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- PDB-3msz: Crystal Structure of Glutaredoxin 1 from Francisella tularensis C... -

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Basic information

Entry
Database: PDB / ID: 3msz
TitleCrystal Structure of Glutaredoxin 1 from Francisella tularensis Complexed with Cacodylate
ComponentsGlutaredoxin 1
KeywordsOXIDOREDUCTASE / alpha-beta sandwich / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


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
CACODYLATE ION / GLUTATHIONE / Glutaredoxin 1
Similarity search - Component
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.053 Å
AuthorsMaltseva, N. / Kim, Y. / Kwon, K. / 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 Complexed with Cacodylate
Authors: Maltseva, N. / Kim, Y. / Kwon, K. / Anderson, W.F. / Joachimiak, A.
History
DepositionApr 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutaredoxin 1
B: Glutaredoxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7416
Polymers20,8972
Non-polymers8444
Water1,54986
1
A: Glutaredoxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8933
Polymers10,4481
Non-polymers4442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glutaredoxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8483
Polymers10,4481
Non-polymers3992
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.139, 49.139, 140.199
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Glutaredoxin 1


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


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#3: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.34 Å3/Da / Density % sol: 47.4 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris pH 8.5, 2.0 M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 27, 2010 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 12949 / Num. obs: 12949 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 28.04 Å2 / Rsym value: 0.13 / Net I/σ(I): 8.2
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 615 / Rsym value: 0.596 / % possible all: 99.7

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
BALBESphasing
PHENIX(phenix.refine: 1.6_289)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 3LGC

3lgc


Resolution: 2.053→40.721 Å / SU ML: 0.14 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.223 625 4.86 %RANDOM
Rwork0.173 ---
all0.175 12862 --
obs0.175 12862 99.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.183 Å2 / ksol: 0.409 e/Å3
Displacement parametersBiso mean: 34.1 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.053→40.721 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1419 0 51 86 1556
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131557
X-RAY DIFFRACTIONf_angle_d1.3292108
X-RAY DIFFRACTIONf_dihedral_angle_d18.298571
X-RAY DIFFRACTIONf_chiral_restr0.083219
X-RAY DIFFRACTIONf_plane_restr0.006278
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.053-2.25950.27521490.19072962311199
2.2595-2.58640.2391640.17512994315899
2.5864-3.25830.26921410.172630723213100
3.2583-40.7290.18891710.165932093380100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.41270.22850.49370.21810.60591.92940.0476-0.0402-0.04790.0351-0.0576-0.0470.2480.0247-0.01390.1850.0006-0.02640.1180.0040.1454-18.444.74295.416
20.8431-0.3245-0.51930.13340.25211.84960.0685-0.00030.10290.0221-0.0513-0.0511-0.19110.1217-0.03960.21540.0119-0.00250.1737-0.00770.2085-16.2273-8.4092-27.3344
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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