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- PDB-5af1: Crystal structure of Candida albicans Mep2 -

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Basic information

Entry
Database: PDB / ID: 5af1
TitleCrystal structure of Candida albicans Mep2
ComponentsMEP2
KeywordsTRANSPORT PROTEIN / MEMBRANE 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: 1.639 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 14, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references / Other
Revision 1.2May 11, 2016Group: Database references / Other
Revision 1.3Oct 24, 2018Group: Advisory / Data collection / Source and taxonomy / Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id
Revision 1.4Jan 10, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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

Downloads & links

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Assembly

Deposited unit
A: MEP2
B: MEP2


Theoretical massNumber of molelcules
Total (without water)98,0672
Polymers98,0672
Non-polymers00
Water9,656536
1
A: MEP2

A: MEP2

A: MEP2


Theoretical massNumber of molelcules
Total (without water)147,1003
Polymers147,1003
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-y+1,x-y-1,z1
crystal symmetry operation3_765-x+y+2,-x+1,z1
Buried area13470 Å2
ΔGint-165.6 kcal/mol
Surface area39690 Å2
MethodPISA
2
B: MEP2

B: MEP2

B: MEP2


Theoretical massNumber of molelcules
Total (without water)147,1003
Polymers147,1003
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_775-x+y+2,-x+2,z1
crystal symmetry operation2_755-y+2,x-y,z1
Buried area13370 Å2
ΔGint-165.1 kcal/mol
Surface area39300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.151, 100.151, 109.990
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11A-2042-

HOH

21B-2050-

HOH

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Components

#1: Protein MEP2


Mass: 49033.496 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CANDIDA ALBICANS (yeast) / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain (production host): DELTA PEP4 / References: UniProt: Q59UP8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 536 / 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: 3.2 Å3/Da / Density % sol: 61 % / Description: NONE
Crystal growpH: 6 / Details: 0.1 M MES PH 6 0.2 M LITHIUM SULPHATE 20% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9796
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.64→29.6 Å / Num. obs: 151150 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 22.9 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 20
Reflection shellResolution: 1.64→1.68 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2 / % possible all: 97

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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: 1.639→29.582 Å / SU ML: 0.14 / σ(F): 1.97 / Phase error: 16.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1591 1997 1.3 %
Rwork0.1364 --
obs0.1367 151123 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.4 Å2
Refinement stepCycle: LAST / Resolution: 1.639→29.582 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6904 0 0 536 7440
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077152
X-RAY DIFFRACTIONf_angle_d1.0099769
X-RAY DIFFRACTIONf_dihedral_angle_d11.5052384
X-RAY DIFFRACTIONf_chiral_restr0.0431063
X-RAY DIFFRACTIONf_plane_restr0.0051213
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6389-1.67990.23911410.229910338X-RAY DIFFRACTION97
1.6799-1.72530.221420.202310715X-RAY DIFFRACTION100
1.7253-1.77610.22831420.182710607X-RAY DIFFRACTION100
1.7761-1.83340.20151440.16910735X-RAY DIFFRACTION100
1.8334-1.89890.16071460.154810666X-RAY DIFFRACTION100
1.8989-1.9750.15211400.150410673X-RAY DIFFRACTION100
1.975-2.06480.17381440.139110687X-RAY DIFFRACTION100
2.0648-2.17360.13921450.13110672X-RAY DIFFRACTION100
2.1736-2.30980.17151360.128610646X-RAY DIFFRACTION100
2.3098-2.4880.14811480.128310675X-RAY DIFFRACTION100
2.488-2.73830.1341380.126110693X-RAY DIFFRACTION100
2.7383-3.13410.16231440.128910686X-RAY DIFFRACTION100
3.1341-3.94720.15781500.126710679X-RAY DIFFRACTION100
3.9472-29.58680.15141370.132810654X-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)
11.23830.11550.09330.9681-0.10150.9584-0.022-0.13920.09980.1218-0.0476-0.099-0.13120.18320.07930.1721-0.0174-0.0260.1344-0.01930.1759108.552711.1288-33.6839
26.0123-4.16330.70315.9277-0.50120.9432-0.4227-0.83370.51540.69130.4206-0.5217-0.4730.1869-0.06270.4149-0.0543-0.09430.3156-0.06340.2834115.075724.7241-26.7889
31.59670.13420.62281.4155-0.27453.0379-0.0868-0.20820.19360.2508-0.0492-0.1302-0.45010.11290.14730.2344-0.0252-0.05720.1538-0.03060.1909108.411315.5629-29.1941
41.88320.3059-0.15311.5146-0.56810.4725-0.0212-0.18750.27110.1817-0.0593-0.0468-0.2540.12720.06990.325-0.035-0.06370.17-0.01410.2615106.974825.3485-37.5938
51.71291.1524-0.56633.1588-0.69911.5242-0.08070.21860.2267-0.24160.03870.0904-0.3485-0.00830.07210.28940.0323-0.05410.16170.0260.259997.608125.2076-54.5244
60.86670.08950.00330.9445-0.09661.0577-0.0419-0.05120.23530.0552-0.02360.1301-0.3354-0.15820.03990.23790.0446-0.0290.1464-0.03350.223890.092720.5673-38.7461
70.8429-0.4859-0.26332.64620.26243.71920.10280.28420.1143-1.0906-0.017-0.5112-0.23930.2398-0.05830.5413-0.04020.06960.40810.0990.3637116.109118.6059-64.5249
80.7888-0.10990.02570.96390.30791.49260.02320.0027-0.0535-0.0125-0.00620.1980.0825-0.27770.00390.1511-0.0195-0.00890.18770.01880.228783.919551.317923.1947
91.2874-0.14330.14551.32730.27011.2210.02280.0082-0.1593-0.0149-0.07010.22120.1669-0.2515-0.02040.2248-0.0749-0.03750.2542-0.01150.298279.943741.004916.9236
102.14160.0225-0.50941.17030.39272.03410.01810.3305-0.2604-0.40250.00250.16490.2529-0.20110.01040.4075-0.0491-0.07450.2698-0.07110.285387.537735.52750.0448
110.7499-0.03430.0480.82270.13481.10620.02730.0889-0.2438-0.10490.00980.04380.3666-0.0629-0.04220.2653-0.0208-0.02770.1371-0.02460.240496.393935.247415.6497
121.03380.8552-0.56112.8526-0.19782.22680.03130.49880.0181-0.85250.16750.40040.086-0.2891-0.16830.5555-0.0303-0.180.6289-0.01940.393376.598551.6517-9.9276
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 4 THROUGH 78 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 79 THROUGH 101 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 102 THROUGH 137 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 138 THROUGH 183 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 184 THROUGH 221 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 222 THROUGH 408 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 409 THROUGH 453 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 3 THROUGH 137 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 138 THROUGH 183 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 184 THROUGH 221 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 222 THROUGH 408 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 409 THROUGH 453 )

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