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- PDB-2y6y: Crystal structure of TtrD from Archaeoglobus fulgidus -

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Basic information

Entry
Database: PDB / ID: 2y6y
TitleCrystal 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: 2.2 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
DepositionJan 27, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2012Group: Other
Revision 1.2Dec 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

Downloads & links

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Assembly

Deposited unit
A: CHAPERONE PROTEIN TTRD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4322
Polymers20,3961
Non-polymers351
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.058, 87.058, 83.392
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein CHAPERONE PROTEIN TTRD


Mass: 20396.436 Da / Num. of mol.: 1
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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsADDITIONAL GLY-ALA AT N-TERMINUS REMAIN FOLLOWING CLEAVAGE OF AFFINITY TAG.

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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: 4.47 Å3/Da / Density % sol: 72.5 % / Description: NONE
Crystal growDetails: PROTEIN BUFFER 50 MM TRIS, 250 MM NACL, PH 7.5; RESERVOIR 4.3 M NACL, 0.1 M HEPES PH 7.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97698
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 13, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97698 Å / Relative weight: 1
ReflectionResolution: 2.2→55.9 Å / Num. obs: 18960 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 9.9 % / Biso Wilson estimate: 35.8 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.1
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.5 / % possible all: 100

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Processing

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

2xol


Resolution: 2.2→55.93 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.921 / SU B: 8.177 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23767 955 5 %RANDOM
Rwork0.21702 ---
obs0.21805 17981 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.414 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20.26 Å20 Å2
2--0.53 Å20 Å2
3----0.79 Å2
Refinement stepCycle: LAST / Resolution: 2.2→55.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1339 0 1 72 1412
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221365
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.131.9741835
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.15161
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.13823.18266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.93715258
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8521511
X-RAY DIFFRACTIONr_chiral_restr0.0860.2203
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211012
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.5551.5814
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.12721311
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.7683551
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0914.5524
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.201→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 86 -
Rwork0.243 1286 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.9719-0.1993-3.64981.02950.12919.21590.195-0.11840.18320.0951-0.1465-0.1059-0.60860.2951-0.04850.3827-0.06250.00790.28280.0140.2039-36.31323.7810.516
214.36776.9278-17.016615.0974-10.865723.16381.61650.83591.3858-1.1374-0.03251.0589-2.1042-0.5445-1.5840.82240.05910.08410.20250.07170.1675-43.82730.29713.037
31.39210.0624-0.44272.6639-0.49491.7739-0.00360.08130.0465-0.1204-0.0638-0.214-0.04340.12140.06740.3326-0.02010.00690.3144-0.00150.219-35.93911.2339.504
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 23
2X-RAY DIFFRACTION2A24 - 47
3X-RAY DIFFRACTION3A48 - 164

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