PDB-7wim: Crystal structure of Arabidopsis thaliana FKBP43 N-terminal domain

ID or keywords:

Entry

Database: PDB / ID: 7wim

Title

Crystal structure of Arabidopsis thaliana FKBP43 N-terminal domain

Components

Peptidyl-prolyl cis-trans isomerase FKBP43

Keywords

CHAPERONE / Nucleoplasmin / Histone chaperone / FKBP / PPIase

Function / homology

Nucleoplasmin-like domain / Nucleoplasmin-like domain / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / Peptidyl-prolyl cis-trans isomerase domain superfamily / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / Peptidyl-prolyl cis-trans isomerase FKBP43

Function and homology information

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.29 Å

Authors

Singh, A.K. / Saharan, K. / Baral, S. / Vasudevan, D.

Funding support

India, 2items

Citation

Journal: Biochim Biophys Acta Gene Regul Mech / Year: 2022
Title: The plant nucleoplasmin AtFKBP43 needs its extended arms for histone interaction.
Authors: Singh, A.K. / Saharan, K. / Baral, S. / Vasudevan, D.

History

Deposition	Jan 3, 2022	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Sep 21, 2022	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7wim.cif.gz	686.2 KB	Display	PDBx/mmCIF format
PDB format	pdb7wim.ent.gz	566.7 KB	Display	PDB format
PDBx/mmJSON format	7wim.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7wim_validation.pdf.gz	610.5 KB	Display	wwPDB validaton report
Full document	7wim_full_validation.pdf.gz	632 KB	Display
Data in XML	7wim_validation.xml.gz	55.2 KB	Display
Data in CIF	7wim_validation.cif.gz	78 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wi/7wim ftp://data.pdbj.org/pub/pdb/validation_reports/wi/7wim	HTTPS FTP

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Related structure data

Related structure data	6j2zS S: Starting model for refinement
Similar structure data	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: Peptidyl-prolyl cis-trans isomerase FKBP43

B: Peptidyl-prolyl cis-trans isomerase FKBP43

C: Peptidyl-prolyl cis-trans isomerase FKBP43

D: Peptidyl-prolyl cis-trans isomerase FKBP43

E: Peptidyl-prolyl cis-trans isomerase FKBP43

F: Peptidyl-prolyl cis-trans isomerase FKBP43

G: Peptidyl-prolyl cis-trans isomerase FKBP43

H: Peptidyl-prolyl cis-trans isomerase FKBP43

I: Peptidyl-prolyl cis-trans isomerase FKBP43

J: Peptidyl-prolyl cis-trans isomerase FKBP43

K: Peptidyl-prolyl cis-trans isomerase FKBP43

L: Peptidyl-prolyl cis-trans isomerase FKBP43

M: Peptidyl-prolyl cis-trans isomerase FKBP43

N: Peptidyl-prolyl cis-trans isomerase FKBP43

O: Peptidyl-prolyl cis-trans isomerase FKBP43

P: Peptidyl-prolyl cis-trans isomerase FKBP43

Q: Peptidyl-prolyl cis-trans isomerase FKBP43

R: Peptidyl-prolyl cis-trans isomerase FKBP43

S: Peptidyl-prolyl cis-trans isomerase FKBP43

T: Peptidyl-prolyl cis-trans isomerase FKBP43

264 kDa, 20 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Peptidyl-prolyl cis-trans isomerase FKBP43

B: Peptidyl-prolyl cis-trans isomerase FKBP43

C: Peptidyl-prolyl cis-trans isomerase FKBP43

D: Peptidyl-prolyl cis-trans isomerase FKBP43

E: Peptidyl-prolyl cis-trans isomerase FKBP43

defined by author&software
Evidence: gel filtration
66 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

F: Peptidyl-prolyl cis-trans isomerase FKBP43

G: Peptidyl-prolyl cis-trans isomerase FKBP43

H: Peptidyl-prolyl cis-trans isomerase FKBP43

I: Peptidyl-prolyl cis-trans isomerase FKBP43

J: Peptidyl-prolyl cis-trans isomerase FKBP43

defined by author&software
66 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

K: Peptidyl-prolyl cis-trans isomerase FKBP43

L: Peptidyl-prolyl cis-trans isomerase FKBP43

M: Peptidyl-prolyl cis-trans isomerase FKBP43

N: Peptidyl-prolyl cis-trans isomerase FKBP43

O: Peptidyl-prolyl cis-trans isomerase FKBP43

defined by author&software
66 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

