PDB-5htf: Crystal Structure of PrsA1 from Listeria monocytogenes

ID or keywords:

Entry

Database: PDB / ID: 5htf

Title

Crystal Structure of PrsA1 from Listeria monocytogenes

Components

Foldase protein PrsA 1

Keywords

CHAPERONE / PrsA / PPIase / post-translocation chaperone / secretion

Function / homology

Function and homology information

peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / plasma membrane
Similarity search - Function

Biological species

Listeria monocytogenes (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.1 Å

Authors

Prehna, G. / Cahoon, L.A. / Freitag, N.E.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	R01 AI083241	United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	AI083241-03S1	United States

Citation

Journal: Mol.Microbiol. / Year: 2016
Title: A structural comparison of Listeria monocytogenes protein chaperones PrsA1 and PrsA2 reveals molecular features required for virulence.
Authors: Cahoon, L.A. / Freitag, N.E. / Prehna, G.

History

Deposition	Jan 26, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 6, 2016	Provider: repository / Type: Initial release
Revision 1.1	Jul 6, 2016	Group: Data collection
Revision 1.2	Jul 13, 2016	Group: Database references
Revision 1.3	Sep 13, 2017	Group: Author supporting evidence / Database references / Derived calculations Category: citation / pdbx_audit_support / pdbx_struct_oper_list Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4	Dec 11, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5	Mar 6, 2024	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

-
Download

PDBx/mmCIF format	5htf.cif.gz	314.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5htf.ent.gz	263 KB	Display	PDB format
PDBx/mmJSON format	5htf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5htf_validation.pdf.gz	453.8 KB	Display	wwPDB validaton report
Full document	5htf_full_validation.pdf.gz	462.3 KB	Display
Data in XML	5htf_validation.xml.gz	23.3 KB	Display
Data in CIF	5htf_validation.cif.gz	33.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ht/5htf ftp://data.pdbj.org/pub/pdb/validation_reports/ht/5htf	HTTPS FTP

-
Related structure data

Similar structure data	6fcu-d 6fcq-d 6fcr-d 6fc4-d 6lbe-d 5ohu-d 6fcs-d 6fbt-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#32 - Aug 2002 Chaperones similarity (1) #261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #163 - Jul 2013 HIV Capsid similarity (1) #245 - May 2020 Spliceosomes similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #29 - May 2002 Penicillin-binding Proteins similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#32 - Aug 2002
Chaperones
similarity (1)
#261 - Sep 2021
DNA-Sequencing Nanopores
similarity (1)
#163 - Jul 2013
HIV Capsid
similarity (1)
#245 - May 2020
Spliceosomes
similarity (1)
#22 - Oct 2001
Photosystem I
similarity (1)
#262 - Oct 2021
Fifty Years of Open Access to PDB Structures
similarity (1)
#29 - May 2002
Penicillin-binding Proteins
similarity (1)
#95 - Nov 2007
Multidrug Resistance Transporters
similarity (1)

Deposited unit

A: Foldase protein PrsA 1

B: Foldase protein PrsA 1

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	65.310, 84.030, 114.770
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Foldase protein PrsA 1 Mass: 31685.072 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: ATCC BAA-679 / EGD-e / Gene: prsA1, lmo1444 / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)star / References: UniProt: Q8Y759, peptidylprolyl isomerase
#2: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.4 Å³/Da / Density % sol: 48.68 %
Crystal grow	Temperature: 278 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 26 mg/mL PrsA1 with a 1:1 mixture of 30% MPD (2-methyl-2,4-pentadiol) 100 mM Na Acetate pH 4.5.

-
Data collection

Diffraction	Mean temperature: 80 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97941 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 20, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97941 Å / Relative weight: 1
Reflection	Resolution: 2.1→19.782 Å / Num. obs: 37408 / % possible obs: 99.5 % / Redundancy: 5.7 % / CC_1/2: 0.999 / R_merge(I) obs: 0.064 / Net I/σ(I): 17.4
Reflection shell	Resolution: 2.1→2.2 Å / Redundancy: 5.8 % / R_merge(I) obs: 0.984 / Mean I/σ(I) obs: 1.9 / % possible all: 99.3

-
Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XDS		data reduction
XDS		data scaling
autoSHARP		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.1→19.782 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.61 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2342	1863	4.98 %
R_work	0.1982	-	-
obs	0.2	37395	99.67 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.1→19.782 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4098	0	16	281	4395

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	4167
X-RAY DIFFRACTION	f_angle_d	0.934	5617
X-RAY DIFFRACTION	f_dihedral_angle_d	14.911	1553
X-RAY DIFFRACTION	f_chiral_restr	0.033	647
X-RAY DIFFRACTION	f_plane_restr	0.003	709

