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- PDB-2jad: Yellow fluorescent protein - glutaredoxin fusion protein -

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Basic information

Entry
Database: PDB / ID: 2jad
TitleYellow fluorescent protein - glutaredoxin fusion protein
ComponentsYELLOW FLUORESCENT PROTEIN GLUTAREDOXIN FUSION PROTEIN
KeywordsELECTRON TRANSPORT / YELLOW FLUORESCENT PROTEIN / REDOX- ACTIVE CENTER / YEAST / GRX1P / TRANSPORT / GLUTAREDOXIN
Function / homology
Function and homology information


protein glutathionylation / glutathione peroxidase / glutathione disulfide oxidoreductase activity / glutathione peroxidase activity / glutathione transferase / glutathione transferase activity / bioluminescence / generation of precursor metabolites and energy / cellular response to oxidative stress / nucleus / cytoplasm
Similarity search - Function
Glutaredoxin subgroup / Glutaredoxin, eukaryotic/virial / Glutaredoxin active site / Glutaredoxin active site. / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP ...Glutaredoxin subgroup / Glutaredoxin, eukaryotic/virial / Glutaredoxin active site / Glutaredoxin active site. / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Glutaredoxin-1 / Green fluorescent protein
Similarity search - Component
Biological speciesAEQUOREA VICTORIA (jellyfish)
SACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsHakansson, K.O. / Winther, J.R.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2007
Title: Structure of Glutaredoxin Grx1P C30S Mutant from Yeast.
Authors: Hakansson, K.O. / Winther, J.R.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Crystallisation of Mutant Forms of Glutaredoxin Grx1P from Yeast
Authors: Hakansson, K.O. / Winther, J.R.
History
DepositionNov 27, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2006Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Version format compliance
Revision 1.2Mar 15, 2017Group: Source and taxonomy
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 12-STRANDED BARREL THIS IS REPRESENTED BY A 13-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: YELLOW FLUORESCENT PROTEIN GLUTAREDOXIN FUSION PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1673
Polymers40,9751
Non-polymers1922
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)132.111, 132.111, 58.722
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 YELLOW FLUORESCENT PROTEIN GLUTAREDOXIN FUSION PROTEIN


Mass: 40975.215 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: THE MUTATED RESIDUE NUMBER 276 CORRESPONDS TO C30S IN GLUTAREDOXIN
Source: (gene. exp.) AEQUOREA VICTORIA (jellyfish), (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P42212, UniProt: P25373
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 3.6 Å3/Da / Density % sol: 66 %
Crystal growpH: 10 / Details: 50MM BICARBONATE PH 10 1.5-1.75M MGSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.115
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 30, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 15714 / % possible obs: 96.7 % / Observed criterion σ(I): -10 / Redundancy: 2.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 5.8
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.1 / % possible all: 95.1

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H6R

1h6r


Resolution: 2.7→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: RESIDUES 237-241 BUILT AS AAAGG AND RESIDUES 242-245 ABSENT DUE TO DISORDER. THE C-TERMINUS WAS ALSO DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.247 -5 %RANDOM
Rwork0.214 ---
obs0.214 15708 96.7 %-
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2753 0 10 55 2818
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0061
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.36
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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