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- PDB-2nsc: Structures of and interactions between domains of trigger factor ... -

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Basic information

Entry
Database: PDB / ID: 2nsc
TitleStructures of and interactions between domains of trigger factor from Themotoga maritima
ComponentsTrigger factor
KeywordsCHAPERONE
Function / homology
Function and homology information


'de novo' cotranslational protein folding / protein unfolding / chaperone-mediated protein folding / protein folding chaperone / regulation of DNA-templated transcription elongation / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / ribosome binding / protein transport / cell cycle ...'de novo' cotranslational protein folding / protein unfolding / chaperone-mediated protein folding / protein folding chaperone / regulation of DNA-templated transcription elongation / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / ribosome binding / protein transport / cell cycle / cell division / DNA binding / cytoplasm
Similarity search - Function
Trigger factor ribosome-binding domain / Transcription elongation factor GreA/GreB, C-terminal domain superfamily / Trigger factor / Trigger factor, C-terminal / Trigger factor, ribosome-binding, bacterial / Trigger factor ribosome-binding domain superfamily / Bacterial trigger factor protein (TF) / Bacterial trigger factor protein (TF) C-terminus / Trigger factor, C-terminal domain superfamily / Trigger factor/SurA domain superfamily ...Trigger factor ribosome-binding domain / Transcription elongation factor GreA/GreB, C-terminal domain superfamily / Trigger factor / Trigger factor, C-terminal / Trigger factor, ribosome-binding, bacterial / Trigger factor ribosome-binding domain superfamily / Bacterial trigger factor protein (TF) / Bacterial trigger factor protein (TF) C-terminus / Trigger factor, C-terminal domain superfamily / Trigger factor/SurA domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsMartinez-Hackert, E. / Hendrickson, W.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: Structures of and interactions between domains of trigger factor from Thermotoga maritima.
Authors: Martinez-Hackert, E. / Hendrickson, W.A.
History
DepositionNov 3, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Nov 29, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_related
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_related.db_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Trigger factor


Theoretical massNumber of molelcules
Total (without water)12,8191
Polymers12,8191
Non-polymers00
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: Trigger factor

A: Trigger factor


Theoretical massNumber of molelcules
Total (without water)25,6382
Polymers25,6382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area4930 Å2
ΔGint-22 kcal/mol
Surface area14120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.214, 75.871, 30.514
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsStrand swapped dimer is probably a construct artifact

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Components

#1: Protein Trigger factor / TF


Mass: 12818.841 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: tig / Plasmid: pet24d / Production host: Escherichia coli (E. coli) / Strain (production host): codonplus RIL / References: UniProt: Q9WZF8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.32 Å3/Da / Density % sol: 46.9 %
Crystal growTemperature: 293 K / pH: 6.5
Details: 15% PEG 4000, 0.2M potassium chloride, 0.1M MES, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.91994
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 13, 2004
RadiationMonochromator: DOUBLE MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91994 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 6440 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 34.2
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 7.756 / % possible all: 99.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å19.62 Å
Translation2.5 Å19.62 Å

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Processing

Software
NameVersionClassificationNB
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→19.62 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.916 / SU B: 12.164 / SU ML: 0.161 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.316 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26 297 4.6 %RANDOM
Rwork0.195 ---
obs-6404 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.98 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å20 Å20 Å2
2--0.39 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms898 0 0 138 1036
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022909
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1642.0021222
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5615108
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.70524.34846
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.80315186
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.532159
X-RAY DIFFRACTIONr_chiral_restr0.0730.2140
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02671
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2170.2381
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.2613
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.276
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.280
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8381.5568
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.292888
X-RAY DIFFRACTIONr_scbond_it2.0943378
X-RAY DIFFRACTIONr_scangle_it3.324.5334
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 17 -
Rwork0.202 424 -
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)
13.30811.76040.20191.1084-0.09090.4767-0.00820.1043-0.0257-0.0618-0.0128-0.0142-0.0158-0.02650.0210.00480.02790.0075-0.0415-0.0133-0.008943.8371-2.577321.4033
22.5856-3.7292.110117.4845-11.21779.3725-0.1973-0.24240.10380.37020.2575-0.0774-0.2764-0.0019-0.0602-0.03010.00740.00840.015-0.0414-0.05742.4689-10.036941.7072
32.6722-2.6833.52268.8326-0.307414.322-0.11050.00810.29580.39670.1394-0.5711-0.0290.9912-0.0289-0.16270.0702-0.06080.0014-0.0030.050852.4335-14.693946.1619
410.9193-3.56895.71541.8353-1.75683.27840.0339-0.2196-0.16720.09930.02440.10540.1886-0.233-0.0584-0.0302-0.00070.02020.0298-0.0177-0.038334.6626-9.294831.204
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 211 - 21
2X-RAY DIFFRACTION1AA84 - 10984 - 109
3X-RAY DIFFRACTION2AA22 - 3922 - 39
4X-RAY DIFFRACTION3AA40 - 6040 - 60
5X-RAY DIFFRACTION4AA61 - 8361 - 83

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