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- PDB-3vfi: Crystal Structure of a Metagenomic Thioredoxin -

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Basic information

Entry
Database: PDB / ID: 3vfi
TitleCrystal Structure of a Metagenomic Thioredoxin
Componentsthioredoxin
KeywordsELECTRON TRANSPORT / Thioredoxin
Function / homology
Function and homology information


protein-disulfide reductase activity
Similarity search - Function
Thioredoxin / Thioredoxin / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative thioredoxin
Similarity search - Component
Biological speciesSilicibacter phage DSS3phi2 (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsCraig, T.K. / Gardberg, A. / Lorimer, D.D. / Burgin Jr., A.B. / Segall, A. / Rohwer, F.
CitationJournal: To be Published
Title: Structure of a Metagenomic Thioredoxin
Authors: Craig, T.K. / Gardberg, A. / Lorimer, D.D. / Burgin Jr., A.B. / Segall, A. / Rohwer, F.
History
DepositionJan 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: thioredoxin


Theoretical massNumber of molelcules
Total (without water)12,0701
Polymers12,0701
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.219, 55.364, 54.435
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein thioredoxin


Mass: 12069.833 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Silicibacter phage DSS3phi2 (virus) / Plasmid: VCID_5533, pEMB31 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C4NT42
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 1.89 Å3/Da / Density % sol: 34.79 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.44
Details: 0.27M Tris-HCL pH 8.44 13.52% (w/v) PEG 1000 13.52% (w/v) PEG 3350 13.52% (w/v) MPD 0.03M NaF 0.03M NaBr 0.03M NaI 0.4uL@ 10mg/mL + 0.4uL, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Dec 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.73→50 Å / Num. all: 10095 / Num. obs: 9812 / % possible obs: 97.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rmerge(I) obs: 0.075 / Χ2: 1.025 / Net I/σ(I): 23.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.73-1.762.10.173550.571172.7
1.76-1.792.50.1424630.62192.4
1.79-1.832.80.1364830.628199.6
1.83-1.862.80.1254890.647199.4
1.86-1.92.90.124920.728199
1.9-1.9530.1054820.8091100
1.95-230.0984990.851199.8
2-2.053.10.0924970.9381100
2.05-2.113.40.1074881.3981100
2.11-2.183.80.1055021.422199.8
2.18-2.264.20.1054951.5181100
2.26-2.354.50.1015041.411100
2.35-2.454.80.1064941.397199.6
2.45-2.584.90.0955031.2251100
2.58-2.755.40.0995171.241100
2.75-2.966.30.1054981.3161100
2.96-3.266.50.0975111.114198.8
3.262-3.736.10.085010.896196.3
3.733-4.6960.0644860.632193.3
4.692-505.90.0475530.325194.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å20.22 Å
Translation2.5 Å20.22 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.4.0phasing
PHENIXrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→50 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2327 461 5%
Rwork0.2008 --
all-9242 -
obs-8781 -
Displacement parametersBiso max: 70.11 Å2 / Biso mean: 25.0787 Å2 / Biso min: 10.46 Å2
Refinement stepCycle: LAST / Resolution: 1.75→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms822 0 0 67 889
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d1.102
X-RAY DIFFRACTIONf_angle_d0.007
LS refinement shellResolution: 1.7501→2.0031 Å
RfactorNum. reflection% reflection
Rfree0.2975 140 -
Rwork0.2239 --
obs-2666 88.6 %

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