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- PDB-5nc8: Shewanella denitrificans Kef CTD in AMP bound form -

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Basic information

Entry
Database: PDB / ID: 5nc8
TitleShewanella denitrificans Kef CTD in AMP bound form
ComponentsPotassium efflux system protein
KeywordsTRANSPORT PROTEIN / KTN/RCK domain / Kef / AMP / Potassium efflux
Function / homology
Function and homology information


: / potassium ion transport / membrane => GO:0016020 / nucleotide binding
Similarity search - Function
K+/H+ exchanger / Sodium/solute symporter superfamily / Cation/H+ exchanger / Sodium/hydrogen exchanger family / Regulator of K+ conductance, N-terminal / TrkA-N domain / RCK N-terminal domain profile. / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold ...K+/H+ exchanger / Sodium/solute symporter superfamily / Cation/H+ exchanger / Sodium/hydrogen exchanger family / Regulator of K+ conductance, N-terminal / TrkA-N domain / RCK N-terminal domain profile. / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Potassium efflux system protein
Similarity search - Component
Biological speciesShewanella denitrificans OS217 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.09 Å
AuthorsPliotas, C. / Naismith, J.H.
CitationJournal: Biochemistry / Year: 2017
Title: Adenosine Monophosphate Binding Stabilizes the KTN Domain of the Shewanella denitrificans Kef Potassium Efflux System.
Authors: Pliotas, C. / Grayer, S.C. / Ekkerman, S. / Chan, A.K.N. / Healy, J. / Marius, P. / Bartlett, W. / Khan, A. / Cortopassi, W.A. / Chandler, S.A. / Rasmussen, T. / Benesch, J.L.P. / Paton, R.S. ...Authors: Pliotas, C. / Grayer, S.C. / Ekkerman, S. / Chan, A.K.N. / Healy, J. / Marius, P. / Bartlett, W. / Khan, A. / Cortopassi, W.A. / Chandler, S.A. / Rasmussen, T. / Benesch, J.L.P. / Paton, R.S. / Claridge, T.D.W. / Miller, S. / Booth, I.R. / Naismith, J.H. / Conway, S.J.
History
DepositionMar 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: 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 / struct_ncs_dom_lim
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Potassium efflux system protein
B: Potassium efflux system protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5844
Polymers52,8902
Non-polymers6942
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint-38 kcal/mol
Surface area15200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.600, 71.600, 140.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: TRP / End label comp-ID: TRP / Refine code: 0 / Auth seq-ID: 407 - 569 / Label seq-ID: 28 - 190

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Potassium efflux system protein


Mass: 26444.777 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella denitrificans OS217 (bacteria)
Gene: Sden_0368 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q12SB3
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM

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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

Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.2M sodium malonate pH7.0 20% w/v PEG 3350 / PH range: 7.0-7.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 3.09→47.62 Å / Num. obs: 6976 / % possible obs: 97.6 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 15.3
Reflection shellResolution: 3.09→3.17 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.651 / Num. unique obs: 425 / % possible all: 85.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
xia2data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EYW containing residues 410 - 570 (omitting all water molecules and ligands with non-conserved residues set to alanine)

