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- PDB-5da4: Structure of a nanobody recognizing the fumarate transporter SLC26Dg -

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Basic information

Entry
Database: PDB / ID: 5da4
TitleStructure of a nanobody recognizing the fumarate transporter SLC26Dg
ComponentsNanobody recognizing the membrane protein SLC26Dg
KeywordsIMMUNE SYSTEM / Membrane transport protein / nanobody complex
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsDutzler, R. / Geertsma, E.R. / Chang, Y. / Shaik, F.R.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: Structure of a prokaryotic fumarate transporter reveals the architecture of the SLC26 family.
Authors: Geertsma, E.R. / Chang, Y.N. / Shaik, F.R. / Neldner, Y. / Pardon, E. / Steyaert, J. / Dutzler, R.
History
DepositionAug 19, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Database references
Revision 1.2Oct 14, 2015Group: Database references
Revision 2.0Jan 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nanobody recognizing the membrane protein SLC26Dg
B: Nanobody recognizing the membrane protein SLC26Dg
C: Nanobody recognizing the membrane protein SLC26Dg


Theoretical massNumber of molelcules
Total (without water)39,9143
Polymers39,9143
Non-polymers00
Water5,134285
1
A: Nanobody recognizing the membrane protein SLC26Dg


Theoretical massNumber of molelcules
Total (without water)13,3051
Polymers13,3051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nanobody recognizing the membrane protein SLC26Dg


Theoretical massNumber of molelcules
Total (without water)13,3051
Polymers13,3051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Nanobody recognizing the membrane protein SLC26Dg


Theoretical massNumber of molelcules
Total (without water)13,3051
Polymers13,3051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.511, 139.511, 196.863
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-295-

HOH

21A-298-

HOH

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Components

#1: Antibody Nanobody recognizing the membrane protein SLC26Dg


Mass: 13304.595 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M Hepes pH 7.5, 200 mM CaCl2, 28% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 76545 / % possible obs: 99.9 % / Redundancy: 14.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 23.5
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 14.7 % / Rmerge(I) obs: 1.357 / Mean I/σ(I) obs: 2.2 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
PHENIXphasing
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WGV

4wgv
PDB Unreleased entry


Resolution: 2.4→19.996 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2417 1992 2.61 %
Rwork0.233 --
obs0.2333 76232 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→19.996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2772 0 0 285 3057
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022826
X-RAY DIFFRACTIONf_angle_d0.5773816
X-RAY DIFFRACTIONf_dihedral_angle_d12.145993
X-RAY DIFFRACTIONf_chiral_restr0.024405
X-RAY DIFFRACTIONf_plane_restr0.003501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.45990.3241410.30665223X-RAY DIFFRACTION100
2.4599-2.52630.31841400.30165223X-RAY DIFFRACTION100
2.5263-2.60050.32171400.29275213X-RAY DIFFRACTION100
2.6005-2.68430.26391410.2825251X-RAY DIFFRACTION100
2.6843-2.780.32251400.28215233X-RAY DIFFRACTION100
2.78-2.89090.26041420.27715254X-RAY DIFFRACTION100
2.8909-3.02210.27731400.26875265X-RAY DIFFRACTION100
3.0221-3.18080.26311420.26365281X-RAY DIFFRACTION100
3.1808-3.37920.26711420.24335258X-RAY DIFFRACTION100
3.3792-3.63870.1951410.22515296X-RAY DIFFRACTION100
3.6387-4.00220.21961430.21025330X-RAY DIFFRACTION100
4.0022-4.57530.20221440.18385356X-RAY DIFFRACTION100
4.5753-5.74170.21081460.20035412X-RAY DIFFRACTION100
5.7417-19.99640.26341500.24295645X-RAY DIFFRACTION100

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