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- PDB-3v5u: Structure of Sodium/Calcium Exchanger from Methanocaldococcus jan... -

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Basic information

Entry
Database: PDB / ID: 3v5u
TitleStructure of Sodium/Calcium Exchanger from Methanocaldococcus jannaschii DSM 2661
ComponentsUncharacterized membrane protein MJ0091
KeywordsMETAL TRANSPORT / lipid cubic phase / cation protein complex / sodium / calcium exchanger / Membrane protein / Alpha Helical / superfamily of cation / cation binding / membrane
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 / Sodium/calcium exchanger membrane region / NCX, central ion-binding domain superfamily / 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 / Sodium/calcium exchanger membrane region / NCX, central ion-binding domain superfamily / 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 / MAD / Resolution: 1.9 Å
AuthorsJiang, Y. / Liao, J. / Li, H. / Zeng, W. / Sauer, D. / Belmares, R.
CitationJournal: 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
DepositionDec 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.pdbx_dist_value / _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_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_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Uncharacterized membrane protein MJ0091
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,55925
Polymers34,2411
Non-polymers4,31824
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.490, 72.879, 96.206
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 34240.574 Da / Num. of mol.: 1 / Mutation: L2V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Strain: DSM 2661 / Gene: MJ0091 / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / References: UniProt: Q57556

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Non-polymers , 7 types, 123 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: 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
#6: Chemical
ChemComp-MYS / PENTADECANE


Mass: 212.415 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C15H32
#7: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


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


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.53 Å3/Da / Density % sol: 51.45 %
Crystal growTemperature: 293 K / Method: lipic cubic phase / pH: 6.5
Details: 42% (v/v) PEG400, 0.1-0.2 M NaAc, 0.1 M MES pH 6.5, lipic cubic phase, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 23-ID-B10.9793
SYNCHROTRONAPS 23-ID-B21.8458
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 18, 2011
RadiationProtocol: SIRAS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
21.84581
ReflectionResolution: 1.9→50 Å / Num. obs: 27923 / % possible obs: 98.9 %
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 8.9 % / Rsym value: 0.88 / % possible all: 97.8

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Processing

Software
NameVersionClassification
HKL-3000data collection
SHARPphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.9→37.673 Å / SU ML: 0.2 / σ(F): 0.13 / Phase error: 18.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2104 1900 7.16 %
Rwork0.1853 --
obs0.1871 26548 93.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80.526 Å2 / ksol: 0.327 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.1713 Å2-0 Å2-0 Å2
2---4.501 Å20 Å2
3----4.6703 Å2
Refinement stepCycle: LAST / Resolution: 1.9→37.673 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2218 0 262 99 2579
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082510
X-RAY DIFFRACTIONf_angle_d1.3753321
X-RAY DIFFRACTIONf_dihedral_angle_d9.761967
X-RAY DIFFRACTIONf_chiral_restr0.059388
X-RAY DIFFRACTIONf_plane_restr0.004384
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.96520.24541610.21382117X-RAY DIFFRACTION82
1.9652-2.04390.23121790.18222282X-RAY DIFFRACTION89
2.0439-2.13690.19481780.16642347X-RAY DIFFRACTION90
2.1369-2.24950.20881850.1592410X-RAY DIFFRACTION93
2.2495-2.39050.22121910.15412460X-RAY DIFFRACTION95
2.3905-2.5750.18431950.15972510X-RAY DIFFRACTION96
2.575-2.83410.22171960.15912543X-RAY DIFFRACTION97
2.8341-3.2440.21022000.16982593X-RAY DIFFRACTION98
3.244-4.08630.20042030.17962634X-RAY DIFFRACTION99
4.0863-37.68010.20712120.21352752X-RAY DIFFRACTION99

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