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- PDB-5zdi: Crystal structure of CsaA chaperone protein from picrophilus torridus -

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Basic information

Entry
Database: PDB / ID: 5zdi
TitleCrystal structure of CsaA chaperone protein from picrophilus torridus
ComponentsProtein secretion chaperonin CsaA
KeywordsCHAPERONE / tRNA-binding protein / Thermoacidophiles
Function / homology
Function and homology information


Probable chaperone CsaA / : / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Protein secretion chaperonin CsaA
Similarity search - Component
Biological speciesPicrophilus torridus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKumari, S. / Sharma, A. / Goel, M.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology , Ministry of Science and Technology (New Delhi, India)BT/Bio-CARe/01/9935/2013-14 India
CitationJournal: To Be Published
Title: Crystal structure of CsaA chaperone protein from picrophilus torridus
Authors: Sharma, A. / Kumari, S. / Verma, V. / Goel, M.
History
DepositionFeb 23, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Protein secretion chaperonin CsaA
B: Protein secretion chaperonin CsaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7063
Polymers23,6132
Non-polymers921
Water4,774265
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Homodimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-25 kcal/mol
Surface area10660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.009, 65.334, 75.588
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 Protein secretion chaperonin CsaA


Mass: 11806.739 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Picrophilus torridus (strain ATCC 700027 / DSM 9790 / JCM 10055 / NBRC 100828) (archaea)
Strain: ATCC 700027 / DSM 9790 / JCM 10055 / NBRC 100828 / Gene: PTO0409 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6L208
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.41 Å3/Da / Density meas: 2.41 Mg/m3 / Density % sol: 49.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20mM Tris buffer pH 8.0, 0.2 M ammonium sul-phate, 1 M NaCl, 25% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 25764 / % possible obs: 98 % / Redundancy: 7.3 % / Χ2: 1.489 / Net I/σ(I): 24.96
Reflection shellResolution: 1.7→1.76 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-2000data scaling
PHASER2.6.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NZH

2nzh


Resolution: 1.7→49.43 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.426 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.11 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22361 1237 4.8 %RANDOM
Rwork0.1829 ---
obs0.18496 24473 97.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.063 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å20 Å20 Å2
2--0.99 Å20 Å2
3----0.29 Å2
Refinement stepCycle: 1 / Resolution: 1.7→49.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1663 0 6 265 1934
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.021722
X-RAY DIFFRACTIONr_bond_other_d0.0030.021714
X-RAY DIFFRACTIONr_angle_refined_deg2.0271.9942329
X-RAY DIFFRACTIONr_angle_other_deg1.05334005
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5315222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.92326.30865
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.11215329
X-RAY DIFFRACTIONr_dihedral_angle_4_deg3.598152
X-RAY DIFFRACTIONr_chiral_restr0.1380.2271
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211869
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02305
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0342.106864
X-RAY DIFFRACTIONr_mcbond_other2.0262.105863
X-RAY DIFFRACTIONr_mcangle_it2.7963.1471079
X-RAY DIFFRACTIONr_mcangle_other2.7983.1471080
X-RAY DIFFRACTIONr_scbond_it3.6282.471858
X-RAY DIFFRACTIONr_scbond_other3.6222.471858
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0343.5511245
X-RAY DIFFRACTIONr_long_range_B_refined6.45627.231893
X-RAY DIFFRACTIONr_long_range_B_other6.35126.621858
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 79 -
Rwork0.307 1571 -
obs--85.85 %

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