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- PDB-4kpp: Crystal Structure of H+/Ca2+ Exchanger CAX -

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Basic information

Entry
Database: PDB / ID: 4kpp
TitleCrystal Structure of H+/Ca2+ Exchanger CAX
ComponentsPutative uncharacterized protein
KeywordsMEMBRANE PROTEIN / transporter
Function / homologySodium/calcium exchanger membrane region / Sodium/calcium exchanger protein / transmembrane transport / membrane => GO:0016020 / metal ion binding / alpha-maltose / OLEIC ACID / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Uncharacterized protein
Function and homology information
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsNishizawa, T. / Ishitani, R. / Nureki, O.
CitationJournal: Science / Year: 2013
Title: Structural basis for the counter-transport mechanism of a H+/Ca2+ exchanger.
Authors: Nishizawa, T. / Kita, S. / Maturana, A.D. / Furuya, N. / Hirata, K. / Kasuya, G. / Ogasawara, S. / Dohmae, N. / Iwamoto, T. / Ishitani, R. / Nureki, O.
History
DepositionMay 14, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Structure summary
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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 / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id / _struct_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 24, 2022Group: Database references / Structure summary / Category: chem_comp / citation / database_2
Item: _chem_comp.pdbx_synonyms / _citation.journal_volume ..._chem_comp.pdbx_synonyms / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein
B: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,22311
Polymers90,0312
Non-polymers2,1919
Water1,38777
1
A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6954
Polymers45,0161
Non-polymers6793
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5287
Polymers45,0161
Non-polymers1,5126
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.954, 97.386, 71.233
Angle α, β, γ (deg.)90.000, 99.370, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 3 molecules AB

#1: Protein Putative uncharacterized protein / membrane transporter


Mass: 45015.613 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea)
Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126
Gene: AF0251, AF_0251 / Plasmid: pET22c / Production host: Escherichia coli (E. coli) / Strain (production host): C41 (DE3) / References: UniProt: O29988
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 85 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-OLB / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
#5: Chemical
ChemComp-OLA / OLEIC ACID / Oleic acid


Mass: 282.461 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C18H34O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.43 Å3/Da / Density % sol: 49.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 10% pentaerythritol propoxylate(5/4 PO/OH), 100mM MES-NaOH, 100mM NH4Cl, 10mM CaCl2, pH 6.5, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: May 13, 2013
RadiationMonochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 33675 / Num. obs: 33675 / % possible obs: 87.7 % / Biso Wilson estimate: 29.53 Å2

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.2_869refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→30.712 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.66 / σ(F): 1.53 / Phase error: 21.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2379 1678 5 %
Rwork0.2019 --
obs0.2038 33570 87.63 %
Solvent computationShrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.767 Å2 / ksol: 0.309 e/Å3
Displacement parametersBiso max: 99.51 Å2 / Biso mean: 35.9865 Å2 / Biso min: 9.54 Å2
Baniso -1Baniso -2Baniso -3
1-1.3796 Å20 Å21.1085 Å2
2---3.1979 Å20 Å2
3---1.8183 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30.712 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5942 0 89 77 6108
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0146165
X-RAY DIFFRACTIONf_angle_d0.7228382
X-RAY DIFFRACTIONf_chiral_restr0.0491041
X-RAY DIFFRACTIONf_plane_restr0.0041004
X-RAY DIFFRACTIONf_dihedral_angle_d13.8942108
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.36770.33621310.26012495262682
2.3677-2.44410.3011400.22882676281689
2.4441-2.53140.25651450.20662761290692
2.5314-2.63270.26341490.19472809295893
2.6327-2.75240.24311480.18422813296193
2.7524-2.89740.22361520.17432900305296
2.8974-3.07880.24921540.1882919307396
3.0788-3.31630.23671540.19182924307897
3.3163-3.64950.2213960.19831831192760
3.6495-4.17650.21661290.19622448257780
4.1765-5.25760.23861210.20592306242776
5.2576-30.71440.20951590.21243010316997
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)
10.70630.29860.07210.53070.77331.001-0.0004-0.0601-0.0289-0.0081-0.05680.01410.1367-0.0457-0.00120.1994-0.0108-0.02340.2286-0.01130.165738.407315.6677175.7699
21.5823-0.4329-0.01451.1122-0.02840.8581-0.0278-0.0928-0.0670.04630.0628-0.03710.0767-0.03240.00010.1619-0.0305-0.00420.1615-0.00670.164660.626316.3359179.1799
30.1105-0.1187-0.14810.05420.21991.4935-0.148-0.04250.11990.0102-0.2408-0.51110.51410.0898-0.25780.24960.0217-0.06780.2401-0.02230.375674.769.5905180.6209
40.3336-0.3532-0.06020.4238-0.22620.9917-0.0730.03660.12870.13280.10830.12020.05450.04090.05130.1102-0.0180.02850.1711-0.04760.180619.058619.2421156.5975
51.36510.8892-0.43371.014-0.42221.0205-0.02180.11150.1015-0.06120.12820.03640.0036-0.06230.02510.11-0.0148-0.00020.1114-0.01810.081236.471921.7865140.5589
60.6785-0.0350.16240.0677-0.0990.1281-0.16270.18750.1964-0.05820.0324-0.11840.192-0.0834-0.04980.3188-0.07350.0380.1641-0.00350.16546.85129.81131.6796
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 2:61 or resseq 189:238)A2 - 61
2X-RAY DIFFRACTION1chain 'A' and (resseq 2:61 or resseq 189:238)A189 - 238
3X-RAY DIFFRACTION2chain 'A' and (resseq 62:188 or resseq 239:356)A62 - 188
4X-RAY DIFFRACTION2chain 'A' and (resseq 62:188 or resseq 239:356)A239 - 356
5X-RAY DIFFRACTION3chain 'A' and (resseq 357:396)A357 - 396
6X-RAY DIFFRACTION4chain 'B' and (resseq 2:58 or resseq 189:238)B2 - 58
7X-RAY DIFFRACTION4chain 'B' and (resseq 2:58 or resseq 189:238)B189 - 238
8X-RAY DIFFRACTION5chain 'B' and (resseq 65:186 or resseq 239:356)B65 - 186
9X-RAY DIFFRACTION5chain 'B' and (resseq 65:186 or resseq 239:356)B239 - 356
10X-RAY DIFFRACTION6chain 'B' and (resseq 357:395)B357 - 395

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