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- PDB-6b21: Crystal structure of AmtB from E. coli bound to TopFluor cardiolipin -

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Basic information

Entry
Database: PDB / ID: 6b21
TitleCrystal structure of AmtB from E. coli bound to TopFluor cardiolipin
ComponentsAmmonia channel
KeywordsMEMBRANE PROTEIN / ammonia channel / AmtB / cardiolipin / transporter
Function / homology
Function and homology information


ammonium transmembrane transport / ammonium channel activity / carbon dioxide transport / identical protein binding / 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-C9V / Ammonium transporter AmtB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.45 Å
AuthorsBoone, C.D. / Laganowsky, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)DP2GM123486 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Allostery revealed within lipid binding events to membrane proteins.
Authors: Patrick, J.W. / Boone, C.D. / Liu, W. / Conover, G.M. / Liu, Y. / Cong, X. / Laganowsky, A.
History
DepositionSep 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2018Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression
Revision 1.2Mar 21, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Mar 28, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ammonia channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8552
Polymers42,3031
Non-polymers1,5521
Water1,38777
1
A: Ammonia channel
hetero molecules

A: Ammonia channel
hetero molecules

A: Ammonia channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,5666
Polymers126,9103
Non-polymers4,6553
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 area10160 Å2
ΔGint-141 kcal/mol
Surface area34050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.780, 138.780, 159.140
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Ammonia channel / Ammonia transporter


Mass: 42303.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: amtB, ybaG, b0451, JW0441 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: P69681
#2: Chemical ChemComp-C9V / [(2R,5R,11R,14S,24E)-14-[(acetyloxy)methyl]-8-{[5-(3,5-dimethyl-1H-pyrrol-2-yl-kappaN)-5-(3,5-dimethyl-2H-pyrrol-2-ylidene-kappaN)pentanoyl]oxy}-5,11-dihydroxy-2-{[(9E)-octadec-9-enoyl]oxy}-5,11,16-trioxo-4,6,10,12,15-pentaoxa-5lambda~5~,11lambda~5~-diphosphatritriacont-24-en-1-yl (9E)-octadec-9-enoatato](difluoro)boron


Mass: 1551.739 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C82H139BF2N2O18P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 3.49 Å3/Da / Density % sol: 64.72 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris, pH 8.0 0.3M Mg-nitrate 22% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.45→56.219 Å / Num. obs: 21583 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 4.547 % / Biso Wilson estimate: 48.47 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rrim(I) all: 0.073 / Χ2: 1.048 / Net I/σ(I): 14.72
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.45-2.514.1680.492.8515900.890.55998.9
2.51-2.584.5560.4183.4115300.9210.47199.1
2.58-2.664.780.3654.0315180.9410.4199.7
2.66-2.744.7750.3264.5714630.9590.36699.9
2.74-2.834.7540.2635.6614490.9730.29599.5
2.83-2.934.650.2176.5913490.9760.24599.5
2.93-3.044.6410.1678.4213390.9860.18899.6
3.04-3.164.7160.13610.2312870.990.15299.5
3.16-3.34.6070.11112.0312270.9920.12599.4
3.3-3.464.4860.08814.911590.9940.09998.9
3.46-3.654.0740.06817.5811140.9950.07897.7
3.65-3.874.2850.05620.6310350.9970.06498.1
3.87-4.144.7460.04826.629990.9980.05498.8
4.14-4.474.2240.04129.239310.9980.04798.6
4.47-4.94.6550.03832.928440.9980.04397.9
4.9-5.484.6840.04131.67720.9980.04697.8
5.48-6.334.5480.03930.416950.9980.04497.7
6.33-7.754.1310.03134.175650.9990.03695
7.75-10.964.7680.02147.034570.9990.02496.4
10.96-56.2194.3310.01948.9426010.02293.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U7G

1u7g


Resolution: 2.45→56.219 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.04
RfactorNum. reflection% reflectionSelection details
Rfree0.2125 1079 5.01 %Random Selection
Rwork0.1699 ---
obs0.1719 21556 98.63 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 239.47 Å2 / Biso mean: 61.6964 Å2 / Biso min: 27.83 Å2
Refinement stepCycle: final / Resolution: 2.45→56.219 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2648 0 107 77 2832
Biso mean--95.4 64.57 -
Num. residues----369
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022817
X-RAY DIFFRACTIONf_angle_d0.6183834
X-RAY DIFFRACTIONf_chiral_restr0.02452
X-RAY DIFFRACTIONf_plane_restr0.003460
X-RAY DIFFRACTIONf_dihedral_angle_d18.294923
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4501-2.56160.26551340.22062532266699
2.5616-2.69660.22461340.193325522686100
2.6966-2.86560.20851340.17612538267299
2.8656-3.08680.22121350.16352580271599
3.0868-3.39740.21371350.16762556269199
3.3974-3.88890.20951340.16562546268098
3.8889-4.89920.18031350.15522565270098
4.8992-56.23360.23341380.17522608274696
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)
10.5730.1562-0.24630.3852-0.11830.1078-0.0922-0.02690.0868-0.0127-0.1073-0.1447-0.1815-0.0413-00.4066-0.01130.01090.35420.03220.36687.86259.981351.584
20.5037-0.3333-0.3441.0299-0.22470.4564-0.0406-0.04840.1056-0.0004-0.0545-0.1176-0.12430.0133-00.4441-0.03910.01650.38070.01690.470610.129321.296756.0514
30.26580.17890.04120.51460.30980.1842-0.041-0.00540.1523-0.0441-0.00020.0992-0.13970.00200.41040.0272-0.02890.3940.04090.4231-10.960615.424150.3704
40.55810.34760.12210.3543-0.03610.11990.1213-0.11090.18730.03140.0521-0.0446-0.35670.33310.00030.63450.014-0.00010.4810.10060.6092-9.317226.576456.5198
50.4571-0.2637-0.07840.1951-0.06740.31560.2998-0.23320.4512-0.1639-0.0291-0.0343-0.77740.37790.00690.6859-0.03680.08390.42630.08320.47446.552632.281250.4061
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 61 )A1 - 61
2X-RAY DIFFRACTION2chain 'A' and (resid 62 through 197 )A62 - 197
3X-RAY DIFFRACTION3chain 'A' and (resid 198 through 301 )A198 - 301
4X-RAY DIFFRACTION4chain 'A' and (resid 302 through 347 )A302 - 347
5X-RAY DIFFRACTION5chain 'A' and (resid 348 through 385 )A348 - 385

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