PDB-6b4p: Crystal Structure of Peptidylprolyl Isomerase from Naegleria fowleri

ID or keywords:

Entry

Database: PDB / ID: 6b4p

Title

Crystal Structure of Peptidylprolyl Isomerase from Naegleria fowleri

Components

Peptidylprolyl Isomerase

Keywords

ISOMERASE / SSGCID / peptidylprolyl isomerase / Naegleria fowleri / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / peptidylprolyl isomerase
Similarity search - Function

Biological species

Naegleria fowleri (brain-eating amoeba)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.55 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal Structure of Peptidylprolyl Isomerase from Naegleria fowleri
Authors: Dranow, D.M. / Mayclin, S.J. / Lorimer, D.D. / Edwards, T.E.

History

Deposition	Sep 27, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 11, 2017	Provider: repository / Type: Initial release
Revision 1.1	Oct 4, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6b4p.cif.gz	111.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6b4p.ent.gz	84.6 KB	Display	PDB format
PDBx/mmJSON format	6b4p.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b4/6b4p ftp://data.pdbj.org/pub/pdb/validation_reports/b4/6b4p	HTTPS FTP

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Related structure data

Related structure data	1r9hS S: Starting model for refinement
Similar structure data	7a6w-2 6rcj-d 6mke-3 6tx7-d 4jfk-d 5ier-4 7a6w-1 6mke-4 3o5j-d 4jfi-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: SSGCID-NafoA.18272.a.B1

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Links

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

Deposited unit

A: Peptidylprolyl Isomerase

B: Peptidylprolyl Isomerase

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

1

A: Peptidylprolyl Isomerase

defined by author
Evidence: gel filtration
14.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Peptidylprolyl Isomerase

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

3

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	37.250, 61.150, 45.760
Angle α, β, γ (deg.)	90.000, 90.280, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Peptidylprolyl Isomerase Mass: 14206.163 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Naegleria fowleri (brain-eating amoeba) Strain: ATCC 30863 / Gene: NF0084240 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A2H4A315*PLUS
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 220 / 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: 1.83 Å³/Da / Density % sol: 32.94 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop Details: NafoA.18272.a.B1.PS38284 at 22.7 mg/ml was mixed 1:1 with Morpheus (h11): 12.5% (w/v) PEG-1000, 12.5% (w/v) PEG-3350, 12.5% (v/v) MPD, 0.1 M bicine/ Trizma base, pH = 8.5, 0.02 M each sodium ...Details: NafoA.18272.a.B1.PS38284 at 22.7 mg/ml was mixed 1:1 with Morpheus (h11): 12.5% (w/v) PEG-1000, 12.5% (w/v) PEG-3350, 12.5% (v/v) MPD, 0.1 M bicine/ Trizma base, pH = 8.5, 0.02 M each sodium L-glutmate, DL-alanine, glycine, DL-lysine/ HCl, DL-serine. Tray: 292677h11, puck: pfe9-9.

Crystal

Density Matthews: 1.83 Å³/Da / Density % sol: 32.94 %

Crystal grow

Temperature: 290 K / Method: vapor diffusion, sitting drop
Details: NafoA.18272.a.B1.PS38284 at 22.7 mg/ml was mixed 1:1 with Morpheus (h11): 12.5% (w/v) PEG-1000, 12.5% (w/v) PEG-3350, 12.5% (v/v) MPD, 0.1 M bicine/ Trizma base, pH = 8.5, 0.02 M each sodium ...

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97872 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 18, 2017 / Details: Beryllium Lenses

Radiation

Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 1.55→45.759 Å / Num. obs: 29144 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 4.246 % / B_iso Wilson estimate: 17.06 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.053 / R_rim(I) all: 0.061 / Χ²: 1.016 / Net I/σ(I): 16.32 / Num. measured all: 123738 / Scaling rejects: 0

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.55-1.59	4.203	0.214	5.45	8923	2185	2123	0.975	0.245	97.2
1.59-1.63	4.316	0.19	6.55	8879	2150	2057	0.98	0.216	95.7
1.63-1.68	4.317	0.158	7.69	8608	2062	1994	0.985	0.181	96.7
1.68-1.73	4.306	0.134	9.17	8439	2021	1960	0.986	0.153	97
1.73-1.79	4.305	0.106	11.06	8179	1972	1900	0.99	0.121	96.3
1.79-1.85	4.283	0.093	12.63	7950	1904	1856	0.992	0.106	97.5
1.85-1.92	4.298	0.08	14.63	7612	1813	1771	0.994	0.092	97.7
1.92-2	4.274	0.07	17.06	7369	1769	1724	0.994	0.08	97.5
2-2.09	4.252	0.065	18.14	7143	1719	1680	0.995	0.075	97.7
2.09-2.19	4.248	0.057	19.98	6754	1627	1590	0.996	0.066	97.7
2.19-2.31	4.266	0.057	21.27	6450	1531	1512	0.995	0.066	98.8
2.31-2.45	4.248	0.052	22.54	6054	1452	1425	0.997	0.059	98.1
2.45-2.62	4.199	0.055	23.29	5656	1367	1347	0.995	0.063	98.5
2.62-2.83	4.198	0.051	23.91	5457	1318	1300	0.995	0.058	98.6
2.83-3.1	4.192	0.05	25.5	4804	1163	1146	0.995	0.057	98.5
3.1-3.47	4.157	0.047	25.99	4373	1060	1052	0.995	0.053	99.2
3.47-4	4.154	0.046	26.48	3934	953	947	0.996	0.052	99.4
4-4.9	4.138	0.044	26.92	3277	796	792	0.997	0.05	99.5
4.9-6.93	4.106	0.045	26.66	2550	625	621	0.996	0.052	99.4
6.93-45.759	3.824	0.049	25.72	1327	360	347	0.993	0.057	96.4

