PDB-4odm: Structure of SlyD from Thermus thermophilus in complex with S2-W2...

ID or keywords:

Entry

Database: PDB / ID: 4odm

Title

Structure of SlyD from Thermus thermophilus in complex with S2-W23A peptide

Components

30S ribosomal protein S2
Peptidyl-prolyl cis-trans isomerase SlyD

Keywords

ISOMERASE / CHAPERONE / FKBP domain / IF domain / peptidyl-prolyl isomerase / PPIase

Function / homology

Function and homology information

peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / ribosomal small subunit assembly / protein refolding / cytosolic small ribosomal subunit / cytoplasmic translation / structural constituent of ribosome / zinc ion binding / metal ion binding / cytoplasm
Similarity search - Function

Biological species

Thermus thermophilus (bacteria)

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.75 Å

Authors

Quistgaard, E.M. / Low, C. / Nordlund, P.

Citation

Journal: BMC Biol. / Year: 2016
Title: Molecular insights into substrate recognition and catalytic mechanism of the chaperone and FKBP peptidyl-prolyl isomerase SlyD.
Authors: Quistgaard, E.M. / Weininger, U. / Ural-Blimke, Y. / Modig, K. / Nordlund, P. / Akke, M. / Low, C.

History

Deposition	Jan 10, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 14, 2015	Provider: repository / Type: Initial release
Revision 1.1	Oct 4, 2017	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4odm.cif.gz	288.4 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	4odm_validation.pdf.gz	542.6 KB	Display	wwPDB validaton report
Full document	4odm_full_validation.pdf.gz	547 KB	Display
Data in XML	4odm_validation.xml.gz	33 KB	Display
Data in CIF	4odm_validation.cif.gz	48.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/od/4odm ftp://data.pdbj.org/pub/pdb/validation_reports/od/4odm	HTTPS FTP

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Related structure data

Related structure data	4odkC 4odlC 4odnC 4odoC 4odpC 4odqC 4odrC C: citing same article (ref.)
Similar structure data	3luo-d 3ltj-d 4odo-1 3asg-2 4phy-d 4ccg-1 6m2c-3 2aug-2 1p1d-d 4zy9-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#157 - Jan 2013 Transfer-Messenger RNA similarity (1) #253 - Jan 2021 Expressome similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #32 - Aug 2002 Chaperones similarity (1) #163 - Jul 2013 HIV Capsid similarity (1) #245 - May 2020 Spliceosomes similarity (1)

Deposited unit

A: Peptidyl-prolyl cis-trans isomerase SlyD

B: Peptidyl-prolyl cis-trans isomerase SlyD

C: Peptidyl-prolyl cis-trans isomerase SlyD

D: Peptidyl-prolyl cis-trans isomerase SlyD

E: 30S ribosomal protein S2

F: 30S ribosomal protein S2

G: 30S ribosomal protein S2

H: 30S ribosomal protein S2

I: 30S ribosomal protein S2

J: 30S ribosomal protein S2

K: 30S ribosomal protein S2

L: 30S ribosomal protein S2

M: 30S ribosomal protein S2

hetero molecules

83.1 kDa, 13 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

B: Peptidyl-prolyl cis-trans isomerase SlyD

G: 30S ribosomal protein S2

H: 30S ribosomal protein S2

hetero molecules

defined by author
20.3 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: Peptidyl-prolyl cis-trans isomerase SlyD

E: 30S ribosomal protein S2

F: 30S ribosomal protein S2

hetero molecules

defined by author
20.4 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Peptidyl-prolyl cis-trans isomerase SlyD

I: 30S ribosomal protein S2

J: 30S ribosomal protein S2

hetero molecules

defined by author
20.3 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Peptidyl-prolyl cis-trans isomerase SlyD

K: 30S ribosomal protein S2

L: 30S ribosomal protein S2

hetero molecules

defined by author
20.4 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

M: 30S ribosomal protein S2

defined by author
1.74 kDa, 1 polymers

Unit cell

Length a, b, c (Å)	184.120, 41.200, 131.520
Angle α, β, γ (deg.)	90.00, 123.13, 90.00
Int Tables number	5
Space group name H-M	C121

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Protein / Protein/peptide , 2 types, 13 molecules ABCDEFGHIJKLM

#1: Protein	Peptidyl-prolyl cis-trans isomerase SlyD / TtSlyD Mass: 16768.693 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: TTHA0346 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SLE7, peptidylprolyl isomerase
#2: Protein/peptide	30S ribosomal protein S2 Mass: 1742.095 Da / Num. of mol.: 9 / Fragment: S2-W23A peptide (UNP residues 20-34) / Mutation: W23A / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) / References: UniProt: P0A7V0

