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- PDB-1b8x: GLUTATHIONE S-TRANSFERASE FUSED WITH THE NUCLEAR MATRIX TARGETING... -

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Basic information

Entry
Database: PDB / ID: 1b8x
TitleGLUTATHIONE S-TRANSFERASE FUSED WITH THE NUCLEAR MATRIX TARGETING SIGNAL OF THE TRANSCRIPTION FACTOR AML-1
ComponentsPROTEIN (AML-1B)
KeywordsSIGNAL PROTEIN / NUCLEAR MATRIX TARGETING SIGNAL PROTEIN
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity / glutathione metabolic process
Similarity search - Function
Signal Protein Aml-1b; Chain A, domain 3 / Signal Protein Aml-1b; Chain A, 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 ...Signal Protein Aml-1b; Chain A, domain 3 / Signal Protein Aml-1b; Chain A, 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 speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsTang, L. / Guo, B. / Van Wijnen, A.J. / Lian, J.B. / Stein, J.L. / Stein, G.S. / Zhou, G.W.
CitationJournal: J.Struct.Biol. / Year: 1998
Title: Preliminary crystallographic study of glutathione S-transferase fused with the nuclear matrix targeting signal of the transcription factor AML-1/CBF-alpha2.
Authors: Tang, L. / Guo, B. / van Wijnen, A.J. / Lian, J.B. / Stein, J.L. / Stein, G.S. / Zhou, G.W.
History
DepositionFeb 3, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Apr 12, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (AML-1B)


Theoretical massNumber of molelcules
Total (without water)32,1241
Polymers32,1241
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: PROTEIN (AML-1B)

A: PROTEIN (AML-1B)


Theoretical massNumber of molelcules
Total (without water)64,2482
Polymers64,2482
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area2620 Å2
ΔGint-19 kcal/mol
Surface area27470 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)93.400, 93.400, 57.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Cell settingtetragonal
Space group name H-MP43212

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Components

#1: Protein PROTEIN (AML-1B)


Mass: 32124.119 Da / Num. of mol.: 1 / Fragment: NMTS FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Cell line: BL21 / Production host: Escherichia coli (E. coli) / References: UniProt: P08515

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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: 2.05 Å3/Da / Density % sol: 50 %
Crystal growpH: 7.5 / Details: pH 7.5
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2PEG 40011
3NA2HPO411
4NAH2PO411
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
240 %PEG40001reservoir
32 %PEG4001reservoir
40.2 M1reservoirNa2HPO4/NaH2PO4

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Data collection

DiffractionMean temperature: 85 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→15 Å / Num. obs: 7449 / % possible obs: 94.9 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Biso Wilson estimate: 41 Å2 / Rsym value: 11 / Net I/σ(I): 3
Reflection shellResolution: 2.7→2.82 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.5 / Rsym value: 25 / % possible all: 87.5
Reflection
*PLUS
Rmerge(I) obs: 0.11
Reflection shell
*PLUS
% possible obs: 87.5 % / Rmerge(I) obs: 0.25

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Processing

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

1gne


Resolution: 2.7→6 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.31 666 10 %RANDOM
Rwork0.209 ---
obs-6061 94.5 %-
Refinement stepCycle: LAST / Resolution: 2.7→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2083 0 0 0 2083
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.005
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_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.051.5
X-RAY DIFFRACTIONx_mcangle_it42
X-RAY DIFFRACTIONx_scbond_it4.232
X-RAY DIFFRACTIONx_scangle_it5.082.5
LS refinement shellResolution: 2.7→2.81 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.36 81 13 %
Rwork0.27 557 -
obs--87.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPH19.PEP
X-RAY DIFFRACTION2TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.209
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor obs: 0.27

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