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHENIX		refinement
PDB_EXTRACT	3.22	data extraction
XDS		data reduction
MoRDa		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1R9H

1r9h

Resolution: 1.55→45.759 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 18.87

	R_factor	Num. reflection	% reflection
R_free	0.1867	2024	6.95 %
R_work	0.1547	-	-
obs	0.1569	29135	97.6 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 72.77 Å² / B_iso mean: 24.657 Å² / B_iso min: 10.6 Å²

Refinement step

Cycle: final / Resolution: 1.55→45.759 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1764	0	0	222	1986
B_iso mean	-	-	-	35.61	-
Num. residues	-	-	-	-	232

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	1851
X-RAY DIFFRACTION	f_angle_d	0.742	2523
X-RAY DIFFRACTION	f_chiral_restr	0.053	279
X-RAY DIFFRACTION	f_plane_restr	0.005	323
X-RAY DIFFRACTION	f_dihedral_angle_d	14.146	1111

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.5499-1.5887	0.2268	146	0.1815	1889	2035	97
1.5887-1.6316	0.2307	151	0.1757	1877	2028	95
1.6316-1.6796	0.2179	134	0.1692	1907	2041	97
1.6796-1.7339	0.2093	143	0.1765	1928	2071	97
1.7339-1.7958	0.2097	150	0.1594	1889	2039	97
1.7958-1.8677	0.2097	128	0.1686	1941	2069	97
1.8677-1.9527	0.1874	123	0.1624	1948	2071	98
1.9527-2.0557	0.1955	135	0.1607	1960	2095	98
2.0557-2.1845	0.1818	174	0.1635	1944	2118	98
2.1845-2.3531	0.2046	153	0.157	1907	2060	98
2.3531-2.5899	0.2051	145	0.1626	1949	2094	98
2.5899-2.9646	0.1838	143	0.1645	1978	2121	99
2.9646-3.7349	0.1712	143	0.1446	1985	2128	99
3.7349-45.7794	0.1662	156	0.1362	2009	2165	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	6.3356	1.1657	-1.6444	0.4883	-0.159	6.735	0.3022	-0.785	0.305	0.7831	0.1789	0.635	-0.4658	-0.5282	-0.2856	0.2356	0.0477	0.0697	0.2673	0.0539	0.2675	2.8982	9.1134	2.9047
2	4.942	-0.1581	-1.9059	1.7089	-1.5234	2.2057	-0.0154	-0.1711	-0.2324	-0.4199	0.5572	0.508	0.4771	-0.3197	-0.5591	0.2156	-0.0446	-0.0691	0.2063	0.0645	0.2014	3.9437	-0.9531	4.2156
3	4.5662	6.0414	0.1338	8.1508	0.2044	2.3904	0.1199	-0.2203	0.1926	0.9341	-0.0066	0.0231	-0.2137	-0.1545	-0.0481	0.2358	0.0251	-0.0624	0.1378	0.0033	0.2015	14.6138	0.3633	15.6017
4	2.6712	-2.0071	2.261	3.2292	-2.0472	6.0486	0.2841	0.206	-0.244	-0.2764	-0.1119	-0.0757	0.4846	0.2264	-0.1991	0.1214	0.0044	-0.0016	0.1072	-0.0164	0.1649	15.9602	-3.7919	-4.6367
5	6.9305	-0.96	-1.8345	1.9794	1.2721	2.8303	0.0092	0.1283	-0.3818	0.3825	0.1847	-0.658	0.7505	0.598	-0.1986	0.2079	0.037	-0.0542	0.1733	-0.0116	0.2505	23.6418	-2.9148	3.5235
6	3.7904	1.2117	-1.4185	4.2261	-1.3847	5.7067	0.103	0.0777	0.0353	0.2509	-0.0668	-0.5134	-0.4701	0.1165	-0.0796	0.1508	-0.0174	-0.0078	0.0845	-0.002	0.1804	17.395	7.8136	4.7781
7	2.0942	-0.4074	1.8192	7.1826	-5.2154	8.54	0.1641	-0.0612	-0.1421	0.0861	0.1016	0.1634	0.2463	-0.2071	-0.2581	0.1127	-0.0044	-0.0067	0.1274	0.0169	0.1403	9.0622	-0.644	5.0604
8	5.4653	1.8232	-2.6519	0.7959	-1.3684	8.1123	-0.1296	0.2599	0.1934	-0.0011	0.0921	-0.0333	-0.4068	-0.0228	0.0296	0.1169	0.0012	0.0204	0.1073	0.0392	0.1327	15.6798	9.8901	-9.6057
9	3.0253	-1.8883	2.4541	3.5807	-2.4865	4.1375	0.2323	-0.0137	-0.1494	0.0298	0.0019	-0.0678	0.4436	0.0742	-0.2979	0.136	0.0023	-0.041	0.1077	-0.0121	0.1495	15.2318	-2.292	4.8092