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Non-polymers , 4 types, 613 molecules

#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 606 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.52 Å³/Da / Density % sol: 51.27 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 19% PEG3350, 8% Tacsimate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9199 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 6, 2013
Radiation	Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9199 Å / Relative weight: 1
Reflection	Resolution: 1.75→29.111 Å / Num. all: 83454 / Num. obs: 83454 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / B_iso Wilson estimate: 26.98 Å² / R_sym value: 0.047 / Net I/σ(I): 18.31
Reflection shell	Resolution: 1.75→1.8 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.42 / Num. unique all: 6009 / R_sym value: 0.766 / % possible all: 97.6

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Processing

Software

Name	Version	Classification
XDS		data scaling
PHASER		phasing
PHENIX	(phenix.refine: 1.8.2_1309)	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.75→29.111 Å / SU ML: 0.23 / σ(F): 1.35 / Phase error: 21.8 / Stereochemistry target values: ML / Details: PDB ENTRY 3LUO

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2083	3312	3.97 %	RANDOM
R_work	0.1764	-	-	-
obs	0.1777	83451	99.11 %	-
all	-	83451	-	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.75→29.111 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5353	0	20	606	5979

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	5575
X-RAY DIFFRACTION	f_angle_d	1.094	7581
X-RAY DIFFRACTION	f_dihedral_angle_d	13.556	2087
X-RAY DIFFRACTION	f_chiral_restr	0.075	817
X-RAY DIFFRACTION	f_plane_restr	0.005	1024

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.75-1.7749	0.3879	129	0.3542	3259	X-RAY DIFFRACTION	98
1.7749-1.8014	0.3635	130	0.3194	3269	X-RAY DIFFRACTION	97
1.8014-1.8296	0.3264	143	0.2767	3240	X-RAY DIFFRACTION	99
1.8296-1.8596	0.3086	139	0.2451	3310	X-RAY DIFFRACTION	99
1.8596-1.8916	0.2641	128	0.2307	3297	X-RAY DIFFRACTION	98
1.8916-1.926	0.2429	141	0.212	3314	X-RAY DIFFRACTION	99
1.926-1.963	0.2316	128	0.2067	3337	X-RAY DIFFRACTION	98
1.963-2.0031	0.2438	142	0.202	3306	X-RAY DIFFRACTION	100
2.0031-2.0466	0.204	142	0.1893	3330	X-RAY DIFFRACTION	100
2.0466-2.0942	0.2248	141	0.179	3293	X-RAY DIFFRACTION	99
2.0942-2.1466	0.2255	133	0.1805	3365	X-RAY DIFFRACTION	100
2.1466-2.2046	0.2241	134	0.1782	3315	X-RAY DIFFRACTION	99
2.2046-2.2695	0.2443	127	0.1831	3356	X-RAY DIFFRACTION	100
2.2695-2.3427	0.2253	145	0.1796	3314	X-RAY DIFFRACTION	99
2.3427-2.4264	0.2419	143	0.1857	3361	X-RAY DIFFRACTION	99
2.4264-2.5235	0.2416	153	0.1803	3300	X-RAY DIFFRACTION	100
2.5235-2.6383	0.2164	153	0.1849	3332	X-RAY DIFFRACTION	99
2.6383-2.7772	0.2279	131	0.1766	3410	X-RAY DIFFRACTION	100
2.7772-2.9511	0.2328	131	0.1835	3350	X-RAY DIFFRACTION	99
2.9511-3.1787	0.1998	144	0.1733	3361	X-RAY DIFFRACTION	99
3.1787-3.4981	0.1885	126	0.1605	3380	X-RAY DIFFRACTION	99
3.4981-4.0032	0.1811	145	0.1556	3390	X-RAY DIFFRACTION	99
4.0032-5.0393	0.1554	136	0.1402	3424	X-RAY DIFFRACTION	99
5.0393-29.1154	0.1792	148	0.1733	3526	X-RAY DIFFRACTION	99

