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- PDB-5hwy: Structural mechanisms of extracellular ion exchange and induced b... -

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Basic information

Entry
Database: PDB / ID: 5hwy
TitleStructural mechanisms of extracellular ion exchange and induced binding-site occlusion in the sodium-calcium exchanger NCX_Mj soaked with 10 mM Na+ and zero Ca2+
ComponentsUncharacterized membrane protein MJ0091
KeywordsMEMBRANE PROTEIN / Na+/Ca2+ exchange / Calcium signalling / membrane transporter / induced conformational change
Function / homology
Function and homology information


calcium, potassium:sodium antiporter activity / calcium ion transmembrane transport / calcium channel activity / intracellular calcium ion homeostasis / plasma membrane
Similarity search - Function
NCX, central ion-binding region / NCX, peripheral helical region / Sodium/potassium/calcium exchanger / NCX, central ion-binding domain superfamily / Sodium/calcium exchanger membrane region / Sodium/calcium exchanger protein / A middle domain of Talin 1 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Helix non-globular / Special ...NCX, central ion-binding region / NCX, peripheral helical region / Sodium/potassium/calcium exchanger / NCX, central ion-binding domain superfamily / Sodium/calcium exchanger membrane region / Sodium/calcium exchanger protein / A middle domain of Talin 1 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Helix non-globular / Special / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / PENTADECANE / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Uncharacterized membrane protein MJ0091
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.098 Å
AuthorsLiao, J. / Jiang, Y.X. / Faraldo-Gomez, J.D.
Citation
Journal: Nat.Struct.Mol.Biol. / Year: 2016
Title: Mechanism of extracellular ion exchange and binding-site occlusion in a sodium/calcium exchanger
Authors: Liao, J. / Marinelli, F. / Lee, C. / Huang, Y. / Faraldo-Gomez, J.D. / Jiang, Y.
#1: Journal: Science / Year: 2012
Title: Structural insight into the ion-exchange mechanism of the sodium/calcium exchanger
Authors: Liao, J. / Li, H. / Zeng, W. / Sauer, D.B. / Belmares, R. / Jiang, Y.
History
DepositionJan 29, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 1.2Nov 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 / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized membrane protein MJ0091
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,91521
Polymers32,0291
Non-polymers3,88620
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint31 kcal/mol
Surface area15960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.213, 71.966, 95.633
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Uncharacterized membrane protein MJ0091


Mass: 32029.131 Da / Num. of mol.: 1 / Fragment: UNP residues 1-300 / Mutation: L2V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (archaea)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
Gene: MJ0091 / Production host: Escherichia coli (E. coli) / References: UniProt: Q57556

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Non-polymers , 6 types, 56 molecules

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


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-MYS / PENTADECANE


Mass: 212.415 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C15H32
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.48 Å3/Da / Density % sol: 50.45 %
Crystal growTemperature: 298 K / Method: lipidic cubic phase / Details: PEG 400

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.098→50 Å / Num. obs: 19305 / % possible obs: 99.9 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.04 / Rrim(I) all: 0.101 / Χ2: 1.393 / Net I/av σ(I): 24.256 / Net I/σ(I): 10.1 / Num. measured all: 117734
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.1460.6989500.8190.3090.7650.927100
2.14-2.1860.5959430.8670.2620.6510.95100
2.18-2.2260.5499450.8610.2430.6020.983100
2.22-2.2660.4599400.9030.2020.5021.028100
2.26-2.3160.3979600.9160.1760.4350.993100
2.31-2.376.10.3259330.9390.1420.3551.05100
2.37-2.4260.3249510.9510.1420.3551.093100
2.42-2.4960.2849510.9650.1240.311.106100
2.49-2.5660.2439620.9680.1070.2661.293100
2.56-2.656.10.219420.9740.0910.2291.318100
2.65-2.746.10.1879670.9820.0810.2041.449100
2.74-2.856.20.1599570.9870.0690.1741.445100
2.85-2.986.20.1339550.990.0580.1451.51100
2.98-3.146.20.1179680.9920.050.1271.684100
3.14-3.336.30.0999760.9950.0420.1081.792100
3.33-3.596.30.0869670.9970.0370.0941.906100
3.59-3.956.30.0739710.9960.0310.0791.893100
3.95-4.526.20.0579900.9980.0240.0621.934100
4.52-5.76.10.0510060.9980.0220.0551.525100
5.7-505.70.04810710.9970.0210.0521.74898.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
SHARPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3V5U

3v5u


Resolution: 2.098→36.022 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2234 1540 8 %
Rwork0.188 17714 -
obs0.1908 19254 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.89 Å2 / Biso mean: 35.7621 Å2 / Biso min: 19.83 Å2
Refinement stepCycle: final / Resolution: 2.098→36.022 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2257 0 156 36 2449
Biso mean--55.59 41.2 -
Num. residues----300
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062455
X-RAY DIFFRACTIONf_angle_d0.9153279
X-RAY DIFFRACTIONf_chiral_restr0.034394
X-RAY DIFFRACTIONf_plane_restr0.005386
X-RAY DIFFRACTIONf_dihedral_angle_d10.282908
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0977-2.16540.23931330.19781537167098
2.1654-2.24280.26821370.194415691706100
2.2428-2.33250.251410.180816151756100
2.3325-2.43870.21851380.174315941732100
2.4387-2.56720.20391370.171615841721100
2.5672-2.7280.20291390.166215951734100
2.728-2.93850.23181390.171315991738100
2.9385-3.23410.2481400.188316121752100
3.2341-3.70170.21671410.187116261767100
3.7017-4.66210.19061440.181816521796100
4.6621-36.02720.24131510.21131731188299

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