10	6.9968	2.1365	-4.0577	3.6807	-3.9261	4.7724	-0.169	0.2591	0.8522	0.1553	-0.1075	-0.2939	-0.4976	0.778	-0.3793	0.1706	-0.075	-0.0088	0.3281	0.0492	0.2771	43.3414	16.4223	-15.6131
11	4.1108	1.9945	2.3554	6.9033	4.5957	8.9621	0.0381	0.8947	-0.2213	-0.611	0.312	-0.7478	0.7547	1.043	-0.2046	0.2852	0.0386	0.0934	0.3918	0.0044	0.2168	42.1922	10.0083	-22.5501
12	2.8317	0.1093	0.2669	1.2194	1.124	1.0831	-0.2623	0.6866	0.3373	-0.9722	-0.1948	-0.1594	-0.4189	0.4789	-0.1333	0.5842	0.0136	0.0594	0.3878	0.1524	0.228	30.6064	19.0486	-29.034
13	1.6454	-1.1846	0.6128	2.3057	-1.6711	1.2943	-0.0877	0.3412	-0.1771	-0.7509	-0.0504	0.0291	-0.0991	0.2119	-0.0722	0.276	-0.0012	-0.1202	0.1259	-0.0238	0.1272	29.2946	5.35	-20.9762
14	7.672	1.137	5.621	5.0327	0.593	4.2182	0.5847	0.1166	-0.8076	-0.198	-0.0048	0.163	0.634	0.1664	-0.6118	0.1967	0.0153	-0.037	0.1992	-0.026	0.2079	30.7775	-1.4955	-16.2062
15	2.4464	-0.5058	0.6736	4.1013	0.5295	4.147	-0.0246	-0.0334	-0.0597	-0.4702	0.045	0.8036	0.1419	-0.3688	0.0488	0.1551	-0.0082	-0.0629	0.1866	0.0394	0.2158	22.9729	11.6694	-20.4233
16	2.7289	0.5238	0.214	2.2078	0.3974	4.3883	0.0099	0.3575	0.1247	-0.4047	-0.0693	-0.0793	-0.0097	0.2915	0.0362	0.1724	-0.0025	0.0268	0.175	0.0275	0.1029	34.4669	12.889	-20.5864
17	6.1803	2.496	-3.2301	8.3123	-3.7682	2.7746	0.1423	-0.4122	0.2907	0.5888	-0.0467	0.037	-0.674	0.1197	-0.114	0.2185	-0.0316	0.0103	0.1827	-0.0011	0.1466	31.4098	12.4727	-5.7492
18	7.7164	1.103	-6.0704	4.6122	-4.7152	8.158	-0.3354	-0.2296	-0.3808	0.0949	0.0134	0.0312	0.1139	-0.0954	0.2808	0.1355	-0.0017	0.0066	0.1406	-0.0072	0.1252	29.1687	3.981	-4.5929
19	3.3153	-0.3641	1.7269	1.9562	-2.7292	4.9741	0.0441	0.4444	-0.0693	-0.6635	0.0426	-0.0734	-0.2179	0.0532	0.0018	0.3292	0.0389	-0.0146	0.2071	-0.0034	0.0984	31.3432	8.8926	-23.847

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 14 )	A	3 - 14
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 15 through 20 )	A	15 - 20
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 21 through 32 )	A	21 - 32
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 33 through 54 )	A	33 - 54
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 55 through 61 )	A	55 - 61
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 62 through 77 )	A	62 - 77
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 78 through 88 )	A	78 - 88
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 89 through 108 )	A	89 - 108
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 109 through 119 )	A	109 - 119
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 3 through 14 )	B	3 - 14
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 15 through 20 )	B	15 - 20
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 21 through 32 )	B	21 - 32
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 33 through 42 )	B	33 - 42
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 43 through 54 )	B	43 - 54
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 55 through 68 )	B	55 - 68
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 69 through 88 )	B	69 - 88
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 89 through 97 )	B	89 - 97
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 98 through 108 )	B	98 - 108
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 109 through 119 )	B	109 - 119

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