PDB-8x6p: Isomerase Protein

ID or keywords:

Entry

Database: PDB / ID: 8x6p

Title

Isomerase Protein

Components

Peptidyl-prolyl cis-trans isomerase FKBP1A

Keywords

ISOMERASE / Proline

Function / homology

Function and homology information

macrolide binding / activin receptor binding / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / transforming growth factor beta receptor binding / cytoplasmic side of membrane / 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: 1.05 Å

Authors

Guven, O. / Demirci, H.

Funding support

Turkey, 1items

Citation

Journal: To Be Published
Title: Isomerase Protein
Authors: Guven, O. / Demirci, H.

History

Deposition	Nov 21, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Dec 20, 2023	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8x6p.cif.gz	109.4 KB	Display	PDBx/mmCIF format
PDB format	pdb8x6p.ent.gz	83.3 KB	Display	PDB format
PDBx/mmJSON format	8x6p.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8x6p_validation.pdf.gz	440.4 KB	Display	wwPDB validaton report
Full document	8x6p_full_validation.pdf.gz	441 KB	Display
Data in XML	8x6p_validation.xml.gz	14.4 KB	Display
Data in CIF	8x6p_validation.cif.gz	20.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x6/8x6p ftp://data.pdbj.org/pub/pdb/validation_reports/x6/8x6p	HTTPS FTP

-
Related structure data

Similar structure data	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	#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

hetero molecules

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

1

A: Peptidyl-prolyl cis-trans isomerase FKBP1A

hetero molecules

A: Peptidyl-prolyl cis-trans isomerase FKBP1A

hetero molecules

defined by author&software
24.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Peptidyl-prolyl cis-trans isomerase FKBP1A

hetero molecules

B: Peptidyl-prolyl cis-trans isomerase FKBP1A

hetero molecules

defined by author&software
24.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	101.850, 36.124, 54.499
Angle α, β, γ (deg.)	90.00, 95.99, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-201- SO4
2	1	B-201- SO4
3	1	A-373- HOH
4	1	B-373- 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 (E. coli) / References: UniProt: P62942
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 326 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.08 Å³/Da / Density % sol: 40.95 %
Crystal grow	Temperature: 300 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: NaCl, Ammonium Sulfate, TRIS

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU PhotonJet-R / Wavelength: 1.54 Å
Detector	Type: RIGAKU HyPix-Arc 150 / Detector: PIXEL / Date: Apr 1, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54 Å / Relative weight: 1
Reflection	Resolution: 1.05→53.9 Å / Num. obs: 101614 / % possible obs: 94.5 % / Redundancy: 3.7 % / CC_1/2: 0.999 / CC star: 0.995 / Net I/σ(I): 16.16
Reflection shell	Resolution: 1.05→1.08 Å / Num. unique obs: 6791 / CC_1/2: 0.075 / CC star: 0.373

-
Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
CrysalisPro		data reduction
CrysalisPro		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.05→22.08 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 28.16 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2237	2000	2.48 %
R_work	0.205	-	-
obs	0.2054	80574	87.39 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.05→22.08 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1680	0	10	326	2016

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	1830
X-RAY DIFFRACTION	f_angle_d	1.132	2489
X-RAY DIFFRACTION	f_dihedral_angle_d	13.129	703
X-RAY DIFFRACTION	f_chiral_restr	0.093	260
X-RAY DIFFRACTION	f_plane_restr	0.009	336

