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- PDB-3e9t: Crystal structure of Apo-form Calx CBD1 domain -

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Basic information

Entry
Database: PDB / ID: 3e9t
TitleCrystal structure of Apo-form Calx CBD1 domain
ComponentsNa/Ca exchange protein
KeywordsMEMBRANE PROTEIN / CBD1 / Calx / Membrane / Transmembrane
Function / homology
Function and homology information


rhabdomere membrane / calcium:sodium antiporter activity / neuromuscular process controlling posture / calcium ion import across plasma membrane / phototransduction / sodium ion transmembrane transport / response to endoplasmic reticulum stress / sarcolemma / calmodulin binding / postsynapse ...rhabdomere membrane / calcium:sodium antiporter activity / neuromuscular process controlling posture / calcium ion import across plasma membrane / phototransduction / sodium ion transmembrane transport / response to endoplasmic reticulum stress / sarcolemma / calmodulin binding / postsynapse / axon / calcium ion binding
Similarity search - Function
CalX-beta domain / Sodium/calcium exchanger protein / Sodium/calcium exchanger domain, C-terminal extension / : / C-terminal extension of sodium/calcium exchanger domain / Na-Ca exchanger/integrin-beta4 / Calx-beta domain / Domains in Na-Ca exchangers and integrin-beta4 / CalX-like domain superfamily / Sodium/calcium exchanger membrane region ...CalX-beta domain / Sodium/calcium exchanger protein / Sodium/calcium exchanger domain, C-terminal extension / : / C-terminal extension of sodium/calcium exchanger domain / Na-Ca exchanger/integrin-beta4 / Calx-beta domain / Domains in Na-Ca exchangers and integrin-beta4 / CalX-like domain superfamily / Sodium/calcium exchanger membrane region / NCX, central ion-binding domain superfamily / Sodium/calcium exchanger protein / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Sodium/calcium exchanger Calx / Sodium/calcium exchanger Calx
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsWu, M. / Zheng, L.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Crystal structures of progressive Ca2+ binding states of the Ca2+ sensor Ca2+ binding domain 1 (CBD1) from the CALX Na+/Ca2+ exchanger reveal incremental conformational transitions.
Authors: Wu, M. / Le, H.D. / Wang, M. / Yurkov, V. / Omelchenko, A. / Hnatowich, M. / Nix, J. / Hryshko, L.V. / Zheng, L.
History
DepositionAug 23, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 5, 2023Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
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 / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.pdbx_dist_value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 22, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Na/Ca exchange protein
B: Na/Ca exchange protein
C: Na/Ca exchange protein
D: Na/Ca exchange protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,45910
Polymers52,2184
Non-polymers2406
Water8,305461
1
A: Na/Ca exchange protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1353
Polymers13,0551
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Na/Ca exchange protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2155
Polymers13,0551
Non-polymers1604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Na/Ca exchange protein


Theoretical massNumber of molelcules
Total (without water)13,0551
Polymers13,0551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Na/Ca exchange protein


Theoretical massNumber of molelcules
Total (without water)13,0551
Polymers13,0551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.086, 76.429, 128.918
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Na/Ca exchange protein


Mass: 13054.530 Da / Num. of mol.: 4 / Fragment: Calx CBD1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Calx, NCX, CG5685 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Bl-21 / References: UniProt: Q24413, UniProt: Q9VDG5*PLUS
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 461 / 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: 2.79 Å3/Da / Density % sol: 55.87 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 6.5
Details: 100 mM Bis-Tris, 200 mM NH4Ac, 10 mM MgCl2, 15% Polyethylene glycol 10,000, pH 6.5, EVAPORATION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Jul 19, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→47.6 Å / Num. obs: 73482 / % possible obs: 98.7 % / Redundancy: 3.8 % / Net I/σ(I): 15.6
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2 / Num. unique all: 23700 / % possible all: 95.8

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→46.73 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.318 / SU ML: 0.06 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22315 3868 5 %RANDOM
Rwork0.19271 ---
obs0.19426 73482 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.117 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.6→46.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3460 0 6 461 3927
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223559
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6341.9624819
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.6015439
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.71623.529187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.44715586
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6431532
X-RAY DIFFRACTIONr_chiral_restr0.1590.2523
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022779
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.220.21665
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.22439
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2373
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3150.277
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2630.254
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8331.52223
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.31723512
X-RAY DIFFRACTIONr_scbond_it2.11431500
X-RAY DIFFRACTIONr_scangle_it3.2194.51301
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 277 -
Rwork0.262 5261 -
obs--100 %
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)
11.26150.52740.07732.19640.5361.2728-0.0426-0.0369-0.0364-0.1159-0.002-0.18570.02180.01290.0446-0.06510.00760.022-0.06520.0111-0.04172.52137.383614.8201
21.2878-0.766-0.48652.08910.7581.9681-0.04240.0055-0.0553-0.0137-0.01470.060.0266-0.05760.057-0.0709-0.0120.0045-0.04820.0036-0.051730.64448.4915.7868
31.5810.5689-0.19031.8911-0.1092.00940.0385-0.2222-0.02910.1924-0.0563-0.00580.0248-0.00710.0178-0.05430.02760.0352-0.05380.0339-0.0725-12.3463-3.244628.6188
42.564-0.84341.16553.8499-0.75442.38120.0427-0.1764-0.2386-0.00610.14810.23860.0484-0.1712-0.1908-0.09010.0173-0.014-0.07310.0439-0.079216.090621.7976-0.3675
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A442 - 550
2X-RAY DIFFRACTION2B442 - 550
3X-RAY DIFFRACTION3C442 - 515
4X-RAY DIFFRACTION3C522 - 549
5X-RAY DIFFRACTION4D442 - 510
6X-RAY DIFFRACTION4D522 - 549

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