3eyw


Resolution: 3.09→29.15 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.867 / SU B: 46.579 / SU ML: 0.386 / Cross valid method: THROUGHOUT / ESU R Free: 0.505 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26042 318 4.6 %RANDOM
Rwork0.2029 ---
obs0.20536 6658 97.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 93.541 Å2
Baniso -1Baniso -2Baniso -3
1-4.51 Å20 Å20 Å2
2--4.51 Å2-0 Å2
3----9.03 Å2
Refinement stepCycle: 1 / Resolution: 3.09→29.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2448 0 46 0 2494
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192540
X-RAY DIFFRACTIONr_bond_other_d0.0040.022451
X-RAY DIFFRACTIONr_angle_refined_deg1.5581.9763444
X-RAY DIFFRACTIONr_angle_other_deg0.97135597
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0025313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.6923.621116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.44615415
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7881518
X-RAY DIFFRACTIONr_chiral_restr0.1590.2393
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022871
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02605
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 9002 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.09→3.17 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 21 -
Rwork0.298 399 -
obs--84.51 %
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)
11.58414.953-2.687816.9774-10.28628.18990.3931-0.7870.03320.1089-1.34940.21640.67740.14030.95630.4193-0.58620.1381.03530.0910.84364.030220.696615.6275
22.4651-4.18681.26729.94080.60244.1159-0.2433-0.6135-0.18680.71970.9008-0.24770.2950.3987-0.65750.1870.0388-0.03680.98510.09380.38865.122319.943720.7729
37.4661-1.06222.49867.1207-0.83018.50680.0117-0.5509-0.63980.4927-0.16960.1770.6701-0.39670.15790.1029-0.03140.0780.07390.11670.47592.664611.017214.4346
47.20280.49791.032119.8081-2.99968.1256-0.2466-0.1916-0.44020.5777-0.3520.50630.7234-0.55880.59860.1458-0.1160.05280.18260.00320.4288-6.5159.30979.4255
52.17971.8295-0.697410.9495-1.84240.5657-0.15320.28620.0502-0.6170.14830.1582-0.0861-0.16190.00490.28120.0646-0.08150.096-0.02120.26412.289129.7711-0.4734
62.55615.2306-0.095518.85366.25825.6085-0.13270.03540.2433-0.39450.32210.2967-0.3069-0.0255-0.18940.22950.0231-0.03190.27020.02430.3235-4.17735.8909-3.8927
716.44561.16890.39621.4852.674516.94350.32830.8183-0.63790.1031-0.6476-0.2163-0.1416-0.31650.31920.16410.0660.00030.3655-0.06630.2874-9.10719.9099-11.5418
89.23444.597-2.292310.31980.88772.0378-0.07330.73490.2808-1.02210.0599-0.1531-0.4205-0.03680.01340.2898-0.0301-0.03260.1350.03060.240512.87336.6289-6.8346
915.1011-6.02170.36524.46921.90237.60440.26730.6223-0.2044-0.805-0.2804-0.07720.04760.34180.0130.3968-0.01650.01080.17390.07490.250711.807937.3061-10.9574
106.1482-5.51693.18510.4119-2.88941.8846-0.0830.02550.5489-1.0142-0.1694-0.2054-0.3665-0.11380.25240.8118-0.06030.13940.6364-0.04230.519523.050137.6069-12.841
116.96582.358-0.3857.8021-2.788110.8915-0.32770.24270.123-0.46360.2116-0.6027-0.29110.52490.11610.0663-0.06130.0920.0677-0.0920.334521.690240.35332.1764
1210.50464.1016-2.2434.1767-1.8981.1510.01120.467-0.2277-0.0635-0.02180.1154-0.0652-0.27970.01060.06380.086-0.05260.2953-0.09850.2966-0.163830.73111.2099
1314.39223.4046-0.35541.8049-1.86883.68720.4455-0.38350.42940.0759-0.28880.1507-0.10940.07-0.15660.21310.07840.00090.2426-0.06350.34773.179337.423817.63
143.64184.96192.499910.02521.46292.8772-0.35880.3334-0.4509-0.76220.8668-0.2905-0.04440.0106-0.5080.40680.07430.03280.39840.01760.316321.43737.258220.6688
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A407 - 421
2X-RAY DIFFRACTION2A422 - 443
3X-RAY DIFFRACTION3A444 - 488
4X-RAY DIFFRACTION4A489 - 501
5X-RAY DIFFRACTION5A502 - 546
6X-RAY DIFFRACTION6A547 - 563
7X-RAY DIFFRACTION7A564 - 569
8X-RAY DIFFRACTION8B407 - 421
9X-RAY DIFFRACTION9B422 - 441
10X-RAY DIFFRACTION10B442 - 464
11X-RAY DIFFRACTION11B465 - 518
12X-RAY DIFFRACTION12B519 - 546
13X-RAY DIFFRACTION13B547 - 564
14X-RAY DIFFRACTION14B565 - 570

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