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- PDB-3lwa: The Crystal Structure of a Secreted Thiol-disulfide Isomerase fro... -

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Basic information

Entry
Database: PDB / ID: 3lwa
TitleThe Crystal Structure of a Secreted Thiol-disulfide Isomerase from Corynebacterium glutamicum to 1.75A
ComponentsSecreted thiol-disulfide isomerase
KeywordsISOMERASE / Thiol-disulfide / thioredoxin / Corynebacterium / glutamicum / PSI / MCSG / Structural Genomics / Midwest Center for Structural Genomics / Protein Structure Initiative
Function / homology
Function and homology information


antioxidant activity / isomerase activity / oxidoreductase activity
Similarity search - Function
: / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thiol-disulfide isomerase and thioredoxins
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.75 Å
AuthorsStein, A.J. / Weger, A. / Hendricks, R. / Cobb, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The Crystal Structure of a Secreted Thiol-disulfide Isomerase from Corynebacterium glutamicum to 1.75A
Authors: Stein, A.J. / Weger, A. / Hendricks, R. / Cobb, G. / Joachimiak, A.
History
DepositionFeb 23, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Secreted thiol-disulfide isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9043
Polymers19,8241
Non-polymers802
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.818, 35.376, 53.718
Angle α, β, γ (deg.)90.000, 96.690, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Secreted thiol-disulfide isomerase / Thiol-disulfide isomerase / thioredoxins


Mass: 19824.275 Da / Num. of mol.: 1 / Fragment: sequence database residues 25-187
Source method: isolated from a genetically manipulated source
Details: pMCSG19 / Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Strain: ATCC 13032 / Gene: cg0520, Cgl0439 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8NT71
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 1.86 Å3/Da / Density % sol: 34 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 16% PEG 8000, 20% Glycerol, 0.04M K3PO4, 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: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2010
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 14734 / % possible obs: 99 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.079 / Χ2: 2.272 / Net I/σ(I): 10.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.75-1.813.70.57314341.31299.3
1.81-1.893.70.37414721.41699.7
1.89-1.973.70.25414641.36199.8
1.97-2.073.70.19214981.513100
2.07-2.23.70.14614601.74799.7
2.2-2.383.70.11814802.03699.5
2.38-2.613.70.09514912.28499.6
2.61-2.993.60.08314752.98498.8
2.99-3.773.50.05814673.40298.3
3.77-503.40.05414934.98395.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.004data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
MLPHAREphasing
RESOLVEphasing
ARP/wARPmodel building
Cootmodel building
RefinementResolution: 1.75→26.68 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.966 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.138 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23 751 5.1 %RANDOM
Rwork0.2 ---
obs0.201 14724 98.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.394 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0.01 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.75→26.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1251 0 2 51 1304
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221279
X-RAY DIFFRACTIONr_angle_refined_deg1.3311.9611754
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.925169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.51525.34558
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.37115181
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.088156
X-RAY DIFFRACTIONr_chiral_restr0.0930.2203
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211003
X-RAY DIFFRACTIONr_mcbond_it0.7731.5836
X-RAY DIFFRACTIONr_mcangle_it1.47421344
X-RAY DIFFRACTIONr_scbond_it2.5923443
X-RAY DIFFRACTIONr_scangle_it4.1934.5408
LS refinement shellResolution: 1.746→1.791 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 53 -
Rwork0.3 954 -
all-1007 -
obs--93.15 %

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