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- PDB-6yt4: Crystal structure of the N112A mutant of the light-driven sodium ... -

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Basic information

Entry
Database: PDB / ID: 6yt4
TitleCrystal structure of the N112A mutant of the light-driven sodium pump KR2 in the pentameric form, pH 8.0
ComponentsSodium pumping rhodopsin
KeywordsMEMBRANE PROTEIN / rhodopsin / retinal / ion transport / sodium pump / mutant
Function / homologyBacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / membrane / EICOSANE / OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / RETINAL / Sodium pumping rhodopsin
Function and homology information
Biological speciesDokdonia eikasta (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKovalev, K. / Maliar, N. / Astashkin, R. / Gordeliy, V.
Funding support Russian Federation, 3items
OrganizationGrant numberCountry
Russian Foundation for Basic Research17-00-00164 Russian Federation
Russian Foundation for Basic Research17-00-00165 Russian Federation
Russian Foundation for Basic Research17-00-00167 Russian Federation
CitationJournal: Crystals / Year: 2020
Title: Crystal Structure of the N112A Mutant of the Light-Driven Sodium Pump KR2
Authors: Maliar, N. / Kovalev, K. / Baeken, C. / Balandin, T. / Astashkin, R. / Rulev, M. / Alekseev, A. / Ilyinsky, N. / Rogachev, A. / Chupin, V. / Dolgikh, D. / Kirpichnikov, M. / Gordeliy, V.
History
DepositionApr 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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

Downloads & links

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Assembly

Deposited unit
A: Sodium pumping rhodopsin
B: Sodium pumping rhodopsin
D: Sodium pumping rhodopsin
E: Sodium pumping rhodopsin
C: Sodium pumping rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,05569
Polymers162,8435
Non-polymers17,21264
Water5,152286
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area43030 Å2
ΔGint-10 kcal/mol
Surface area40370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.840, 239.700, 134.580
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
22D
13A
23E
14A
24C
15B
25D
16B
26E
17B
27C
18D
28E
19D
29C
110E
210C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSAA3 - 2713 - 271
21LYSLYSBB3 - 2713 - 271
12SERSERAA3 - 2703 - 270
22SERSERDC3 - 2703 - 270
13SERSERAA3 - 2703 - 270
23SERSERED3 - 2703 - 270
14LEULEUAA3 - 2693 - 269
24LEULEUCE3 - 2693 - 269
15SERSERBB3 - 2703 - 270
25SERSERDC3 - 2703 - 270
16SERSERBB3 - 2703 - 270
26SERSERED3 - 2703 - 270
17LEULEUBB3 - 2693 - 269
27LEULEUCE3 - 2693 - 269
18LYSLYSDC3 - 2713 - 271
28LYSLYSED3 - 2713 - 271
19LEULEUDC3 - 2693 - 269
29LEULEUCE3 - 2693 - 269
110LEULEUED3 - 2693 - 269
210LEULEUCE3 - 2693 - 269

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10

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Components

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Protein / Sugars , 2 types, 10 molecules ABDEC

#1: Protein
Sodium pumping rhodopsin


Mass: 32568.557 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dokdonia eikasta (bacteria) / Gene: NaR / Production host: Escherichia coli (E. coli) / References: UniProt: N0DKS8
#5: Sugar
ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 6 types, 345 molecules

#2: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H40O4
#3: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C18H34O2
#4: Chemical...
ChemComp-LFA / EICOSANE / LIPID FRAGMENT


Mass: 282.547 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C20H42
#6: Chemical
ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C20H28O
#7: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.22 Å3/Da / Density % sol: 61.74 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 8 / Details: 1.2 M NaMal pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9999 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.4→47.85 Å / Num. obs: 77168 / % possible obs: 94 % / Redundancy: 40.7 % / CC1/2: 0.943 / Rmerge(I) obs: 0.216 / Rpim(I) all: 0.035 / Net I/σ(I): 19.6
Reflection shellResolution: 2.4→2.455 Å / Redundancy: 40.2 % / Rmerge(I) obs: 2.734 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3858 / CC1/2: 0.821 / Rpim(I) all: 0.436

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YC3

6yc3


Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.944 / SU B: 7.81 / SU ML: 0.171 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.315 / ESU R Free: 0.218
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2168 3767 4.9 %RANDOM
Rwork0.1864 ---
obs0.1879 73219 93.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 146.44 Å2 / Biso mean: 42.133 Å2 / Biso min: 19.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å20 Å20 Å2
2---1.39 Å20 Å2
3---0.45 Å2
Refinement stepCycle: final / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10796 0 683 286 11765
Biso mean--73.25 43.79 -
Num. residues----1349
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01311825
X-RAY DIFFRACTIONr_bond_other_d00.01711461
X-RAY DIFFRACTIONr_angle_refined_deg1.041.64515874
X-RAY DIFFRACTIONr_angle_other_deg1.0841.57626458
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.85551364
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.91322.239527
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.19151746
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0631525
X-RAY DIFFRACTIONr_chiral_restr0.0370.21463
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212666
X-RAY DIFFRACTIONr_gen_planes_other00.022617
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A99010.04
12B99010.04
21A99260.03
22D99260.03
31A98920.04
32E98920.04
41A98490.03
42C98490.03
51B98940.04
52D98940.04
61B98810.05
62E98810.05
71B98210.04
72C98210.04
81D99350.03
82E99350.03
91D98830.03
92C98830.03
101E98380.04
102C98380.04
LS refinement shellResolution: 2.4→2.461 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 196 -
Rwork0.273 4057 -
all-4253 -
obs--72 %

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