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- PDB-7tbs: Crystal Structure of the Glutaredoxin 2 from Francisella tularensis -

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Basic information

Entry
Database: PDB / ID: 7tbs
TitleCrystal Structure of the Glutaredoxin 2 from Francisella tularensis
ComponentsGlutaredoxin 2
KeywordsTRANSPORT PROTEIN / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homologyGlutaredoxin 2, C-terminal / Glutaredoxin 2, C terminal domain / Glutathione S-transferase, N-terminal domain / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / glutathione metabolic process / Thioredoxin-like superfamily / Glutaredoxin 2
Function and homology information
Biological speciesFrancisella tularensis subsp. tularensis SCHU S4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.96 Å
AuthorsKim, Y. / Zhou, M. / Grimshaw, S. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Crystal Structure of the Glutaredoxin 2 from Francisella tularensis
Authors: Kim, Y. / Zhou, M. / Grimshaw, S. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionDec 22, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 5, 2022Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutaredoxin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5666
Polymers28,1461
Non-polymers4205
Water1,982110
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.989, 83.164, 84.089
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-494-

HOH

21A-510-

HOH

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Components

#1: Protein Glutaredoxin 2


Mass: 28146.467 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis SCHU S4 (bacteria)
Strain: SCHU S4 / Schu 4 / Gene: grxB, FTT_0650c / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Gold / References: UniProt: Q5NH24
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.38 Å3/Da / Density % sol: 48.23 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M lithium sulfate, 0.1 M HEPES pH 7.5, 25 % (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 7, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 19617 / % possible obs: 98.7 % / Redundancy: 7.6 % / Biso Wilson estimate: 27.08 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.171 / Net I/σ(I): 16.6
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.729 / Mean I/σ(I) obs: 2.32 / Num. unique obs: 817 / % possible all: 84.6

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MLPHAREphasing
RefinementMethod to determine structure: SAD / Resolution: 1.96→42.04 Å / SU ML: 0.2267 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.4211
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2168 974 5.12 %
Rwork0.1819 18065 -
obs0.1837 19039 97.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.44 Å2
Refinement stepCycle: LAST / Resolution: 1.96→42.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1838 0 21 110 1969
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021930
X-RAY DIFFRACTIONf_angle_d0.58152618
X-RAY DIFFRACTIONf_chiral_restr0.0439278
X-RAY DIFFRACTIONf_plane_restr0.004335
X-RAY DIFFRACTIONf_dihedral_angle_d13.7124719
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.060.3121190.25822243X-RAY DIFFRACTION85.86
2.06-2.190.25031280.21122566X-RAY DIFFRACTION97.75
2.19-2.360.2671270.18482585X-RAY DIFFRACTION98.76
2.36-2.60.20971500.18422613X-RAY DIFFRACTION99.46
2.6-2.970.21171500.18722625X-RAY DIFFRACTION99.68
2.97-3.740.19461470.17452659X-RAY DIFFRACTION100
3.75-42.040.20651530.16692774X-RAY DIFFRACTION99.86
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)
10.342791162759-0.341376405712-0.01186891393590.2487872470420.02250148788970.4251109582460.013155762424-0.4097446639210.06228793451150.17597349526-0.0295197601546-0.411077632669-0.4539669193840.419191925301-0.03766006127510.386656963921-0.0899248153882-0.04292104020170.3695632668110.002775551550140.305364801195-2.18328919997-13.1877242849-15.8631060047
20.228833115952-0.08672537117470.3526955279761.983158250280.1603864004061.348936946870.0851409153318-0.110153301087-0.0552230567490.0592058822409-0.0443489283718-0.002146201381140.12819899966-0.0168702232315-0.007797175536670.195930081303-0.0414274832191-0.02827392692120.2221700414110.03976543985590.237451603878-8.07992154234-18.6650675753-14.1260344215
32.70235912484-1.585840441921.859424848571.58224624704-1.694629511311.78912075906-0.21254099911-0.2316220574550.08571153330990.3798232294970.09413682601170.00352303723788-0.478435448133-0.1288900628670.1133079440150.270172953474-0.00962468401235-0.02131081633260.25491646187-0.001132657720440.225778510623-12.9509163285-3.34371780581-11.1565211792
41.09170354239-1.15068099197-0.7797921531434.007008477061.841830033912.82341996699-0.27957425818-0.122740946572-0.2090249121980.4052285704920.160385782360.4802597555560.2610113056140.107377329041-0.006583839116080.277823186654-0.04312498925320.03520659594520.2774484695240.03596690783610.284191241893-26.2200188066-9.83817691501-30.2867503954
51.52799390503-0.4956768409971.776889706845.07429404177-1.308197096564.607067367880.3410443567690.130948044788-0.184073661488-0.792030803487-0.226447304081-0.1305330877510.801766201319-0.0289227055559-0.1959999973970.388794174076-0.00600125924308-0.04107279502940.269410520458-0.02984774838260.276571087777-11.6044578195-25.2753899642-31.0104797845
62.0001459099-0.1508977451081.064773434834.13225659253-4.346175394687.329098703740.247705472893-0.677683846003-0.7271073120230.4575680431250.1271976417620.07967702352190.823186620102-0.360854172284-0.3458083393060.441126183843-0.0587386951946-0.07208313157480.3741732696380.03142095687070.469883431827-22.3468137102-24.8499509511-37.5088225061
72.020261781211.105753568460.8153913652417.03227122052.645589317183.56625615983-0.1893266082180.1518904796480.0407367582974-0.303657255419-0.02184171017050.653239156440.0332753080733-0.3883359130620.005379996730310.173068540505-0.0255250089799-0.02087318102760.2436796034880.04101661607790.230215833752-24.5433210404-5.04047928878-38.2957832924
82.97627573045-0.1279559140210.3591148178612.30512611362-1.228633899414.21429429223-0.0677298828741-0.1451897940790.6080834458360.255147189932-0.0990364845987-0.0172629757115-1.040318757120.4814311895710.07020004953380.445387432923-0.0672322004276-0.04847570528460.269633772994-0.01791147182720.325641917325-13.15724810635.18439295965-22.4119391336
91.15593326716-0.310527424337-0.08784868708031.4086166458-0.3495788422441.59469380369-0.01551408848970.0658610575403-0.06624793398760.110489976593-2.14779582021E-5-0.1828669617110.4095952952870.06708862140290.04185048179350.205354925222-0.00879935046749-0.02126714067510.1947609537910.007009497083450.210616550214-15.4369419855-7.49926013964-30.201305457
101.175881220670.1408978435670.5067800240981.76801595074-0.5589779368591.744540798050.05908782416350.1391333959090.233543607164-0.0922137813436-0.120371180197-0.381646123093-0.07406031739210.3365227384520.1120662639550.166518968755-0.0298195646657-0.00775881854570.2286229003890.01673587170850.228952051725-7.59328082854-3.19255479208-29.6688572649
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid -21 through 9 )-21 - 91 - 16
22chain 'A' and (resid 10 through 61 )10 - 6117 - 68
33chain 'A' and (resid 62 through 83 )62 - 8369 - 90
44chain 'A' and (resid 84 through 100 )84 - 10091 - 107
55chain 'A' and (resid 101 through 128 )101 - 128108 - 135
66chain 'A' and (resid 129 through 143 )129 - 143136 - 150
77chain 'A' and (resid 144 through 160 )144 - 160151 - 167
88chain 'A' and (resid 161 through 172 )161 - 172168 - 179
99chain 'A' and (resid 173 through 195 )173 - 195180 - 202
1010chain 'A' and (resid 196 through 214 )196 - 214203 - 221

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