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 (%)
2.1-2.1567	0.3174	124	0.3059	2688	X-RAY DIFFRACTION	100
2.1567-2.2201	0.3235	137	0.2701	2699	X-RAY DIFFRACTION	99
2.2201-2.2917	0.2881	121	0.2528	2680	X-RAY DIFFRACTION	99
2.2917-2.3735	0.2694	135	0.2353	2729	X-RAY DIFFRACTION	100
2.3735-2.4683	0.2763	152	0.2122	2687	X-RAY DIFFRACTION	100
2.4683-2.5804	0.2457	140	0.202	2707	X-RAY DIFFRACTION	100
2.5804-2.7162	0.2418	153	0.1994	2722	X-RAY DIFFRACTION	100
2.7162-2.8858	0.2616	150	0.2144	2710	X-RAY DIFFRACTION	100
2.8858-3.1079	0.274	135	0.2133	2747	X-RAY DIFFRACTION	100
3.1079-3.4192	0.2359	142	0.2045	2729	X-RAY DIFFRACTION	100
3.4192-3.9106	0.2069	153	0.1775	2753	X-RAY DIFFRACTION	100
3.9106-4.9145	0.2146	165	0.1667	2774	X-RAY DIFFRACTION	100
4.9145-19.7833	0.2125	156	0.1907	2907	X-RAY DIFFRACTION	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	0.3963	0.0287	0.2034	0.1228	0.1242	0.1349	0.1993	-1.583	0.5947	1.9615	-0.1816	-0.0705	-0.3504	0.1521	0.0056	0.9144	-0.0915	-0.1304	0.7319	0.0164	0.5236	19.3665	-33.157	12.6945
2	0.6752	0.7905	0.186	1.2087	0.4756	1.0553	0.0839	-0.2195	-0.1182	0.3245	-0.0018	-0.2587	0.2107	-0.1051	0	0.339	0.0427	-0.0932	0.3647	-0.0098	0.3575	20.9508	-17.8642	3.8549
3	0.2215	-0.1884	0.2026	0.4307	-0.0262	0.0801	-0.1771	0.5532	0.5419	-0.5831	0.0056	0.4648	0.0557	0.496	-0.0194	0.3525	0.0204	0.0023	0.7529	0.1395	0.5454	2.7167	-2.9963	-4.8791
4	0.0661	0.0073	0.0924	0.0812	0.0334	0.0946	0.9387	1.5724	-0.5566	-0.7083	-0.5709	0.1305	-0.2185	-0.5564	-0.0004	0.8801	-0.057	0.0441	1.0827	-0.0955	0.8462	0.8227	-13.5078	-15.3995
5	1.6596	-0.4347	0.084	0.2565	-0.0396	1.4289	-0.1745	0.4433	-0.1734	-0.3908	0.1071	0.7739	0.4025	-0.0524	-0.0001	0.3951	-0.0136	-0.0604	0.4687	-0.0054	0.4705	10.4311	-8.3687	-5.6212
6	0.1273	-0.5164	0.6183	0.4933	-0.5444	0.2846	-0.0401	0.4828	0.5735	0.1351	-0.4675	-0.3654	0.0354	0.7824	-0.0027	0.5759	-0.0105	-0.1031	0.4395	-0.0021	0.5033	11.7875	15.7928	-17.264
7	4.1764	-0.3737	0.3963	4.2477	0.1119	3.7897	-0.0368	-0.1397	0.1745	0.6641	0.0205	-0.2838	0.2338	0.0632	-0.0033	0.4242	-0.003	-0.1024	0.27	0.0151	0.2686	0.5622	-3.7595	-35.0758
8	0.4328	0.037	0.0347	0.2083	-0.0864	0.2063	0.337	0.0953	-0.668	-0.6195	0.0348	1.299	0.6273	-0.3126	-0.0146	0.6769	0.0581	-0.1786	0.3773	-0.0344	0.4794	1.5568	19.3629	-19.7708
9	0.1694	-1.0509	0.1643	1.0104	-0.6149	1.09	0.1879	0.2998	0.1603	-0.2928	-0.2384	-0.1741	0.1221	0.4211	0.0002	0.3773	0.0247	-0.0612	0.365	0.031	0.3788	18.9163	4.7072	-7.9241
10	0.6526	0.8518	-0.1884	1.4542	-0.7363	0.8801	-0.4074	0.1987	-0.2329	-0.3994	-0.0368	-1.2827	0.5288	0.7144	-0.0936	0.4297	0.091	-0.0542	0.4825	-0.0038	0.5603	30.7541	-10.7337	1.9632
11	0.3757	-0.2204	0.3419	0.2019	-0.1502	0.6671	-0.1217	-0.8194	0.4734	0.8954	-0.2345	0.2964	-0.0082	-0.558	-0.0004	0.5331	0.0254	-0.1107	0.4854	-0.0827	0.4532	22.2566	-12.6723	11.5024
12	0.4032	0.4519	0.1973	0.4976	0.6111	1.1284	-0.0594	-0.0692	-0.3414	0.1796	0.2993	0.7519	0.0463	0.1587	0.0002	0.3306	-0.0163	-0.1032	0.3589	-0.0061	0.467	18.7304	-31.1279	-0.1882
13	0.116	0.1574	0.1812	0.2362	0.1447	0.4166	0.0656	0.6457	-0.8358	-0.1588	0.4019	-0.5874	-0.7658	0.4942	0.0172	0.3389	0.0125	-0.07	0.5473	-0.0625	0.7437	31.9326	-44.8041	-5.2885
14	0.015	0.0258	0.0407	-0.0055	-0.0161	1.0413	0.2597	0.8494	-0.0209	-0.4399	-0.3638	-1.3092	-1.3014	0.58	0.0082	0.8439	0.1435	0.1534	1.2812	0.1746	0.8931	37.8507	-32.8818	-16.4942
15	1.5645	-0.1777	-1.0541	1.2186	-1.9391	3.6266	0.0895	0.5804	-0.1651	-0.877	-0.2148	-0.817	-0.6273	0.3666	0.0015	0.6122	0.0407	0.1264	0.7536	-0.0061	0.6525	27.9828	-38.3165	-17.5162
16	0.0785	-0.2091	0.0445	0.1088	-0.0128	0.0398	-0.2098	0.0451	0.8255	0.1504	0.2753	-0.1609	-0.9283	0.0143	-0.0009	1.6671	-0.1724	-0.0393	1.2357	0.1309	1.7345	28.7725	-18.9669	-43.3913
17	0.0866	-0.1064	0.211	0.1761	-0.1335	0.3481	-0.4255	-1.0499	0.4843	0.1496	0.2976	-0.0821	0.1155	0.1509	-0.0016	1.1132	-0.1805	0.1221	1.3493	-0.1698	1.305	26.4662	-31.9832	-38.22
18	0.12	0.0342	0.1886	0.1327	-0.3243	0.9105	-0.0878	0.8045	0.6457	-0.3612	-0.6661	0.3824	-0.2621	0.0631	-0.0012	1.3967	-0.0217	0.0626	1.0295	-0.0402	1.3569	26.7007	-31.1627	-41.1698
19	1.6642	-0.1769	1.1883	2.2103	-0.642	1.0514	0.0172	0.4254	-0.3797	-0.4178	-0.0947	-0.5431	0.4107	-0.0106	0.0118	0.3394	0.0444	0.0082	0.4624	-0.0376	0.5732	19.3382	-45.0858	-14.7657
20	0.8423	0.0397	0.1792	0.6013	0.2387	0.3375	0.0081	0.0857	0.2482	0.0789	-0.2615	0.2486	0.3373	-0.3453	0	0.3671	0.027	0.0495	0.4092	-0.0001	0.458	8.8237	-35.2905	-2.0528

