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- PDB-1bg5: CRYSTAL STRUCTURE OF THE ANKYRIN BINDING DOMAIN OF ALPHA-NA,K-ATP... -

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Basic information

Entry
Database: PDB / ID: 1bg5
TitleCRYSTAL STRUCTURE OF THE ANKYRIN BINDING DOMAIN OF ALPHA-NA,K-ATPASE AS A FUSION PROTEIN WITH GLUTATHIONE S-TRANSFERASE
ComponentsFUSION PROTEIN OF ALPHA-NA,K-ATPASE WITH GLUTATHIONE S-TRANSFERASE
KeywordsANKYRIN BINDING / ATPASE / GLUTATHIONE-S-TRANSFERASE / CARRIER CRYSTALLIZATION / ION TRANSPORT
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity / glutathione metabolic process
Similarity search - Function
Fusion Protein Of Alpha-na,k-atpase With Glutathione S-transferase; domain 3 / Fusion Protein Of Alpha-na,k-atpase With Glutathione S-transferase; Domain 3 / Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like ...Fusion Protein Of Alpha-na,k-atpase With Glutathione S-transferase; domain 3 / Fusion Protein Of Alpha-na,k-atpase With Glutathione S-transferase; Domain 3 / Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Glutaredoxin / Glutaredoxin / Few Secondary Structures / Irregular / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Glutathione S-transferase class-mu 26 kDa isozyme
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsZhang, Z. / Devarajan, P. / Morrow, J.S.
CitationJournal: J.Biol.Chem. / Year: 1998
Title: Structure of the ankyrin-binding domain of alpha-Na,K-ATPase.
Authors: Zhang, Z. / Devarajan, P. / Dorfman, A.L. / Morrow, J.S.
History
DepositionJun 5, 1998Processing site: BNL
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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Assembly

Deposited unit
A: FUSION PROTEIN OF ALPHA-NA,K-ATPASE WITH GLUTATHIONE S-TRANSFERASE


Theoretical massNumber of molelcules
Total (without water)29,5281
Polymers29,5281
Non-polymers00
Water2,648147
1
A: FUSION PROTEIN OF ALPHA-NA,K-ATPASE WITH GLUTATHIONE S-TRANSFERASE

A: FUSION PROTEIN OF ALPHA-NA,K-ATPASE WITH GLUTATHIONE S-TRANSFERASE


Theoretical massNumber of molelcules
Total (without water)59,0562
Polymers59,0562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666-y+1,-x+1,-z+3/21
Unit cell
Length a, b, c (Å)92.170, 92.170, 57.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein FUSION PROTEIN OF ALPHA-NA,K-ATPASE WITH GLUTATHIONE S-TRANSFERASE / MAB


Mass: 29528.209 Da / Num. of mol.: 1
Fragment: RESIDUES 1-218 FROM GLUTATHIONE S-TRANSFERASE, RESIDUES 219-254 FROM MINIMAL ALPHA-NA,K-ATPASE ANKYRIN BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cellular location: PLASMA MEMBRANE / Fragment: RESIDUES 219-254 / Organ: BLOOD / Plasmid: PGEX-2T / Production host: Escherichia coli (E. coli) / References: UniProt: P08515
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.1 Å3/Da / Density % sol: 41 %
Crystal growpH: 8.8 / Details: pH 8.8
Crystal grow
*PLUS
Temperature: i R.T. / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mMTris-HCl1drop
2150 mM1dropNaCl
32 mMbeta-mercaptoethanol1drop
430 %PEG40001reservoir
5100 mMbis-tris-propane1reservoir
6150 mM1reservoirNaCl
70.04 Mbeta-mercaptoethanol1reservoir

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jun 1, 1996 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→8 Å / Num. obs: 7078 / % possible obs: 86 % / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Rmerge(I) obs: 0.058 / Rsym value: 0.097 / Net I/σ(I): 10.7
Reflection shellResolution: 2.6→2.71 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.05 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.346 / % possible all: 81
Reflection shell
*PLUS
% possible obs: 81 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GTA

1gta


Resolution: 2.6→8 Å / Rfactor Rfree error: 0.1 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.359 75 4 %RANDOM
Rwork0.193 ---
obs0.193 6577 86 %-
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2208 0 0 134 2342
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.547
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d29.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.678
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.6→2.71 Å / Rfactor Rfree error: 0.1 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.4 6 4 %
Rwork0.2468 712 -
obs--81 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1SPACEGROUP.LIBTOPHCSDX.PRO
X-RAY DIFFRACTION2PROTEIN_REP.PARAMTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg29.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.678
LS refinement shell
*PLUS
Rfactor obs: 0.2468

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