PDB-9w8l: Isomerase at 200K

ID or keywords:

Entry

Database: PDB / ID: 9w8l

Title

Isomerase at 200K

Components

Peptidyl-prolyl cis-trans isomerase FKBP1A

Keywords

ISOMERASE / Immunnophilin

Function / homology

Function and homology information

macrolide binding / activin receptor binding / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / cytoplasmic side of membrane / transforming growth factor beta receptor binding / TGFBR1 LBD Mutants in Cancer / type I transforming growth factor beta receptor binding / negative regulation of activin receptor signaling pathway / heart trabecula formation / I-SMAD binding ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Guven, O. / DeMirci, H.

Funding support

1items

Citation

Journal: To Be Published
Title: Isomerase at 200K
Authors: Guven, O. / DeMirci, H.

History

Deposition	Aug 7, 2025	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Aug 20, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9w8l.cif.gz	100 KB	Display	PDBx/mmCIF format
PDB format	pdb9w8l.ent.gz	77.2 KB	Display	PDB format
PDBx/mmJSON format	9w8l.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9w8l_validation.pdf.gz	435.3 KB	Display	wwPDB validaton report
Full document	9w8l_full_validation.pdf.gz	438.3 KB	Display
Data in XML	9w8l_validation.xml.gz	13 KB	Display
Data in CIF	9w8l_validation.cif.gz	16.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/w8/9w8l ftp://data.pdbj.org/pub/pdb/validation_reports/w8/9w8l	HTTPS FTP

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Related structure data

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	#230 - Feb 2019 Initiation Factor eIF4E similarity (1) #60 - Dec 2004 Ubiquitin similarity (2) #44 - Aug 2003 Calmodulin similarity (1) #163 - Jul 2013 HIV Capsid similarity (2) #196 - Apr 2016 Lead Poisoning similarity (1) #28 - Apr 2002 Anthrax Toxin similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1) #245 - May 2020 Spliceosomes similarity (1)

Deposited unit

A: Peptidyl-prolyl cis-trans isomerase FKBP1A

B: Peptidyl-prolyl cis-trans isomerase FKBP1A

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

1

A: Peptidyl-prolyl cis-trans isomerase FKBP1A

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

2

B: Peptidyl-prolyl cis-trans isomerase FKBP1A

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

Unit cell

Length a, b, c (Å)	101.780, 36.095, 54.952
Angle α, β, γ (deg.)	90.00, 96.15, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-218- HOH
2	1	B-228- HOH

#1: Protein	Peptidyl-prolyl cis-trans isomerase FKBP1A Mass: 11967.705 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP1A Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P62942
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.1 Å³/Da / Density % sol: 41.33 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: NaCl, Ammonium Sulfate, TRIS

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Data collection

Diffraction	Mean temperature: 200 K / Serial crystal experiment: N
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU PhotonJet-R / Wavelength: 1.54 Å
Detector	Type: RIGAKU HyPix-3000 / Detector: PIXEL / Date: Oct 2, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54 Å / Relative weight: 1
Reflection	Resolution: 2→17.65 Å / Num. obs: 13294 / % possible obs: 88.55 % / Redundancy: 1.8 % / CC_1/2: 0.999 / Net I/σ(I): 22.38
Reflection shell	Resolution: 2→2.071 Å / Num. unique obs: 1030 / CC_1/2: 0.948

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
PDB_EXTRACT		data extraction
CrysalisPro		data reduction
CrysalisPro	1.171.42.35a	data scaling
PHASER	2.8.3	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2→17.65 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 0.07 / Phase error: 35.23 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.3107	1210	9.99 %
R_work	0.2535	-	-
obs	0.2592	12108	88.72 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2→17.65 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1680	0	0	115	1795

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	1718
X-RAY DIFFRACTION	f_angle_d	0.711	2316
X-RAY DIFFRACTION	f_dihedral_angle_d	11.127	652
X-RAY DIFFRACTION	f_chiral_restr	0.046	246
X-RAY DIFFRACTION	f_plane_restr	0.006	304

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 (%)
2-2.08	0.3554	116	0.3192	1043	X-RAY DIFFRACTION	78
2.08-2.17	0.3997	125	0.2934	1122	X-RAY DIFFRACTION	83
2.17-2.29	0.297	118	0.2916	1063	X-RAY DIFFRACTION	79
2.29-2.43	0.3198	131	0.2693	1185	X-RAY DIFFRACTION	87
2.43-2.62	0.3062	143	0.2829	1280	X-RAY DIFFRACTION	94
2.62-2.88	0.3175	144	0.285	1289	X-RAY DIFFRACTION	95
2.88-3.3	0.36	147	0.2659	1330	X-RAY DIFFRACTION	97
3.3-4.14	0.3052	136	0.2216	1220	X-RAY DIFFRACTION	89
4.15-17.65	0.2402	150	0.2	1366	X-RAY DIFFRACTION	96

