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

ID or keywords:

Entry

Database: PDB / ID: 2nsb

Title

Structures of and interactions between domains of trigger factor from Themotoga maritima

Components

Trigger factor

Keywords

CHAPERONE

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 / protein transport / ribosome binding / cell cycle ...
Similarity search - Function

Biological species

Thermotoga maritima (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 3.2 Å

Authors

Martinez-Hackert, E. / Hendrickson, W.A.

Citation

Journal: 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

Deposition	Nov 3, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 27, 2007	Provider: repository / Type: Initial release
Revision 1.1	Apr 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Derived calculations / Version format compliance
Revision 1.3	Dec 27, 2023	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2nsb.cif.gz	58.2 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	2nsb_validation.pdf.gz	424 KB	Display	wwPDB validaton report
Full document	2nsb_full_validation.pdf.gz	426.5 KB	Display
Data in XML	2nsb_validation.xml.gz	6.8 KB	Display
Data in CIF	2nsb_validation.cif.gz	7.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ns/2nsb ftp://data.pdbj.org/pub/pdb/validation_reports/ns/2nsb	HTTPS FTP

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Related structure data

Related structure data	2nsaC 2nscC C: citing same article (ref.)
Similar structure data	2nsc-d 2rax-1 2km7-d 2dgc-1 1wwa-1 3cto-7 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#32 - Aug 2002 Chaperones similarity (1) #163 - Jul 2013 HIV Capsid similarity (1) #245 - May 2020 Spliceosomes similarity (1)

Deposited unit

A: Trigger factor

12.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

2

A: Trigger factor

defined by software
25.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	48.092, 86.553, 32.954
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

#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

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.68 Å³/Da / Density % sol: 54.1 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / pH: 6.5 Details: 14% PEG 4000, 0.2M potassium chloride 0.2M, 0.1M MES, pH 6.5, VAPOR DIFFUSION, temperature 293K

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Data collection

Diffraction

ID	Crystal-ID
1	1
2	1
3	1

Diffraction source

Source:

SYNCHROTRON / Site:

NSLS

/ Beamline: X4A / Wavelength: 0.97917, 0.97884, 0.96864

Detector

Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 24, 2005
Details: KOHZU double crystal monochromator with a sagittally focused second crystal.

Radiation

Monochromator: double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97917	1
2	0.97884	1
3	0.96864	1

Reflection

D res high: 3.2 Å / D res low: 50 Å

Redundancy (%)	ID	Av σ(I) over netI	Number	R_merge(I) obs	Χ²	Num. obs	% possible obs
3	1	28.3	11956	0.029	1.22	4052	91.8
2.9	2	26.2	11895	0.03	1.22	4042	91.6
1.5	3	21.1	5195	0.029	1.2	3450	78.1

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
6.89	50	90.2	1	0.022	1.029	3.3
5.47	6.89	97.3	1	0.027	1.13	3.4
4.78	5.47	98.2	1	0.029	1.207	3.4
4.34	4.78	99.1	1	0.03	1.159	3.5
4.03	4.34	99.3	1	0.033	1.449	3.4
3.79	4.03	98.7	1	0.036	1.292	3.1
3.6	3.79	95.6	1	0.053	1.508	2.7
3.45	3.6	93.8	1	0.067	1.072	2.3
3.31	3.45	77	1	0.072	0.996	1.9
3.2	3.31	68.2	1	0.126	1.019	1.8
6.89	50	89.5	2	0.023	1.06	3.3
5.47	6.89	95.4	2	0.028	1.125	3.4
4.78	5.47	97.9	2	0.029	1.155	3.4
4.34	4.78	99.3	2	0.032	1.254	3.5
4.03	4.34	99.3	2	0.036	1.459	3.4
3.79	4.03	98.5	2	0.041	1.323	3.1
3.6	3.79	95.6	2	0.058	1.398	2.7
3.45	3.6	94.1	2	0.073	1.106	2.3
3.31	3.45	77.4	2	0.086	1.117	1.9
3.2	3.31	68.5	2	0.137	0.888	1.8
6.89	50	82.1	3	0.023	1.2	1.6
5.47	6.89	88.4	3	0.026	1.315	1.6
4.78	5.47	88.9	3	0.027	1.156	1.6
4.34	4.78	90.8	3	0.031	1.298	1.6
4.03	4.34	91.4	3	0.034	1.523	1.6
3.79	4.03	84.9	3	0.037	1.132	1.5
3.6	3.79	81	3	0.06	1.076	1.4
3.45	3.6	72.3	3	0.076	0.98	1.4
3.31	3.45	54.5	3	0.096	0.552	1.2
3.2	3.31	47.1	3	0.155	0.701	1.2

Reflection

Resolution: 3.2→50 Å / Num. obs: 2373 / % possible obs: 91.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / R_merge(I) obs: 0.029 / Net I/σ(I): 28.3

