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- PDB-4bwz: Crystal structure of the sodium proton antiporter, NapA -

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Basic information

Entry
Database: PDB / ID: 4bwz
TitleCrystal structure of the sodium proton antiporter, NapA
ComponentsNA(+)/H(+) ANTIPORTER
KeywordsTRANSPORT PROTEIN / HIGH PH / OUTWARD-FACING
Function / homology
Function and homology information


antiporter activity / proton transmembrane transport / identical protein binding / membrane / metal ion binding
Similarity search - Function
Na+/H+ antiporter like fold - #20 / Na+/H+ antiporter like fold / Sodium/solute symporter superfamily / Cation/H+ exchanger / Sodium/hydrogen exchanger family / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Na(+)/H(+) antiporter
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.984 Å
AuthorsLee, C. / Drew, D. / Cameron, A.D.
CitationJournal: Nature / Year: 2013
Title: A two-domain elevator mechanism for sodium/proton antiport.
Authors: Lee, C. / Kang, H.J. / von Ballmoos, C. / Newstead, S. / Uzdavinys, P. / Dotson, D.L. / Iwata, S. / Beckstein, O. / Cameron, A.D. / Drew, D.
History
DepositionJul 5, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2013Group: Database references
Revision 1.2Oct 2, 2013Group: Database references
Revision 1.3Jan 17, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.page_last ..._citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_conn.ptnr2_label_seq_id / _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: NA(+)/H(+) ANTIPORTER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3623
Polymers41,2311
Non-polymers1312
Water00
1
A: NA(+)/H(+) ANTIPORTER
hetero molecules

A: NA(+)/H(+) ANTIPORTER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,7246
Polymers82,4622
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3970 Å2
ΔGint-157.1 kcal/mol
Surface area29910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.750, 82.150, 191.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein NA(+)/H(+) ANTIPORTER / NAPA


Mass: 41231.059 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Plasmid: PWALDOGFPE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): LEMO21 / References: UniProt: Q72IM4
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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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: 3.6 Å3/Da / Density % sol: 66 % / Description: NONE
Crystal growpH: 7.8
Details: 0.001 M ZINC SULPHATE, 0.05 M HEPES PH 7.8 AND 22% PEG 600

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARRESEARCH / Detector: CCD / Date: May 18, 2012
RadiationMonochromator: SI(III) DOUBLE CRYSTAL MONOCHOMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.98→64 Å / Num. obs: 12265 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 11 % / Biso Wilson estimate: 90.16 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.8
Reflection shellResolution: 2.98→3.06 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 2.8 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: MIRAS
Starting model: NONE

Resolution: 2.984→47.953 Å / SU ML: 0.32 / σ(F): 1.36 / Phase error: 27.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2482 1085 4.7 %
Rwork0.2224 --
obs0.2237 12231 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.984→47.953 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2822 0 2 0 2824
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082873
X-RAY DIFFRACTIONf_angle_d1.1263907
X-RAY DIFFRACTIONf_dihedral_angle_d15.7651002
X-RAY DIFFRACTIONf_chiral_restr0.068499
X-RAY DIFFRACTIONf_plane_restr0.005484
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.984-3.11980.33291220.29552757X-RAY DIFFRACTION100
3.1198-3.28420.35631420.26862746X-RAY DIFFRACTION100
3.2842-3.48990.28181620.23782693X-RAY DIFFRACTION100
3.4899-3.75930.2611160.22392728X-RAY DIFFRACTION100
3.7593-4.13740.26441340.21242723X-RAY DIFFRACTION100
4.1374-4.73570.27271500.20122714X-RAY DIFFRACTION100
4.7357-5.96460.24381280.22632743X-RAY DIFFRACTION100
5.9646-47.95870.18821310.21452722X-RAY DIFFRACTION99

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