P: Peptidyl-prolyl cis-trans isomerase FKBP43

Q: Peptidyl-prolyl cis-trans isomerase FKBP43

R: Peptidyl-prolyl cis-trans isomerase FKBP43

S: Peptidyl-prolyl cis-trans isomerase FKBP43

T: Peptidyl-prolyl cis-trans isomerase FKBP43

defined by author&software
66 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	53.058, 203.914, 94.547
Angle α, β, γ (deg.)	90.00, 96.14, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Peptidyl-prolyl cis-trans isomerase FKBP43 / PPIase FKBP43 / FK506-binding protein 43 / AtFKBP43 / Immunophilin FKBP43 / Rotamase Mass: 13192.855 Da / Num. of mol.: 20 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: FKBP43, At3g12340, F28J15.1, MQC3.15, T2E22.33 / Plasmid: pET22b+ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F4J9Q6, peptidylprolyl isomerase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Peptidyl-prolyl cis-trans isomerase FKBP43 / PPIase FKBP43 / FK506-binding protein 43 / AtFKBP43 / Immunophilin FKBP43 / Rotamase

Mass: 13192.855 Da / Num. of mol.: 20
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Arabidopsis thaliana (thale cress) / Gene: FKBP43, At3g12340, F28J15.1, MQC3.15, T2E22.33 / Plasmid: pET22b+ / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F4J9Q6, peptidylprolyl isomerase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 9 / 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: 1.93 Å³/Da / Density % sol: 36.18 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 M ammonium acetate, 0.1 M Tris (pH 8.5), 25% (w/v) Polyethylene glycol 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9794 Å
Detector	Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Aug 31, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 2.29→48.28 Å / Num. obs: 88501 / % possible obs: 100 % / Redundancy: 6.6 % / CC_1/2: 0.99 / Net I/σ(I): 10.4
Reflection shell	Resolution: 2.3→2.42 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 8417 / CC_1/2: 0.89 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(1.14_3260: ???)	refinement
XDS		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6J2Z

6j2z

Resolution: 2.29→47 Å / SU ML: 0.34 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 33.4 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.258	4430	5.03 %
R_work	0.223	-	-
obs	0.224	88104	99 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.29→47 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13365	0	0	9	13374

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	13588
X-RAY DIFFRACTION	f_angle_d	0.673	18485
X-RAY DIFFRACTION	f_dihedral_angle_d	9.721	7920
X-RAY DIFFRACTION	f_chiral_restr	0.047	2262
X-RAY DIFFRACTION	f_plane_restr	0.004	2333