Reflection shell

Resolution: 3.2→3.31 Å / Redundancy: 1.8 % / R_merge(I) obs: 0.126 / Num. unique all: 302 / % possible all: 68.2

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Phasing

Phasing

Method:

MAD

Phasing set

ID
1
2
3

Phasing MAD set

Clust-ID	Expt-ID	Set-ID	Wavelength (Å)	F double prime refined	F prime refined
1	3 wavelength	1	0.9788	5.56	-6.71
1	3 wavelength	2	0.9792	4.19	-12.08
1	3 wavelength	3	0.9686	3.71	-0.98

Phasing MAD set site

ID	Cartn x (Å)	Cartn y (Å)	Cartn z (Å)	Atom type symbol	B iso	Occupancy
1	11.765	15.182	17.049	SE	60	0.49
2	30.582	38.6	16.749	SE	60	0.2
3	34.134	9.354	3.771	SE	60	0.34

Phasing dm

FOM : 0.79 / FOM acentric: 0.8 / FOM centric: 0.73 / Reflection: 1890 / Reflection acentric: 1404 / Reflection centric: 486

Phasing dm shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
10-19.785	0.97	0.97	0.97	81	41	40
6.3-10	0.92	0.94	0.88	272	172	100
5-6.3	0.88	0.91	0.8	324	233	91
4.4-5	0.88	0.9	0.81	325	245	80
3.8-4.4	0.73	0.76	0.64	548	438	110
3.5-3.8	0.55	0.6	0.34	340	275	65

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Processing

Software

Name	Version	Classification
SOLVE		phasing
RESOLVE	2.06	phasing
REFMAC	5.2.0019	refinement
PDB_EXTRACT	2	data extraction
ADSC	QUANTUM	data collection
DENZO		data reduction
CCP4	(SCALA)	data scaling

Refinement

Method to determine structure:

MAD / Resolution: 3.2→19.8 Å / Cor.coef. F_o:F_c: 0.901 / Cor.coef. F_o:F_c free: 0.922 / SU B: 57.322 / SU ML: 0.412 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.551
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.262	224	9.6 %	RANDOM
R_work	0.256	-	-	-
all	0.262	-	-	-
obs	-	2343	100 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 101.166 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.38 Å²	0 Å²	0 Å²
2-	-	-0.31 Å²	0 Å²
3-	-	-	-0.06 Å²

Refinement step

Cycle: LAST / Resolution: 3.2→19.8 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	898	0	0	0	898

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	909
X-RAY DIFFRACTION	r_angle_refined_deg	1.208	2.002	1222
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	1.093	5	108
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	43.104	24.348	46
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.455	15	186
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.079	15	9
X-RAY DIFFRACTION	r_chiral_restr	0.077	0.2	140
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	671
X-RAY DIFFRACTION	r_nbd_refined	0.299	0.2	399
X-RAY DIFFRACTION	r_nbtor_refined	0.343	0.2	625
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.164	0.2	22
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.302	0.2	64
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.155	0.2	12
X-RAY DIFFRACTION	r_mcbond_it	1.752	1.5	545
X-RAY DIFFRACTION	r_mcangle_it	3.261	2	888
X-RAY DIFFRACTION	r_scbond_it	1.891	3	364
X-RAY DIFFRACTION	r_scangle_it	3.18	4.5	334

LS refinement shell

Resolution: 3.201→3.282 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.329	8	-
R_work	0.328	120	-
obs	-	128	100 %

Refinement TLS params.

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

ID	L11 (°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)
1	0.4642	0.7328	-0.3318	1.1625	-0.596	1.1773	-0.1514	0.0192	-0.1503	-0.0171	0.143	-0.0649	-0.1598	-0.0463	0.0085	0.7562	-0.0155	0.0633	0.6027	0.0251	0.8107	41.525	39.3401	7.8227
2	3.4456	-3.5447	2.2277	21.8997	-15.288	20.4498	-0.4784	-1.4012	0.064	2.5331	0.8046	1.582	-1.1697	-0.0905	-0.3262	0.5289	0.0033	0.1423	0.7304	0.0217	0.7915	40.641	32.1217	29.1211
3	19.1354	7.302	-16.1705	5.2124	-3.3408	16.9659	1.2821	-1.8568	0.4718	0.7602	-1.6633	-0.4665	0.6017	2.6579	0.3812	1.0629	0.1682	-0.1137	0.9383	-0.0856	0.5532	51.2222	29.2278	33.5375
4	1.8668	2.416	4.8382	3.6832	6.1894	12.5488	-0.8327	-0.7434	-0.5744	0.3811	0.548	0.2821	-0.2216	-0.2278	0.2847	0.5666	-0.0265	0.0159	0.7827	0.1595	0.631	33.1295	31.3466	17.8853

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

ID	Refine TLS-ID	Auth seq-ID	Label seq-ID
1	1	1 - 21	1 - 21
2	1	84 - 109	84 - 109
3	2	22 - 39	22 - 39
4	3	40 - 60	40 - 60
5	4	61 - 83	61 - 83

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