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	1.1822	0.5772	-0.366	1.9567	-1.0158	1.1986	-0.0301	0.0153	0.0132	-0.0741	0.056	0.0679	-0.0197	-0.1155	-0.0212	0.1749	0.0471	-0.0179	0.2079	-0.0311	0.1892	40.5624	6.3415	32.209
2	1.7222	-0.6062	0.0946	2.4768	0.8979	1.1869	-0.0215	0.0854	0.1074	-0.1261	0.0777	-0.0803	-0.112	0.0333	-0.0474	0.1807	-0.0444	-0.0126	0.2187	0.003	0.2005	17.7059	3.9839	27.7106
3	1.3502	-0.3188	0.0703	0.8237	0.5762	2.3016	-0.0138	0.2574	0.1742	-0.0986	-0.0148	-0.1162	-0.1733	0.162	0.0136	0.1582	-0.0245	0.0171	0.1636	0.0462	0.1764	-23.317	-10.1802	23.2948
4	2.0185	0.4507	-1.7686	0.4518	-0.3241	3.1039	-0.0896	0.0851	-0.0835	-0.0654	-0.0135	-0.0632	0.1249	0.0301	0.1016	0.2035	0.0252	-0.0147	0.1707	-0.0103	0.2428	-10.1672	10.5842	30.6873
5	1.0299	0.9919	-1.1519	3.882	-4.1574	4.4726	-0.0253	-0.256	-0.1489	1.1575	0.073	0.1703	-0.2181	0.1449	-0.1812	0.6164	0.0396	0.0863	0.3545	0.0103	0.3951	42.1669	6.7721	34.4955
6	4.89	0.5102	-0.7204	5.4723	-1.2986	2.0832	0.2326	-0.5953	-0.23	0.0986	-0.0974	0.69	-0.3686	-0.7236	-0.2116	0.2293	0.0601	-0.0278	0.4461	-0.034	0.2787	32.0595	0.4101	57.062
7	8.6508	-2.325	-6.0266	0.6353	1.6353	4.2242	-0.1422	0.4723	-0.5314	0.3155	0.1309	-0.1478	-0.1794	0.0838	0.1031	0.4341	-0.0116	0.079	0.3928	-0.0352	0.4196	20.3074	6.1083	27.9185
8	4.937	-2.9173	-4.2371	4.8701	3.6453	8.3577	0.2904	0.4786	0.0416	-0.2749	0.4311	-0.4754	-0.5557	1.176	-0.5639	0.5742	-0.1347	0.0789	0.8087	-0.0664	0.3257	28.5091	-0.8111	3.0516
9	6.1881	0.9166	-1.4372	4.9616	-0.753	7.1831	0.0759	0.7426	0.488	-0.7106	0.0454	0.162	-0.9716	-0.1354	-0.0738	0.4013	0.0003	0.0318	0.2854	0.0574	0.2703	-25.0066	-7.72	20.8513
10	1.3028	2.0612	-2.3088	3.2524	-3.646	4.0827	0.0527	0.0303	0.2702	-0.1916	0.0494	-0.3068	-0.3533	0.8453	-0.2457	0.6907	-0.2467	0.013	0.6974	0.1508	0.3834	-16.4102	0.6669	-2.2187
11	5.6285	-1.2302	-0.7628	1.8789	0.4971	1.3731	-0.0689	-1.3404	-0.0927	0.6674	0.2236	-0.1054	-0.2282	0.3926	-0.0511	0.3911	0.0133	-0.0057	0.4499	-0.0174	0.348	-8.7664	13.0741	32.8428
12	3.5565	-0.8864	-1.3744	5.9062	2.7618	9.504	-0.0399	-0.7043	0.131	0.2139	-0.0753	0.4376	-0.0082	-0.7771	0.217	0.1669	-0.0059	-0.0181	0.3014	-0.0072	0.2641	-25.0204	19.9439	52.8007
13	2.3623	0.3051	-0.365	6.2133	0.5189	1.8762	-0.3316	0.0293	0.2312	0.0916	-0.1957	-0.0692	-0.0226	-0.0865	0.1995	0.8634	-0.0839	0.0232	0.7342	0.114	0.8127	23.2141	4.9312	20.3304

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A'
2	X-RAY DIFFRACTION	2	chain 'B'
3	X-RAY DIFFRACTION	3	chain 'C'
4	X-RAY DIFFRACTION	4	chain 'D'
5	X-RAY DIFFRACTION	5	chain 'E'
6	X-RAY DIFFRACTION	6	chain 'F'
7	X-RAY DIFFRACTION	7	chain 'G'
8	X-RAY DIFFRACTION	8	chain 'H'
9	X-RAY DIFFRACTION	9	chain 'I'
10	X-RAY DIFFRACTION	10	chain 'J'
11	X-RAY DIFFRACTION	11	chain 'K'
12	X-RAY DIFFRACTION	12	chain 'L'
13	X-RAY DIFFRACTION	13	chain 'M'

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