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 (%)
2.294-2.3198	0.3572	137	0.3057	2337	X-RAY DIFFRACTION	84
2.3198-2.347	0.3229	134	0.298	2759	X-RAY DIFFRACTION	99
2.347-2.3757	0.3109	140	0.2933	2800	X-RAY DIFFRACTION	99
2.3757-2.4057	0.3427	149	0.2856	2845	X-RAY DIFFRACTION	99
2.4057-2.4374	0.3338	132	0.2973	2732	X-RAY DIFFRACTION	99
2.4374-2.4708	0.3679	151	0.2873	2794	X-RAY DIFFRACTION	100
2.4708-2.5061	0.3287	146	0.3019	2831	X-RAY DIFFRACTION	100
2.5061-2.5435	0.347	134	0.2919	2819	X-RAY DIFFRACTION	99
2.5435-2.5832	0.3454	157	0.2959	2782	X-RAY DIFFRACTION	99
2.5832-2.6256	0.3437	140	0.3024	2825	X-RAY DIFFRACTION	99
2.6256-2.6708	0.3556	143	0.3054	2779	X-RAY DIFFRACTION	99
2.6708-2.7194	0.3977	161	0.3005	2768	X-RAY DIFFRACTION	99
2.7194-2.7717	0.3016	143	0.2802	2834	X-RAY DIFFRACTION	100
2.7717-2.8283	0.2997	143	0.2584	2768	X-RAY DIFFRACTION	100
2.8283-2.8898	0.3167	150	0.2656	2784	X-RAY DIFFRACTION	99
2.8898-2.957	0.3162	172	0.2549	2834	X-RAY DIFFRACTION	99
2.957-3.0309	0.2906	153	0.2616	2738	X-RAY DIFFRACTION	100
3.0309-3.1128	0.3017	168	0.2566	2811	X-RAY DIFFRACTION	100
3.1128-3.2044	0.2789	127	0.236	2808	X-RAY DIFFRACTION	100
3.2044-3.3078	0.2509	124	0.2399	2850	X-RAY DIFFRACTION	100
3.3078-3.426	0.2685	149	0.2268	2787	X-RAY DIFFRACTION	100
3.426-3.5631	0.2699	153	0.222	2842	X-RAY DIFFRACTION	100
3.5631-3.7252	0.2452	136	0.217	2799	X-RAY DIFFRACTION	100
3.7252-3.9216	0.2314	159	0.2048	2798	X-RAY DIFFRACTION	100
3.9216-4.1671	0.2194	138	0.1954	2846	X-RAY DIFFRACTION	100
4.1671-4.4886	0.2121	154	0.1746	2819	X-RAY DIFFRACTION	100
4.4886-4.9399	0.186	134	0.1511	2825	X-RAY DIFFRACTION	100
4.9399-5.6537	0.1844	164	0.1749	2802	X-RAY DIFFRACTION	100
5.6537-7.1191	0.2581	175	0.2077	2811	X-RAY DIFFRACTION	100
7.1191-47	0.2389	164	0.2198	2847	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	2.259	2.0429	0.351	3.2197	-0.1675	4.2635	-0.3654	-1.0156	0.9589	0.9436	0.2849	0.385	-0.6006	-0.0498	0.1241	0.9188	0.2394	-0.0794	0.9286	-0.2955	0.4348	7.0762	8.566	24.4445
2	4.222	1.5329	-0.0725	5.9064	-0.5207	4.5532	-0.3514	-0.2163	0.8059	0.5847	0.0476	-0.6004	-0.3614	-0.075	0.2597	0.4825	0.081	-0.2146	0.3773	-0.09	0.6819	19.9061	15.0827	10.4971
3	1.5146	0.7424	-0.151	2.6536	0.7814	2.5497	-0.2878	-0.5515	-0.1573	0.7908	0.185	0.6051	0.0446	-0.3989	0.0465	0.5442	0.1167	0.1365	0.616	0.089	0.3154	2.2984	-8.8924	20.0781
4	4.6674	-0.0677	0.6463	6.7145	-0.5467	4.2214	-0.0878	-0.0471	-0.4471	-0.1524	0.1643	-0.0953	0.224	-0.038	-0.0613	0.2461	0.019	0.0345	0.2787	0.0139	0.2811	11.4159	-14.6897	3.8791
5	4.3335	-0.8376	1.78	4.8136	-1.8	4.333	-0.13	0.4393	-0.0441	-0.3834	0.004	-0.6136	-0.1858	0.3151	0.0965	0.3706	0.0265	0.0935	0.3734	-0.0438	0.5451	21.6774	0.7154	-2.5048
6	2.5694	-0.462	-0.7633	5.0753	-2.0756	3.972	-0.0177	-0.3892	0.3053	0.9442	0.1535	0.7599	-0.529	-0.2925	-0.1046	0.6097	0.039	0.1295	0.3763	-0.0864	0.4603	-12.0624	19.6432	-21.8678
7	5.6435	-0.3724	0.6331	6.7277	-0.5814	3.9405	-0.1873	0.0881	0.5914	0.0256	0.0425	-0.0725	-0.2964	-0.0884	0.1443	0.3515	0.0168	0.0164	0.2278	0.0091	0.3655	-0.8779	25.8317	-37.0734
8	4.6612	-0.3002	-0.3363	3.0928	0.4903	2.904	-0.1809	-0.0946	-0.3681	0.5273	0.0424	0.9882	-0.026	-0.3546	0.1292	0.4071	0.0456	0.1173	0.3097	0.0141	0.4798	-17.4438	1.5313	-25.5804
9	4.8083	1.3124	-0.1058	5.7953	0.0404	3.5328	-0.0826	0.4845	-0.2637	-0.5662	0.0754	0.5674	0.2387	-0.1681	-0.014	0.4171	0.0202	-0.0489	0.3216	-0.0697	0.2964	-9.1458	-4.0791	-42.4197
10	3.0705	0.4601	0.4755	6.3775	-1.1206	4.9046	-0.0335	0.6177	-0.0432	-0.9613	-0.1225	0.0066	0.0546	-0.1064	0.0724	0.417	0.0324	0.0636	0.3997	-0.0478	0.3112	0.9289	11.3191	-49.6762
11	4.8014	0.4932	0.151	4.2801	0.5867	1.1468	0.2174	-0.1586	-0.903	-0.6345	-0.0856	1.7511	0.3624	-0.3999	-0.0987	0.6328	0.0011	-0.2633	0.6129	0.0801	1.2984	-2.1365	-62.6107	-14.2284
12	1.8416	-1.0611	-0.0549	4.4207	0.4027	3.8311	0.0339	-0.4114	-0.505	0.0277	0.3589	0.6261	0.6224	-0.2757	-0.2913	0.4827	-0.031	-0.1261	0.4825	0.2008	0.8744	14.8395	-70.0035	-7.1609
13	4.502	-1.702	0.2464	4.7722	0.9931	2.3548	0.2337	-0.2124	-0.8106	-0.371	-0.1944	1.5651	0.2239	-0.6556	-0.0202	0.3601	0.0069	-0.092	0.61	0.0964	0.8576	-3.8485	-44.4957	-8.3591
14	3.8921	-1.4527	1.263	5.2853	0.2409	5.1243	-0.0458	-0.4189	-0.193	0.297	0.2457	0.1096	-0.2488	-0.2313	-0.1837	0.2488	0.0365	0.0769	0.3823	0.0973	0.3959	10.9909	-39.6543	2.6848
15	2.2508	-1.4198	0.8882	4.8036	1.6122	6.7104	0.0419	-0.3206	0.0045	0.6129	0.3472	-0.0474	0.4133	0.1187	-0.3445	0.3352	0.0121	-0.0004	0.4069	0.1091	0.6006	21.7171	-55.869	4.099
16	2.7519	1.2198	0.8949	6.372	-0.7008	4.2207	-0.2422	-0.0275	0.1578	-0.6805	-0.0554	2.1061	0.3242	-0.6025	0.309	0.7303	-0.0235	-0.2017	0.5697	-0.1859	1.2537	-24.7956	-52.8629	-57.589
17	3.2235	-0.7017	-0.9566	8.3568	1.0292	4.4295	-0.1041	-0.1641	-0.1394	-0.1742	-0.2038	0.5883	0.355	-0.2173	0.3006	0.3995	0.028	0.0342	0.3321	-0.0759	0.7607	-7.7875	-59.4748	-51.9487
18	3.4408	0.3762	0.5344	4.6243	1.5225	0.5785	-0.205	-0.1404	-0.021	-1.1842	-0.8588	2.6253	-0.5047	-0.9084	0.519	0.4959	0.1005	-0.3089	0.6846	-0.3858	1.6847	-25.5125	-34.2894	-51.7861
19	3.7217	-0.7587	0.1411	7.1884	1.8804	3.2441	0.0821	-0.221	-0.0627	0.1324	-0.0859	0.6304	-0.1423	-0.1483	-0.0573	0.4297	-0.0005	0.0517	0.3716	-0.1028	0.4332	-10.2249	-29.186	-43.0947
20	5.1627	-0.7439	-0.3919	8.3968	3.9242	6.2306	-0.2065	-0.2521	-0.0628	1.1762	0.3148	-1.138	0.5312	0.3851	-0.007	0.5226	0.0773	-0.0708	0.3561	-0.0427	0.7045	-0.1648	-45.2803	-41.6476