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	2.409	-0.2417	-0.9094	3.9019	1.2674	3.9866	-0.1824	-0.6577	-0.3358	0.7591	0.2371	0.0556	0.6488	0.2278	-0.0075	0.3059	-0.0127	0.0084	0.3522	0.0436	0.1918	-19.4593	-24.5051	10.0323
2	1.5538	1.0201	-0.7541	0.7982	-0.5323	3.5345	-0.3616	0.4405	-0.824	-0.4234	-0.082	0.4428	0.5732	0.1895	0.2496	0.2069	-0.0091	0.0704	0.475	-0.0649	0.2879	-27.751	-19.2057	-3.1388
3	1.999	-0.8874	1.9836	0.6601	-0.4219	2.5239	0.0389	0.1801	0.1733	0.1499	-0.1378	0.0779	-0.0772	-0.2421	0.025	0.2153	-0.0939	0.0801	0.2771	0.0416	0.2147	-13.6928	-13.7607	3.6505
4	2.6715	1.8309	-0.8819	4.547	0.7237	2.6538	-0.0356	-0.3069	0.3393	0.7549	-0.3246	-0.1445	0.1713	-0.2293	0.0008	0.3004	0.0211	-0.0235	0.3947	-0.0429	0.2206	-5.5809	-16.261	11.791
5	0.2607	0.2562	0.2345	0.2568	0.2393	0.2204	0.1357	0.0142	0.477	0.2823	-0.2954	-0.2459	-0.3039	0.109	-0.0361	0.3908	-0.159	0.0638	0.3497	0.0713	0.3973	-11.461	-5.6507	3.5357
6	2.2089	0.1202	-0.3608	0.5294	-0.2382	0.8636	-0.1336	0.414	-0.2045	-0.1836	0.0104	0.1437	0.0953	-0.0994	0.1214	0.1947	-0.0419	0.0236	0.3659	-0.0158	0.1538	-16.8309	-20.2822	-2.6612
7	4.2075	-1.5089	-0.5355	0.9703	0.0509	1.0028	0.0416	0.1898	0.0997	-0.258	-0.1516	0.0396	0.2794	-0.1407	0.0777	0.2297	-0.0786	0.0324	0.2528	-0.0278	0.1561	-10.1815	-25.0936	5.8674
8	0.0743	0.029	0.0045	0.0151	0.0082	-0.0047	-0.146	0.1904	-0.0431	-0.6215	-0.0529	-0.6696	-0.6141	0.7222	0.0891	-0.1594	-0.2391	0.3122	0.6455	-0.0754	0.1583	2.703	-19.597	4.2201
9	0.9702	-0.498	0.2491	0.4746	-0.0156	0.613	0.0113	0.0516	-0.0744	-0.0131	-0.0719	0.0662	0.0629	0.0718	0.0183	0.1663	-0.0325	0.0432	0.4245	0.0235	0.1692	-12.8578	-18.2309	4.441
10	4.2042	-0.7818	-1.6476	4.4296	1.6058	4.3738	-0.3808	-0.7242	-0.5447	0.578	0.3161	-0.1145	0.6421	-0.105	0.0689	0.3894	-0.039	0.0201	0.1981	0.1107	0.3497	-22.4944	-8.5561	37.2484
11	0.7709	-0.2151	-0.0826	0.4174	0.8434	2.5217	-0.0096	0.6035	-0.1491	-0.179	-0.1	0.5188	0.2716	-0.1267	-0.3537	0.0622	-0.0188	-0.2592	0.2801	-0.1666	0.4548	-30.6131	-3.2698	24.0177
12	2.5113	-0.3746	1.2566	1.1873	-0.4665	2.7495	0.465	0.0712	0.4351	-0.1054	-0.0443	0.1348	-0.2421	-0.2853	0.5169	0.1491	-0.0429	-0.0697	0.0078	-0.1036	0.2614	-16.6606	2.1098	30.9944
13	1.7893	1.0811	-0.591	1.1288	0.3854	1.3933	-0.2281	-0.512	0.4152	0.7257	0.0951	0.2202	0.0484	0.3697	0.0321	0.5667	0.0317	-0.028	0.547	-0.0252	0.43	-10.3409	3.0757	37.0513
14	4.5195	-0.8178	-0.2823	1.3945	-1.7382	3.222	-0.3213	-0.1231	0.6088	0.0086	-0.017	-0.2813	-0.411	-0.2093	0.0391	0.282	0.03	-0.0511	0.1234	0.091	0.2485	-16.8773	5.613	23.9302
15	4.456	-0.1214	-1.8956	1.0023	0.2728	1.1178	-0.2846	0.7211	-0.8293	-0.2446	-0.2566	0.1494	0.3648	-0.4656	-0.1338	0.2099	-0.0098	0.0401	0.0135	0.0504	0.1563	-17.819	-7.2366	23.9543
16	3.657	-1.3471	0.25	0.8912	-0.332	0.1185	-0.1163	-0.7047	0.0171	0.5892	-0.0307	-0.0876	-0.0144	0.2691	0.0496	0.1823	0.0057	-0.0543	-0.156	0.0324	0.2329	-16.8547	-7.2247	32.4857
17	1.9311	-0.8349	0.7263	1.3207	-0.2981	0.8927	-0.0364	-0.3478	0.3422	-0.0637	0.1098	-0.1492	-0.0781	0.2202	0.0658	0.1892	0.0212	0.0235	0.1443	0.0241	0.1603	-12.7711	-2.6065	31.7208

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 9 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 10 through 21 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 22 through 31 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 32 through 39 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 40 through 46 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 47 through 71 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 72 through 86 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 87 through 91 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 92 through 108 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 1 through 9 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 10 through 21 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 22 through 31 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 32 through 43 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 44 through 50 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 51 through 66 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 67 through 86 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 87 through 108 )

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