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- PDB-1n1c: Crystal Structure Of The Dimeric TorD Chaperone From Shewanella M... -

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Basic information

Entry
Database: PDB / ID: 1n1c
TitleCrystal Structure Of The Dimeric TorD Chaperone From Shewanella Massilia
ComponentsTorA specific chaperone
KeywordsCHAPERONE / TORD / 3D-domain swapping
Function / homology
Function and homology information


protein folding / protein complex oligomerization / cytoplasm
Similarity search - Function
Four Helix Bundle (Hemerythrin (Met), subunit A) - #1820 / Chaperone TorD / HscB, C-terminal domain superfamily / HscB, C-terminal domain / DMSO/Nitrate reductase chaperone / TorD-like superfamily / Nitrate reductase delta subunit / Monooxygenase / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Chaperone protein TorD
Similarity search - Component
Biological speciesShewanella massilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsTranier, S. / Iobbi-Nivol, C. / Mortier-Barriere, I. / Birck, C. / Mejean, V. / Samama, J.-P.
Citation
Journal: Structure / Year: 2003
Title: A Novel Protein Fold and Extreme Domain Swapping in the Dimeric TorD Chaperone from Shewanella massilia
Authors: Tranier, S. / Iobbi-Nivol, C. / Birck, C. / Ilbert, M. / Mortier-Barriere, I. / Mejean, V. / Samama, J.P.
#1: Journal: Protein Sci. / Year: 2002
Title: Characterization And Multiple Molecular Forms Of TorD From Shewanella Massilia, The Putative Chaperone Of The Molybdoenzyme TorA
Authors: Tranier, S. / Mortier-Barriere, I. / Ilbert, M. / Birck, C. / Iobbi-Nivol, C. / Mejean, V. / Samama, J.-P.
#2: Journal: J.Biol.Chem. / Year: 1998
Title: TorD, a cytoplasmic chaperone that interacts with the unfolded trimethylamine N-oxide reductase enzyme (TorA) in Escherichia coli
Authors: Pommier, J. / Mejean, V. / Giordano, G. / Iobbi-Nivol, C.
History
DepositionOct 17, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 13, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TorA specific chaperone
B: TorA specific chaperone
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6174
Polymers49,3092
Non-polymers3092
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10260 Å2
ΔGint-101 kcal/mol
Surface area19730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.958, 93.441, 95.136
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 TorA specific chaperone


Mass: 24654.322 Da / Num. of mol.: 2 / Mutation: H8P/F147C/F163V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella massilia (bacteria) / Gene: torD / Plasmid: pet-22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3-PLYSS / References: UniProt: O87949
#2: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL / Dithiothreitol


Mass: 154.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 3.08 Å3/Da / Density % sol: 59.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: ammonium sulfate 1.6M, MES 100mM; Crystals were obtained by mixing 1 microl (1.2mg.ml-1) of protein solution with an equal volume of reservoir solution; Crystal Size (300x200x100 microM3), ...Details: ammonium sulfate 1.6M, MES 100mM; Crystals were obtained by mixing 1 microl (1.2mg.ml-1) of protein solution with an equal volume of reservoir solution; Crystal Size (300x200x100 microM3), pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11.2 mg/mlprotein1drop
220 mMTris-HCl1droppH8.0
3240 mM1dropNaCl
410 mMdithiothreitol1drop
51.7 Mammonium sulfate1reservoir
6100 mMMES1reservoirpH6.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.97856, 0.95370, 0.97872
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 21, 2000
RadiationMonochromator: DOUBLE CRYSTAL FOCUSSING MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978561
20.95371
30.978721
ReflectionResolution: 2.4→54.2 Å / Num. all: 23325 / Num. obs: 23239 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 41.5 Å2 / Rmerge(I) obs: 0.033 / Net I/σ(I): 14
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.177 / Mean I/σ(I) obs: 3.6 / Num. unique all: 3365 / % possible all: 98.9
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 54.23 Å / Num. measured all: 85570
Reflection shell
*PLUS
% possible obs: 98.9 % / Mean I/σ(I) obs: 3.6

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.4→19.96 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1119 4.8 %RANDOM
Rwork0.224 ---
obs0.224 23149 98.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.4924 Å2 / ksol: 0.341965 e/Å3
Displacement parametersBiso mean: 43.8 Å2
Baniso -1Baniso -2Baniso -3
1-10.14 Å20 Å20 Å2
2---1.81 Å20 Å2
3----8.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3115 0 16 144 3275
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d19.7
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_mcbond_it0.993
X-RAY DIFFRACTIONc_mcangle_it1.775
X-RAY DIFFRACTIONc_scbond_it2.767
X-RAY DIFFRACTIONc_scangle_it3.9810
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.304 178 4.7 %
Rwork0.29 3646 -
obs--99 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2.4 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.87

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