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESSEQ 2:97)
2	X-RAY DIFFRACTION	2	(CHAIN B AND RESSEQ 2:97)
3	X-RAY DIFFRACTION	3	(CHAIN C AND RESSEQ 2:97)
4	X-RAY DIFFRACTION	4	(CHAIN D AND RESSEQ 2:97)
5	X-RAY DIFFRACTION	5	(CHAIN E AND RESSEQ 2:97)
6	X-RAY DIFFRACTION	6	(CHAIN F AND RESSEQ 2:97)
7	X-RAY DIFFRACTION	7	(CHAIN G AND RESSEQ 2:97)
8	X-RAY DIFFRACTION	8	(CHAIN H AND RESSEQ 2:97)
9	X-RAY DIFFRACTION	9	(CHAIN I AND RESSEQ 2:97)
10	X-RAY DIFFRACTION	10	(CHAIN J AND RESSEQ 2:97)
11	X-RAY DIFFRACTION	11	(CHAIN K AND RESSEQ 2:97)
12	X-RAY DIFFRACTION	12	(CHAIN L AND RESSEQ 2:97)
13	X-RAY DIFFRACTION	13	(CHAIN M AND RESSEQ 2:97)
14	X-RAY DIFFRACTION	14	(CHAIN N AND RESSEQ 2:97)
15	X-RAY DIFFRACTION	15	(CHAIN O AND RESSEQ 2:97)
16	X-RAY DIFFRACTION	16	(CHAIN P AND RESSEQ 2:97)
17	X-RAY DIFFRACTION	17	(CHAIN Q AND RESSEQ 2:97)
18	X-RAY DIFFRACTION	18	(CHAIN R AND RESSEQ 2:97)
19	X-RAY DIFFRACTION	19	(CHAIN S AND RESSEQ 2:97)
20	X-RAY DIFFRACTION	20	(CHAIN T AND RESSEQ 2:97)

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Movie

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Structure viewers

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Viewer log

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This page

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Open data

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Basic information

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Structure visualization

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Download

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Validation report

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Related structure data

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Links

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Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

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Data collection

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About Yorodumi

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News

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

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

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Jul 12, 2017. Major update of PDB

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Yorodumi