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- PDB-6ej6: Crystal structure of the N240A mutant of Candida albicans Mep2 -

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Basic information

Entry
Database: PDB / ID: 6ej6
TitleCrystal structure of the N240A mutant of Candida albicans Mep2
ComponentsAmmonium transporter
KeywordsMEMBRANE PROTEIN / ammonium transporter / Candida albicans / signalling mutant
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: 1.65 Å
Authorsvan den Berg, B.
CitationJournal: To Be Published
Title: Crystal structure of the N240A mutant of Candida albicans Mep2
Authors: van den Berg, B.
History
DepositionSep 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ammonium transporter


Theoretical massNumber of molelcules
Total (without water)52,7461
Polymers52,7461
Non-polymers00
Water5,729318
1
A: Ammonium transporter

A: Ammonium transporter

A: Ammonium transporter


Theoretical massNumber of molelcules
Total (without water)158,2393
Polymers158,2393
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area13470 Å2
ΔGint-167 kcal/mol
Surface area40540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.623, 104.623, 160.974
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-608-

HOH

21A-803-

HOH

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Components

#1: Protein Ammonium transporter


Mass: 52746.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (strain SC5314 / ATCC MYA-2876) (yeast)
Gene: MEP2, orf19.5672, CAALFM_C400430WA / Production host: Saccharomyces cerevisiae S288c (yeast) / References: UniProt: Q59UP8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / Source method: isolated from a natural source / Formula: H2O

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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: 3.21 Å3/Da / Density % sol: 61.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 50 mM Tris pH 8 30% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M-F / 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: 1.65→26.8 Å / Num. obs: 77396 / % possible obs: 84.4 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 13.9
Reflection shellResolution: 1.65→1.69 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 2 / Num. unique obs: 5527 / % possible all: 80.1

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AF1

5af1


Resolution: 1.65→26.8 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 19.06
RfactorNum. reflection% reflection
Rfree0.194 1997 2.58 %
Rwork0.1783 --
obs0.1787 77385 97.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.65→26.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3481 0 0 318 3799
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133649
X-RAY DIFFRACTIONf_angle_d1.1194995
X-RAY DIFFRACTIONf_dihedral_angle_d2.6362744
X-RAY DIFFRACTIONf_chiral_restr0.077548
X-RAY DIFFRACTIONf_plane_restr0.008619
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6502-1.69150.24251400.26475337X-RAY DIFFRACTION97
1.6915-1.73720.2481470.2425492X-RAY DIFFRACTION99
1.7372-1.78830.24791390.23285408X-RAY DIFFRACTION99
1.7883-1.8460.24141430.21375416X-RAY DIFFRACTION98
1.846-1.9120.23951410.20295170X-RAY DIFFRACTION94
1.912-1.98850.20581470.1885486X-RAY DIFFRACTION100
1.9885-2.0790.21061440.195489X-RAY DIFFRACTION100
2.079-2.18860.20121460.17585513X-RAY DIFFRACTION100
2.1886-2.32560.1971410.17095449X-RAY DIFFRACTION99
2.3256-2.5050.19941440.17285409X-RAY DIFFRACTION98
2.505-2.75690.18591390.16355071X-RAY DIFFRACTION92
2.7569-3.15530.17351480.16365482X-RAY DIFFRACTION100
3.1553-3.97330.18761450.165455X-RAY DIFFRACTION99
3.9733-26.83250.17431330.17995211X-RAY DIFFRACTION94

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