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- PDB-5aex: Crystal structure of Saccharomyces cerevisiae Mep2 -

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Basic information

Entry
Database: PDB / ID: 5aex
TitleCrystal structure of Saccharomyces cerevisiae Mep2
ComponentsAMMONIUM TRANSPORTER MEP2
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


positive regulation of filamentous growth of a population of unicellular organisms / pseudohyphal growth / nitrogen utilization / ammonium transmembrane transport / ammonium channel activity / 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
PHOSPHATE ION / Ammonium transporter MEP2
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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 1.3Jan 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: AMMONIUM TRANSPORTER MEP2
B: AMMONIUM TRANSPORTER MEP2
C: AMMONIUM TRANSPORTER MEP2
D: AMMONIUM TRANSPORTER MEP2
E: AMMONIUM TRANSPORTER MEP2
F: AMMONIUM TRANSPORTER MEP2
H: AMMONIUM TRANSPORTER MEP2
I: AMMONIUM TRANSPORTER MEP2
J: AMMONIUM TRANSPORTER MEP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)489,25918
Polymers488,4049
Non-polymers8559
Water00
1
A: AMMONIUM TRANSPORTER MEP2
B: AMMONIUM TRANSPORTER MEP2
C: AMMONIUM TRANSPORTER MEP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,0866
Polymers162,8013
Non-polymers2853
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14760 Å2
ΔGint-195.6 kcal/mol
Surface area38460 Å2
MethodPISA
2
D: AMMONIUM TRANSPORTER MEP2
E: AMMONIUM TRANSPORTER MEP2
F: AMMONIUM TRANSPORTER MEP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,0866
Polymers162,8013
Non-polymers2853
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14690 Å2
ΔGint-194.5 kcal/mol
Surface area38270 Å2
MethodPISA
3
H: AMMONIUM TRANSPORTER MEP2
I: AMMONIUM TRANSPORTER MEP2
J: AMMONIUM TRANSPORTER MEP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,0866
Polymers162,8013
Non-polymers2853
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14530 Å2
ΔGint-195.1 kcal/mol
Surface area36500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.692, 232.350, 279.189
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
AMMONIUM TRANSPORTER MEP2 / MEP2


Mass: 54267.148 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: W303 DELTA PEP4 / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain (production host): W303 DELTA PEP4 / References: UniProt: P41948
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: PO4

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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: 3.5 Å3/Da / Density % sol: 65 % / Description: NONE
Crystal growpH: 6.5
Details: 0.1 M MES PH 6.0, 0.2 M AMMONIUM PHOSPHATE DIBASIC 30% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 3.2→49 Å / Num. obs: 111848 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 90.77 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.6
Reflection shellResolution: 3.2→3.25 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 2 / % 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 2B2J

2b2j


Resolution: 3.2→49.276 Å / SU ML: 0.33 / σ(F): 1.33 / Phase error: 24.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2409 2451 2.2 %
Rwork0.1894 --
obs0.1905 111734 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.55 Å2
Refinement stepCycle: LAST / Resolution: 3.2→49.276 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30531 0 45 0 30576
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01231432
X-RAY DIFFRACTIONf_angle_d1.15442855
X-RAY DIFFRACTIONf_dihedral_angle_d14.30810419
X-RAY DIFFRACTIONf_chiral_restr0.0514800
X-RAY DIFFRACTIONf_plane_restr0.0065281
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.26160.30471330.2546047X-RAY DIFFRACTION100
3.2616-3.32810.32821250.25045984X-RAY DIFFRACTION100
3.3281-3.40050.29951410.2396016X-RAY DIFFRACTION100
3.4005-3.47960.26751380.21625973X-RAY DIFFRACTION100
3.4796-3.56650.2731340.20566030X-RAY DIFFRACTION100
3.5665-3.66290.28311320.20185999X-RAY DIFFRACTION100
3.6629-3.77070.23711390.18886029X-RAY DIFFRACTION100
3.7707-3.89240.23571310.186005X-RAY DIFFRACTION100
3.8924-4.03140.26161370.17816073X-RAY DIFFRACTION100
4.0314-4.19270.21151370.16496021X-RAY DIFFRACTION100
4.1927-4.38340.22171360.16016055X-RAY DIFFRACTION100
4.3834-4.61440.20971350.15376049X-RAY DIFFRACTION100
4.6144-4.90330.21751370.16426095X-RAY DIFFRACTION100
4.9033-5.28140.22561360.16776080X-RAY DIFFRACTION100
5.2814-5.81220.22751400.18336136X-RAY DIFFRACTION100
5.8122-6.65150.26041380.19276124X-RAY DIFFRACTION100
6.6515-8.37350.19911380.18446188X-RAY DIFFRACTION100
8.3735-49.28220.26161440.22016379X-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)
11.78080.2771-0.16981.8207-0.11692.2261-0.0433-0.0244-0.00450.11690.022-0.26420.08810.31380.03210.48580.0133-0.0730.62660.01580.5819-29.272-29.515150.4019
21.868-0.43860.08172.3251-0.30441.2325-0.0214-0.0801-0.194-0.02590.27310.64050.1477-0.4342-0.22440.5283-0.0723-0.06410.6590.13010.7596-60.6725-40.743952.411
31.7308-0.0287-0.52192.4065-0.06731.1567-0.02890.4267-0.3081-0.90450.02370.38360.4713-0.0512-0.01460.9222-0.0759-0.14390.7372-0.05880.6635-41.6789-48.973826.2288
41.7226-0.3313-0.03452.0611-0.75742.0419-0.04480.20080.0442-0.1022-0.1815-0.7848-0.10330.31820.1790.4705-0.01260.01720.5860.03880.8453-7.9296-80.840477.9429
51.20840.25010.04612.2847-0.6392.01840.00830.3549-0.0667-0.83970.02940.08750.37040.031-0.020.75420.01520.02810.692-0.08270.6354-25.7852-100.008557.1382
61.20210.4382-0.18692.09250.06371.82180.01480.00680.0429-0.01050.08730.4479-0.2202-0.4004-0.07120.44850.06690.01360.57710.05630.6772-39.6291-88.487885.3237
72.05710.2766-0.5412.27750.65041.3274-0.3137-0.56410.06860.6070.2602-0.41640.20020.46150.05830.91010.2224-0.0821.0354-0.04180.6156-46.1102-118.0877-3.0804
81.63940.0772-0.72321.0541-0.54812.0801-0.37-0.6686-0.23290.70.08190.29240.1035-0.41370.21861.28980.30020.28411.25320.07510.7818-77.1287-120.98718.9014
91.9039-0.2972-0.19561.3533-0.5051.8204-0.4307-0.6385-0.82380.54440.1773-0.04560.8790.02870.13221.47830.24250.34141.03560.37251.2157-58.914-147.93042.4871
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 2 THROUGH 457)
2X-RAY DIFFRACTION2(CHAIN B AND RESID 2 THROUGH 457)
3X-RAY DIFFRACTION3(CHAIN C AND RESID 2 THROUGH 457)
4X-RAY DIFFRACTION4(CHAIN D AND RESID 3 THROUGH 457)
5X-RAY DIFFRACTION5(CHAIN E AND RESID 2 THROUGH 457)
6X-RAY DIFFRACTION6(CHAIN F AND RESID 2 THROUGH 457)
7X-RAY DIFFRACTION7(CHAIN H AND RESID 2 THROUGH 456)
8X-RAY DIFFRACTION8(CHAIN I AND RESID 3 THROUGH 454)
9X-RAY DIFFRACTION9(CHAIN J AND RESID 2 THROUGH 454)

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