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 (%)
1.05-1.08	0.4029	113	0.4248	4425	X-RAY DIFFRACTION	69
1.08-1.11	0.4289	116	0.3729	4590	X-RAY DIFFRACTION	72
1.11-1.14	0.3153	121	0.3321	4768	X-RAY DIFFRACTION	75
1.14-1.17	0.2934	129	0.3052	5027	X-RAY DIFFRACTION	78
1.17-1.22	0.2653	132	0.2726	5194	X-RAY DIFFRACTION	82
1.22-1.27	0.2619	139	0.2557	5471	X-RAY DIFFRACTION	86
1.27-1.32	0.2991	141	0.2414	5565	X-RAY DIFFRACTION	87
1.32-1.39	0.2452	150	0.2145	5882	X-RAY DIFFRACTION	92
1.39-1.48	0.2351	153	0.202	5959	X-RAY DIFFRACTION	93
1.48-1.59	0.2182	153	0.1875	6047	X-RAY DIFFRACTION	94
1.59-1.75	0.2023	161	0.1766	6288	X-RAY DIFFRACTION	98
1.75-2.01	0.218	161	0.1708	6370	X-RAY DIFFRACTION	99
2.01-2.53	0.1894	163	0.1829	6400	X-RAY DIFFRACTION	99
2.53-22.08	0.1864	168	0.1732	6588	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	2.885	-1.1288	-2.6319	5.1274	2.5791	4.1236	-0.3315	-0.3916	-0.2461	0.4105	0.3453	0.0845	0.3307	0.2255	-0.0345	0.102	0.0027	0.0191	0.0682	0.0151	0.0623	-19.0671	-20.2581	9.9697
2	4.2717	0.2468	-2.2623	1.0034	-0.1823	5.6394	-0.0803	0.2973	-0.2018	-0.1448	0.0214	0.1309	0.1594	-0.0641	0.1087	0.0692	0.0039	-0.0145	0.057	-0.0057	0.0785	-26.916	-15.5425	-3.7432
3	4.1551	-1.2429	3.4381	1.8273	-0.4377	3.2819	-0.1109	-0.0429	0.0785	0.0446	0.0959	-0.0677	-0.1838	-0.0018	0.0115	0.065	-0.0173	0.0138	0.0614	0.0013	0.0818	-14.6312	-8.7639	2.6474
4	4.8084	-3.5554	3.1736	6.574	-2.6911	6.2178	-0.2117	-0.0773	0.2668	0.4311	-0.1134	-0.2357	-0.253	0.139	0.3131	0.091	-0.0244	-0.0126	0.0933	-0.0117	0.0971	-7.1821	-8.8193	9.62
5	2.9025	0.2619	1.0962	2.3367	3.3262	5.5247	-0.1791	0.1625	0.2442	-0.7246	0.272	-0.2149	-0.6937	0.2694	-0.1005	0.115	-0.0126	-0.0078	0.0767	0.0077	0.0987	-14.2225	-5.918	-3.417
6	8.1936	-0.2219	4.7535	4.6327	-1.5785	7.9026	0.0739	0.5777	-0.0338	-0.3531	-0.0534	-0.0071	0.1213	0.4358	-0.006	0.0738	0.0113	0.0113	0.1046	0.0034	0.0739	-12.0664	-16.8288	-7.0808
7	6.4596	-1.7281	-0.7436	0.7069	0.0516	1.0537	-0.0488	0.1278	-0.1311	0.0304	-0.0181	0.0379	0.0085	0.0044	0.0645	0.0722	-0.0048	0.0064	0.0417	0.0038	0.0638	-19.7937	-17.4859	0.9036
8	2.0576	1.6751	-0.4266	2.0576	0.2604	1.1367	-0.233	-0.1653	0.1404	0.305	0.1285	-0.076	-0.0075	0.1241	0.0126	0.0741	0.0086	0.003	0.0709	0.0027	0.0511	-16.8369	-15.972	9.2288
9	7.8366	-2.2778	0.9423	0.6716	-0.1217	2.0303	0.0541	0.0055	-0.4273	-0.0202	-0.0256	0.0041	0.0998	-0.0215	-0.0235	0.0712	-0.0009	0.0001	0.0667	-0.0003	0.0797	-5.6621	-24.0306	3.695
10	6.5545	1.4492	-1.8207	1.8377	-0.8037	3.1067	0.0547	-0.2645	-0.0636	0.0567	-0.0353	-0.0144	0.0287	0.1149	-0.0279	0.0649	0.0085	0.0001	0.0851	-0.0028	0.0588	0.5383	-18.8814	6.9123
11	4.6115	-2.2438	2.4693	1.7677	-1.3588	2.8718	-0.0399	0.0222	0.093	0.0176	0.0523	0.0649	-0.1847	0.0009	0.013	0.0649	-0.0141	0.0059	0.0309	0.0065	0.0774	-18.8151	-9.6634	1.8973
12	3.16	-0.9277	-0.5169	1.6755	0.0511	3.0584	0.0077	-0.08	-0.2557	0.0282	0.0151	0.1562	0.0644	-0.0058	-0.0237	0.0637	-0.0321	0.0137	0.0381	-0.0104	0.0989	-26.8169	-0.4774	30.049
13	3.5241	-0.9144	1.3957	3.3392	-0.168	3.1115	-0.0903	-0.1622	0.1109	0.1912	0.007	-0.172	-0.0703	0.1375	0.0589	0.0609	-0.016	0.01	0.0954	0.0171	0.0755	-14.2032	6.8037	29.4245
14	4.02	-0.9419	-0.0806	0.6464	0.2647	0.1671	-0.0142	-0.2754	-0.1017	0.0693	0.0197	0.0095	0.0156	0.0453	-0.0046	0.0847	-0.0051	0.0014	0.0982	0.0171	0.0537	-15.1819	-0.5582	30.9641

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 30 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 31 through 43 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 44 through 50 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 51 through 57 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 58 through 71 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 72 through 77 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 78 through 86 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 87 through 97 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 98 through 108 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 1 through 21 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 22 through 57 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 58 through 108 )

-
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://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