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 21:29)
2	X-RAY DIFFRACTION	2	(chain A and resid 30:66)
3	X-RAY DIFFRACTION	3	(chain A and resid 67:80)
4	X-RAY DIFFRACTION	4	(chain A and resid 81:90)
5	X-RAY DIFFRACTION	5	(chain A and resid 91:118)
6	X-RAY DIFFRACTION	6	(chain A and resid 119:136)
7	X-RAY DIFFRACTION	7	(chain A and resid 137:228)
8	X-RAY DIFFRACTION	8	(chain A and resid 229:237)
9	X-RAY DIFFRACTION	9	(chain A and resid 238:267)
10	X-RAY DIFFRACTION	10	(chain A and resid 268:282)
11	X-RAY DIFFRACTION	11	(chain B and resid 23:41)
12	X-RAY DIFFRACTION	12	(chain B and resid 42:63)
13	X-RAY DIFFRACTION	13	(chain B and resid 64:71)
14	X-RAY DIFFRACTION	14	(chain B and resid 72:84)
15	X-RAY DIFFRACTION	15	(chain B and resid 85:135)
16	X-RAY DIFFRACTION	16	(chain B and resid 136:179)
17	X-RAY DIFFRACTION	17	(chain B and resid 180:206)
18	X-RAY DIFFRACTION	18	(chain B and resid 207:237)
19	X-RAY DIFFRACTION	19	(chain B and resid 238:267)
20	X-RAY DIFFRACTION	20	(chain B and resid 268:289)

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi