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- PDB-4nh2: Crystal structure of AmtB from E. coli bound to phosphatidylglycerol -

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Basic information

Entry
Database: PDB / ID: 4nh2
TitleCrystal structure of AmtB from E. coli bound to phosphatidylglycerol
ComponentsAmmonia channel
KeywordsMEMBRANE PROTEIN / protein lipid / ammonia/ammonium channel
Function / homology
Function and homology information


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
Chem-P6L / Ammonium transporter
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLaganowsky, A. / Reading, E. / Allison, T.M. / Robinson, C.V.
CitationJournal: Nature / Year: 2014
Title: Membrane proteins bind lipids selectively to modulate their structure and function.
Authors: Laganowsky, A. / Reading, E. / Allison, T.M. / Ulmschneider, M.B. / Degiacomi, M.T. / Baldwin, A.J. / Robinson, C.V.
History
DepositionNov 4, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references / Source and taxonomy
Revision 1.2Nov 20, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: Ammonia channel
B: Ammonia channel
C: Ammonia channel
D: Ammonia channel
E: Ammonia channel
F: Ammonia channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)259,79714
Polymers253,8216
Non-polymers5,9768
Water2,000111
1
A: Ammonia channel
D: Ammonia channel
F: Ammonia channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,8987
Polymers126,9103
Non-polymers2,9884
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11710 Å2
ΔGint-157 kcal/mol
Surface area34830 Å2
MethodPISA
2
B: Ammonia channel
C: Ammonia channel
E: Ammonia channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,8987
Polymers126,9103
Non-polymers2,9884
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12570 Å2
ΔGint-162 kcal/mol
Surface area34850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.190, 201.190, 232.450
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 1 - 385 / Label seq-ID: 1 - 385

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14AA
24EE
15AA
25FF
16BB
26CC
17BB
27DD
18BB
28EE
19BB
29FF
110CC
210DD
111CC
211EE
112CC
212FF
113DD
213EE
114DD
214FF
115EE
215FF

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Ammonia channel / Ammonia transporter


Mass: 42303.473 Da / Num. of mol.: 6 / Fragment: UNP RESIDUES 26-428
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: BL21(DE3) / Gene: AMTB / Plasmid: pET15 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A140NCU4*PLUS
#2: Chemical
ChemComp-P6L / (2S)-3-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-2-[(6E)-HEXADEC-6-ENOYLOXY]PROPYL (8E)-OCTADEC-8-ENOATE


Mass: 746.991 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C40H75O10P / Comment: phospholipid*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.68 Å3/Da / Density % sol: 54.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 15% PEG 4000, 0.8M potassium formate, 0.1M sodium acetate pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.432
11-1/2H+1/2K, 3/2H+1/2K, -L20.287
11-1/2H-1/2K, -3/2H+1/2K, -L30.281
ReflectionResolution: 2.3→40 Å / Num. obs: 119767 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -3 / Biso Wilson estimate: 40.041 Å2 / Rmerge(I) obs: 0.124 / Net I/σ(I): 13.66
Reflection shell

Diffraction-ID: 1

Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.3-2.360.9071.2042.4859395888085491.20496.3
2.36-2.420.9360.0112.964394866384231.02597.2
2.42-2.490.9480.0113.666609832982130.80498.6
2.49-2.570.9640.0114.4967643814181020.60999.5
2.57-2.660.9810.0115.5773949788778750.47199.8
2.66-2.750.9840.0116.7682684764076400.394100
2.75-2.850.9910.0118.2583535740274010.304100
2.85-2.970.990.0119.9884950706670650.259100
2.97-3.10.9960.01112.6589822687568730.19100
3.1-3.250.9960.01114.4886030653465330.168100
3.25-3.430.9970.01117.3681205619261920.131100
3.43-3.640.9980.01120.6981443594259410.114100
3.64-3.890.9980.01123.4270575554755440.09699.9
3.89-4.20.9980.01127.869583516451630.086100
4.2-4.60.9980.01129.4560880476347630.078100
4.6-5.140.9990.01130.5555180433443330.078100
5.14-5.940.9980.01127.1948797385138510.084100
5.94-7.270.9990.01129.5143330330233020.073100
7.27-10.290.9990.01133.2231533255025490.057100
10.29-38.740.9990.01135.9516765148714550.05597.8

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
GDAdata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1U7G

1u7g


Resolution: 2.3→38.74 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.2254 / WRfactor Rwork: 0.1922 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.6937 / SU B: 6.834 / SU ML: 0.166 / SU R Cruickshank DPI: 0.0578 / SU Rfree: 0.0439 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2338 5951 5 %RANDOM
Rwork0.2017 ---
obs0.2033 119766 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 139.57 Å2 / Biso mean: 45.5591 Å2 / Biso min: 13.26 Å2
Baniso -1Baniso -2Baniso -3
1--32.35 Å2-0 Å2-0 Å2
2---37.46 Å2-0 Å2
3---69.81 Å2
Refinement stepCycle: LAST / Resolution: 2.3→38.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15856 0 293 111 16260
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01916497
X-RAY DIFFRACTIONr_bond_other_d0.0080.0216234
X-RAY DIFFRACTIONr_angle_refined_deg1.671.95422459
X-RAY DIFFRACTIONr_angle_other_deg1.313336963
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.08952181
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.82423.23483
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.931152278
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5541523
X-RAY DIFFRACTIONr_chiral_restr0.0950.22708
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0218579
X-RAY DIFFRACTIONr_gen_planes_other0.0070.023816
X-RAY DIFFRACTIONr_mcbond_it4.3464.3958778
X-RAY DIFFRACTIONr_mcbond_other4.3464.3958777
X-RAY DIFFRACTIONr_mcangle_it6.1216.57110941
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A207980.08
12B207980.08
21A210250.07
22C210250.07
31A207470.08
32D207470.08
41A208250.08
42E208250.08
51A208980.07
52F208980.07
61B211880.08
62C211880.08
71B211880.07
72D211880.07
81B211470.07
82E211470.07
91B213160.07
92F213160.07
101C212570.07
102D212570.07
111C212630.08
112E212630.08
121C213700.07
122F213700.07
131D210330.08
132E210330.08
141D211860.07
142F211860.07
151E209650.08
152F209650.08
LS refinement shellResolution: 2.299→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 417 -
Rwork0.341 7971 -
all-8388 -
obs--95.13 %

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