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- PDB-5ah3: Crystal structure of the Mep2 mutant R452D,S453D from Candida albicans -

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Basic information

Entry
Database: PDB / ID: 5ah3
TitleCrystal structure of the Mep2 mutant R452D,S453D from Candida albicans
ComponentsMEP2
KeywordsTRANSPORT PROTEIN / MEMBRANE / MEMBRANE PROTEIN AMMONIUM TRANSPORTER MEP2 CANDIDA ALBICANS
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: 2.4 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 4, 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 / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MEP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1886
Polymers52,7751
Non-polymers2,4135
Water2,324129
1
A: MEP2
hetero molecules

A: MEP2
hetero molecules

A: MEP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,56418
Polymers158,3263
Non-polymers7,23815
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 area19790 Å2
ΔGint-218.6 kcal/mol
Surface area43000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.678, 112.678, 251.146
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-2020-

HOH

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Components

#1: Protein MEP2


Mass: 52775.328 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CANDIDA ALBICANS (yeast) / Plasmid: 83NU / Production host: SACCHAROMYCES CEREVISIAE W303 (yeast) / Variant (production host): DELTA PEP4 / References: UniProt: Q59UP8
#2: Sugar
ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C22H42O11 / Comment: detergent*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsDECYL-BETA-D-MALTOPYRANOSIDE (DMU): MOST DETERGENT MOLECULES ONLY HAVE PARTIAL DENSITY
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: 4.3 Å3/Da / Density % sol: 71 % / Description: NONE
Crystal growpH: 5 / Details: 0.1 M SODIUM ACETATE 15-20% PEG400

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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: Jul 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.4→83 Å / Num. obs: 37790 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 10.8 % / Biso Wilson estimate: 35.3 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 7.6
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.99 / Mean I/σ(I) obs: 1.9 / % 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 5AEZ

5aez


Resolution: 2.4→48.791 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 20.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2 1834 4.9 %
Rwork0.1735 --
obs0.1748 37561 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→48.791 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3424 0 91 129 3644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083625
X-RAY DIFFRACTIONf_angle_d1.0584935
X-RAY DIFFRACTIONf_dihedral_angle_d14.0291201
X-RAY DIFFRACTIONf_chiral_restr0.044545
X-RAY DIFFRACTIONf_plane_restr0.005599
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.4650.30771420.26032660X-RAY DIFFRACTION98
2.465-2.53750.23751270.23112653X-RAY DIFFRACTION99
2.5375-2.61940.24381390.20762704X-RAY DIFFRACTION99
2.6194-2.7130.21141210.1952682X-RAY DIFFRACTION99
2.713-2.82160.22781500.19052704X-RAY DIFFRACTION99
2.8216-2.950.21211250.17732711X-RAY DIFFRACTION99
2.95-3.10550.21781490.1732705X-RAY DIFFRACTION100
3.1055-3.30010.19721530.17152732X-RAY DIFFRACTION100
3.3001-3.55480.20691370.1752747X-RAY DIFFRACTION100
3.5548-3.91240.17441500.15232765X-RAY DIFFRACTION100
3.9124-4.47820.17641380.14792798X-RAY DIFFRACTION100
4.4782-5.64070.1811450.14782841X-RAY DIFFRACTION100
5.6407-48.80110.20021580.19163025X-RAY DIFFRACTION99
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)
10.60150.0242-0.01280.4868-0.11680.57050.03460.04730.0483-0.0201-0.00130.1375-0.0586-0.3553-0.02770.2880.0269-0.00530.39790.01480.35236.710235.370523.4927
23.94581.0030.08471.7717-0.65722.4218-0.1088-0.65240.27240.20490.0840.2528-0.3025-0.621700.530.07730.04450.6377-0.00130.373435.01621.184151.7334
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 4 THROUGH 408 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 409 THROUGH 454 )

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