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- PDB-2xol: High resolution structure of TtrD from Archaeoglobus fulgidus -

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Basic information

Entry
Database: PDB / ID: 2xol
TitleHigh resolution structure of TtrD from Archaeoglobus fulgidus
ComponentsCHAPERONE PROTEIN TTRD
KeywordsCHAPERONE / TAT SYSTEM
Function / homologyTorD-like / TorD-like / DMSO/Nitrate reductase chaperone / TorD-like superfamily / Nitrate reductase delta subunit / Orthogonal Bundle / Mainly Alpha / cytoplasm / Tat proofreading chaperone TtrD
Function and homology information
Biological speciesARCHAEOGLOBUS FULGIDUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsDawson, A. / Coulthurst, S.J. / Sargent, F. / Hunter, W.N.
CitationJournal: Biochemistry / Year: 2012
Title: Conserved Signal Peptide Recognition Systems Across the Prokaryotic Domains.
Authors: Coulthurst, S.J. / Dawson, A. / Hunter, W.N. / Sargent, F.
History
DepositionAug 18, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2012Group: Other
Revision 1.2Mar 7, 2012Group: Other
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: CHAPERONE PROTEIN TTRD
B: CHAPERONE PROTEIN TTRD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8553
Polymers40,7932
Non-polymers621
Water7,080393
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-10.1 kcal/mol
Surface area16540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.763, 52.537, 64.947
Angle α, β, γ (deg.)90.00, 91.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CHAPERONE PROTEIN TTRD /


Mass: 20396.436 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARCHAEOGLOBUS FULGIDUS (archaea) / Plasmid: PET15BTEV_TTRD / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O30077
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 393 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsADDITIONAL GA AT N-TERMINUS LEFT AFTER CLEAVAGE OF PURIFICATION TA

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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: 2.63 Å3/Da / Density % sol: 53.2 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.2 M SODIUM FORMATE, 20% PEG 3350, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.977
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.35→64.69 Å / Num. obs: 89700 / % possible obs: 96.9 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 14.78 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.6
Reflection shellResolution: 1.35→1.42 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 4.2 / % possible all: 94.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IDG

2idg


Resolution: 1.35→64.93 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.499 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.17751 4523 5 %RANDOM
Rwork0.15116 ---
obs0.15248 85158 96.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.751 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20.17 Å2
2--0.2 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.35→64.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2782 0 4 393 3179
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222926
X-RAY DIFFRACTIONr_bond_other_d0.0010.022106
X-RAY DIFFRACTIONr_angle_refined_deg1.2771.9733932
X-RAY DIFFRACTIONr_angle_other_deg0.89535114
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5185340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.87623.243148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.37215576
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5781526
X-RAY DIFFRACTIONr_chiral_restr0.0790.2435
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023153
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02625
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_it2.41.51716
X-RAY DIFFRACTIONr_mcbond_other0.9531.5682
X-RAY DIFFRACTIONr_mcangle_it3.59822786
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.08231210
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.3354.51145
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.3415032
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 324 -
Rwork0.196 6125 -
obs--94.3 %

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