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- PDB-4cz9: Structure of the sodium proton antiporter PaNhaP from Pyrococcus ... -

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Basic information

Entry
Database: PDB / ID: 4cz9
TitleStructure of the sodium proton antiporter PaNhaP from Pyrococcus abyssii at pH 4.
ComponentsNA+/H+ ANTIPORTER, PUTATIVE
KeywordsMEMBRANE PROTEIN / TRANSPORTER / EXCHANGER / CPA
Function / homologySodium/solute symporter superfamily / Cation/H+ exchanger / Sodium/hydrogen exchanger family / antiporter activity / proton transmembrane transport / membrane / Chem-OOC / Na+/H+ antiporter, putative
Function and homology information
Biological speciesPYROCOCCUS ABYSSI GE5 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsWoehlert, D. / Kuhlbrandt, W. / Yildiz, O.
CitationJournal: Elife / Year: 2014
Title: Structure and substrate ion binding in the sodium/proton antiporter PaNhaP.
Authors: Wohlert, D. / Kuhlbrandt, W. / Yildiz, O.
History
DepositionApr 16, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Database references / Other
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc / pdbx_database_status
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _pdbx_database_status.recvd_author_approval
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NA+/H+ ANTIPORTER, PUTATIVE
B: NA+/H+ ANTIPORTER, PUTATIVE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,6143
Polymers93,1432
Non-polymers4711
Water181
1
A: NA+/H+ ANTIPORTER, PUTATIVE
B: NA+/H+ ANTIPORTER, PUTATIVE
hetero molecules

A: NA+/H+ ANTIPORTER, PUTATIVE
B: NA+/H+ ANTIPORTER, PUTATIVE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,2286
Polymers186,2864
Non-polymers9412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
Buried area10130 Å2
ΔGint-111.6 kcal/mol
Surface area69180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.566, 109.566, 209.626
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

#1: Protein NA+/H+ ANTIPORTER, PUTATIVE / PANHAP ANTIPORTER


Mass: 46571.613 Da / Num. of mol.: 2 / Fragment: TRANSPORTER DOMAIN, RESIDUES 1-422
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PYROCOCCUS ABYSSI GE5 (archaea) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: Q9UZ55
#2: Chemical ChemComp-OOC / octyl 4-O-beta-D-allopyranosyl-1-thio-beta-D-altropyranoside / N-BETA-OCTYL-THIO-MALTOSIDE


Mass: 470.575 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H38O10S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 3.39 Å3/Da / Density % sol: 61 % / Description: NONE
Crystal growpH: 4 / Details: pH 4.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.97795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97795 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 33232 / % possible obs: 100 % / Observed criterion σ(I): 1.9 / Redundancy: 9.2 % / Rmerge(I) obs: 0.02 / Net I/σ(I): 19.9
Reflection shellResolution: 3.5→3.72 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.9 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4CZ8

4cz8


Resolution: 3.5→50 Å / σ(F): 1.9
RfactorNum. reflection% reflection
Rfree0.263 1782 5 %
Rwork0.242 --
obs-33232 100 %
Refinement stepCycle: LAST / Resolution: 3.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6560 0 31 1 6592

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