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- PDB-1jfu: CRYSTAL STRUCTURE OF THE SOLUBLE DOMAIN OF TLPA FROM BRADYRHIZOBI... -

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Basic information

Entry
Database: PDB / ID: 1jfu
TitleCRYSTAL STRUCTURE OF THE SOLUBLE DOMAIN OF TLPA FROM BRADYRHIZOBIUM JAPONICUM
ComponentsTHIOL:DISULFIDE INTERCHANGE PROTEIN TLPA
KeywordsMEMBRANE PROTEIN / THIOREDOXIN-LIKE / DOUBLE DISULFIDE BRIDGE
Function / homology
Function and homology information


cytochrome complex assembly / disulfide oxidoreductase activity / plasma membrane
Similarity search - Function
: / Redoxin / Redoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily ...: / Redoxin / Redoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thiol:disulfide interchange protein TlpA
Similarity search - Component
Biological speciesBradyrhizobium japonicum (bacteria)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 1.6 Å
AuthorsCapitani, G. / Rossmann, R. / Sargent, D.F. / Gruetter, M.G. / Richmond, T.J. / Hennecke, H.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Structure of the soluble domain of a membrane-anchored thioredoxin-like protein from Bradyrhizobium japonicum reveals unusual properties.
Authors: Capitani, G. / Rossmann, R. / Sargent, D.F. / Grutter, M.G. / Richmond, T.J. / Hennecke, H.
History
DepositionJun 22, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 19, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 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

Downloads & links

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Assembly

Deposited unit
A: THIOL:DISULFIDE INTERCHANGE PROTEIN TLPA
B: THIOL:DISULFIDE INTERCHANGE PROTEIN TLPA


Theoretical massNumber of molelcules
Total (without water)39,5782
Polymers39,5782
Non-polymers00
Water9,998555
1
A: THIOL:DISULFIDE INTERCHANGE PROTEIN TLPA


Theoretical massNumber of molelcules
Total (without water)19,7891
Polymers19,7891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: THIOL:DISULFIDE INTERCHANGE PROTEIN TLPA


Theoretical massNumber of molelcules
Total (without water)19,7891
Polymers19,7891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.62, 75.15, 82.99
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein THIOL:DISULFIDE INTERCHANGE PROTEIN TLPA


Mass: 19788.889 Da / Num. of mol.: 2 / Fragment: SOLUBLE DOMAIN OF TLPA (RESIDUES 36-221)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bradyrhizobium japonicum (bacteria) / Gene: TLPA / Plasmid: PMAL-P / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P43221
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 555 / 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: 1.99 Å3/Da / Density % sol: 38.28 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 9
Details: Bicine, NaCl, PEG550 MME, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 280K
Crystal grow
*PLUS
Temperature: 7 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.1 MBicine1reservoir
20.1 M1reservoirNaCl
330 %PEG550 MME1reservoir
416 mg/mlprotein1dropin water

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 4, 1999 / Details: OSMIC Confocal Max-Flux
RadiationMonochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→15 Å / Num. obs: 36890 / % possible obs: 86.7 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 16.2
Reflection shellResolution: 1.6→1.67 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.5 / Num. unique all: 3346 / % possible all: 64

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
REFMACrefinement
RefinementMethod to determine structure: SIRAS / Resolution: 1.6→15 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflectionSelection details
Rfree0.234 1863 RANDOM
Rwork0.181 --
obs-36890 -
Displacement parametersBiso mean: 19.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å20 Å2
2---0.09 Å20 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2671 0 0 555 3226
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d1.56
X-RAY DIFFRACTIONp_bond_d0.013
X-RAY DIFFRACTIONp_mcangle_it1.54
X-RAY DIFFRACTIONp_mcbond_it0.88
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
1.6-1.640.39820.33X-RAY DIFFRACTION188464
2.06-2.150.21110.18X-RAY DIFFRACTION222397.1
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 15 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.181
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 19.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d1.56
X-RAY DIFFRACTIONp_mcbond_it0.88
X-RAY DIFFRACTIONp_mcangle_it1.54

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