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- PDB-4cz8: Structure of the sodium proton antiporter PaNhaP from Pyrococcus ... -

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Basic information

Entry
Database: PDB / ID: 4cz8
TitleStructure of the sodium proton antiporter PaNhaP from Pyrococcus abyssii at pH 8.
ComponentsNA+/H+ ANTIPORTER, PUTATIVE
KeywordsMEMBRANE PROTEIN / ANTIPORTER / TRANSPORTER / EXCHANGER / CPA
Function / homologySodium/solute symporter superfamily / Cation/H+ exchanger / Sodium/hydrogen exchanger family / antiporter activity / proton transmembrane transport / membrane / CITRATE ANION / PHOSPHATIDYLETHANOLAMINE / Na+/H+ antiporter, putative
Function and homology information
Biological speciesPYROCOCCUS ABYSSI GE5 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.15 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 1.1Mar 4, 2015Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _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: NA+/H+ ANTIPORTER, PUTATIVE
B: NA+/H+ ANTIPORTER, PUTATIVE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,6949
Polymers93,8002
Non-polymers1,8947
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7540 Å2
ΔGint-41.8 kcal/mol
Surface area33980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.493, 107.944, 107.928
Angle α, β, γ (deg.)90.00, 95.19, 90.00
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 NA+/H+ ANTIPORTER, PUTATIVE / PANHAP ANTIPORTER


Mass: 46899.875 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: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 10 molecules

#3: Chemical ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H80NO8P / Comment: phospholipid*YM
#4: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE


Mass: 163.215 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.37 Å3/Da / Density % sol: 61 % / Description: NONE
Crystal growpH: 8 / Details: pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97874
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97874 Å / Relative weight: 1
ReflectionResolution: 3.15→50 Å / Num. obs: 38952 / % possible obs: 99.5 % / Observed criterion σ(I): 1.5 / Redundancy: 10.8 % / Biso Wilson estimate: 120.43 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 11.9
Reflection shellResolution: 3.15→3.35 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.5 / % possible all: 99.2

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Processing

Software
NameClassification
PARROTmodel building
XDSdata reduction
Aimlessdata scaling
SHELXDphasing
CRANK2phasing
REFMACphasing
PARROTphasing
BUCCANEERphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 3.15→48.487 Å / SU ML: 0.44 / σ(F): 1.91 / Phase error: 36.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2756 2108 5.1 %
Rwork0.2387 --
obs0.2407 40991 96.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 133 Å2
Refinement stepCycle: LAST / Resolution: 3.15→48.487 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6582 0 129 4 6715
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036851
X-RAY DIFFRACTIONf_angle_d0.7589303
X-RAY DIFFRACTIONf_dihedral_angle_d12.7342514
X-RAY DIFFRACTIONf_chiral_restr0.0521143
X-RAY DIFFRACTIONf_plane_restr0.0031103
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1501-3.22340.4347980.34372274X-RAY DIFFRACTION82
3.2234-3.30390.42691410.32272343X-RAY DIFFRACTION89
3.3039-3.39330.38421340.32192566X-RAY DIFFRACTION94
3.3933-3.49310.3851210.31842554X-RAY DIFFRACTION96
3.4931-3.60580.32241520.29232638X-RAY DIFFRACTION98
3.6058-3.73460.33741470.27152575X-RAY DIFFRACTION97
3.7346-3.88410.32291340.25472662X-RAY DIFFRACTION99
3.8841-4.06080.28831470.23112640X-RAY DIFFRACTION99
4.0608-4.27470.25011470.21872646X-RAY DIFFRACTION99
4.2747-4.54240.32651400.21942687X-RAY DIFFRACTION99
4.5424-4.89280.26181710.20862637X-RAY DIFFRACTION100
4.8928-5.38460.30771240.2272677X-RAY DIFFRACTION99
5.3846-6.16240.32021650.26542640X-RAY DIFFRACTION100
6.1624-7.75890.26211550.25472691X-RAY DIFFRACTION100
7.7589-48.49240.2021320.21572653X-RAY DIFFRACTION99

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