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- PDB-2yjm: Structure of TtrD from Archaeoglobus fulgidus -

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Basic information

Entry
Database: PDB / ID: 2yjm
TitleStructure of TtrD from Archaeoglobus fulgidus
ComponentsTTRD
KeywordsCHAPERONE
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 / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsDawson, A. / Coulthurst, S.J. / Hunter, W.N. / Sargent, F.
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
DepositionMay 20, 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: TTRD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6042
Polymers20,3961
Non-polymers2071
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.160, 37.930, 49.120
Angle α, β, γ (deg.)90.00, 94.16, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: 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-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsADDITIONAL GA AT N-TERMINUS FROM AFFINITY TAG CLEAVAGE.

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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: 2.08 Å3/Da / Density % sol: 40.8 % / Description: NONE
Crystal growpH: 7.5
Details: PROTEIN BUFFER: 50 MM TRIS, 250 MM NACL, 5 MM GMP-PNP; RESERVOIR: 0.1 M CHES PH 9.5, 20% W/V PEG 8K.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU CCD / Detector: CCD / Date: Aug 28, 2009 / Details: MIRRORS
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.84→35.01 Å / Num. obs: 13256 / % possible obs: 90.6 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 24.4 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.9
Reflection shellResolution: 1.84→1.94 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 4.3 / % possible all: 84.7

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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 2IDG

2idg


Resolution: 1.84→48.99 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.921 / SU B: 6.655 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.193 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24515 680 5.1 %RANDOM
Rwork0.21414 ---
obs0.21575 12576 89.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.209 Å2
Baniso -1Baniso -2Baniso -3
1--1.75 Å20 Å2-1.12 Å2
2--0.7 Å20 Å2
3---0.89 Å2
Refinement stepCycle: LAST / Resolution: 1.84→48.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1356 0 13 88 1457
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221397
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9841.981878
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3345164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.86123.23568
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.64515260
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3431511
X-RAY DIFFRACTIONr_chiral_restr0.0720.2205
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211035
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_it0.4591.5826
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.88621329
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.483571
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5164.5549
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: 1.841→1.889 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.435 42 -
Rwork0.303 823 -
obs--80.32 %
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)
13.43922.58150.48263.44950.57210.90810.0907-0.3604-0.21860.1783-0.147-0.14520.1151-0.04180.05630.12580.00270.00450.11310.02980.1108-11.23-5.03419.35
22.18810.31850.49741.5081-0.04811.3484-0.0016-0.18120.08770.0589-0.0147-0.0424-0.04450.03390.01630.13520.0050.02040.0888-0.00740.1152-13.0333.3612.093
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 27
2X-RAY DIFFRACTION2A28 - 163

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