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- PDB-3lgc: Crystal Structure of Glutaredoxin 1 from Francisella tularensis -

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Basic information

Entry
Database: PDB / ID: 3lgc
TitleCrystal Structure of Glutaredoxin 1 from Francisella tularensis
ComponentsGlutaredoxin 1
KeywordsUNKNOWN FUNCTION / alpha-beta sandwich / Structural Genomics / structural genomics of infectious diseases / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


protein-disulfide reductase activity / cell redox homeostasis
Similarity search - Function
Glutaredoxin, GrxC / Glutaredoxin subgroup / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily ...Glutaredoxin, GrxC / Glutaredoxin subgroup / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.77 Å
AuthorsMaltseva, N. / Kim, Y. / Papazisi, L. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of Glutaredoxin 1 from Francisella tularensis
Authors: Maltseva, N. / Kim, Y. / Papazisi, L. / Anderson, W.F. / Joachimiak, A.
History
DepositionJan 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutaredoxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7334
Polymers10,4481
Non-polymers2843
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.437, 66.437, 63.116
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Glutaredoxin 1


Mass: 10448.485 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis (bacteria)
Strain: SCHU S4 / Gene: FTT0533c, FTT_0533c, grxA / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21magic / References: UniProt: Q5NHD0
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.85 Å3/Da / Density % sol: 68.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M magnesium chloride, 0.1 M Tris pH 8.5, 20 % PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 4, 2009 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.77→33.2 Å / Num. all: 4103 / Num. obs: 4103 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 12.1 % / Biso Wilson estimate: 45.6 Å2 / Rsym value: 0.175 / Net I/σ(I): 7.2
Reflection shellResolution: 2.77→2.82 Å / Redundancy: 12.2 % / Mean I/σ(I) obs: 6 / Num. unique all: 189 / Rsym value: 0.847 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXmodel building
MLPHAREphasing
DMmodel building
SOLVEphasing
RESOLVEmodel building
PHENIX(phenix.refine: 1.4_147)refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.77→33.2 Å / SU ML: 0.31 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.223 184 4.52 %random
Rwork0.175 ---
all0.177 4075 --
obs0.177 4075 99.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 8.077 Å2 / ksol: 0.256 e/Å3
Displacement parametersBiso mean: 51.7 Å2
Baniso -1Baniso -2Baniso -3
1--4.8993 Å20 Å20 Å2
2---4.8993 Å2-0 Å2
3---3.7544 Å2
Refinement stepCycle: LAST / Resolution: 2.77→33.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms760 0 16 30 806
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014794
X-RAY DIFFRACTIONf_angle_d1.4621075
X-RAY DIFFRACTIONf_dihedral_angle_d20.029287
X-RAY DIFFRACTIONf_chiral_restr0.09111
X-RAY DIFFRACTIONf_plane_restr0.008139
LS refinement shellResolution: 2.7682→33.2209 Å
RfactorNum. reflection% reflection
Rfree0.2227 184 -
Rwork0.1752 3891 -
obs-4075 100 %
Refinement TLS params.Method: refined / Origin x: 38.1741 Å / Origin y: 7.7438 Å / Origin z: 6.5028 Å
111213212223313233
T0.0858 Å2-0.0229 Å20.013 Å2-0.0387 Å20.0166 Å2--0.0538 Å2
L1.8049 °2-1.4734 °2-0.0055 °2-1.8641 °2-0.6014 °2--1.2523 °2
S0.0223 Å °-0.1764 Å °0.1764 Å °-0.1845 Å °-0.1382 Å °-0.1629 Å °0.0961 Å °0.0626 Å °0.095 Å °
Refinement TLS groupSelection details: Chain A

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