL / Date: Aug 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3.4→96.65 Å / Num. obs: 10453 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 9.3 % / Biso Wilson estimate: 132.97 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.6
Reflection shellResolution: 3.4→3.67 Å / Redundancy: 9.7 % / Rmerge(I) obs: 1.17 / Mean I/σ(I) obs: 2.5 / % possible all: 100

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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: 3.4→96.655 Å / SU ML: 0.44 / σ(F): 1.33 / Phase error: 34.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2892 1051 10.17 %
Rwork0.2356 --
obs0.2409 10439 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.4→96.655 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3030 0 0 0 3030
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093138
X-RAY DIFFRACTIONf_angle_d1.2834284
X-RAY DIFFRACTIONf_dihedral_angle_d14.5621021
X-RAY DIFFRACTIONf_chiral_restr0.043471
X-RAY DIFFRACTIONf_plane_restr0.004524
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4001-3.55480.38741330.27241150X-RAY DIFFRACTION100
3.5548-3.74230.28481230.24161154X-RAY DIFFRACTION100
3.7423-3.97670.26551250.22411154X-RAY DIFFRACTION99
3.9767-4.28380.28591290.19641165X-RAY DIFFRACTION100
4.2838-4.71490.2291310.18371163X-RAY DIFFRACTION100
4.7149-5.39710.23041370.19281166X-RAY DIFFRACTION100
5.3971-6.79950.29421370.27131182X-RAY DIFFRACTION100
6.7995-96.69370.32721360.25851254X-RAY DIFFRACTION100

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