[English] 日本語
Yorodumi
- PDB-8x6p: Isomerase Protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8x6p
TitleIsomerase Protein
ComponentsPeptidyl-prolyl cis-trans isomerase FKBP1A
KeywordsISOMERASE / Proline
Function / homology
Function and homology information


macrolide binding / activin receptor binding / cytoplasmic side of membrane / transforming growth factor beta receptor binding / TGFBR1 LBD Mutants in Cancer / signaling receptor inhibitor activity / type I transforming growth factor beta receptor binding / negative regulation of activin receptor signaling pathway / heart trabecula formation / terminal cisterna ...macrolide binding / activin receptor binding / cytoplasmic side of membrane / transforming growth factor beta receptor binding / TGFBR1 LBD Mutants in Cancer / signaling receptor inhibitor activity / type I transforming growth factor beta receptor binding / negative regulation of activin receptor signaling pathway / heart trabecula formation / terminal cisterna / ryanodine receptor complex / I-SMAD binding / regulation of amyloid precursor protein catabolic process / protein maturation by protein folding / 'de novo' protein folding / ventricular cardiac muscle tissue morphogenesis / negative regulation of phosphoprotein phosphatase activity / FK506 binding / mTORC1-mediated signalling / TGF-beta receptor signaling activates SMADs / Calcineurin activates NFAT / regulation of immune response / protein peptidyl-prolyl isomerization / supramolecular fiber organization / heart morphogenesis / regulation of ryanodine-sensitive calcium-release channel activity / sarcoplasmic reticulum membrane / T cell activation / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / sarcoplasmic reticulum / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / calcium ion transmembrane transport / negative regulation of transforming growth factor beta receptor signaling pathway / Z disc / SARS-CoV-1 activates/modulates innate immune responses / regulation of protein localization / protein folding / positive regulation of protein binding / protein refolding / positive regulation of canonical NF-kappaB signal transduction / Potential therapeutics for SARS / transmembrane transporter binding / amyloid fibril formation / membrane / cytosol / cytoplasm
Similarity search - Function
FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase FKBP1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsGuven, O. / Demirci, H.
Funding support Turkey, 1items
OrganizationGrant numberCountry
Other government Turkey
CitationJournal: To Be Published
Title: Isomerase Protein
Authors: Guven, O. / Demirci, H.
History
DepositionNov 21, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase FKBP1A
B: Peptidyl-prolyl cis-trans isomerase FKBP1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1284
Polymers23,9352
Non-polymers1922
Water5,873326
1
A: Peptidyl-prolyl cis-trans isomerase FKBP1A
hetero molecules

A: Peptidyl-prolyl cis-trans isomerase FKBP1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1284
Polymers23,9352
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area1470 Å2
ΔGint-48 kcal/mol
Surface area11210 Å2
MethodPISA
2
B: Peptidyl-prolyl cis-trans isomerase FKBP1A
hetero molecules

B: Peptidyl-prolyl cis-trans isomerase FKBP1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1284
Polymers23,9352
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area1460 Å2
ΔGint-47 kcal/mol
Surface area11100 Å2
MethodPISA
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 number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-201-

SO4

21B-201-

SO4

31A-373-

HOH

41B-373-

HOH

-
Components

#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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 326 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

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

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU PhotonJet-R / Wavelength: 1.54 Å
DetectorType: RIGAKU HyPix-Arc 150 / Detector: PIXEL / Date: Apr 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.05→53.9 Å / Num. obs: 101614 / % possible obs: 94.5 % / Redundancy: 3.7 % / CC1/2: 0.999 / CC star: 0.995 / Net I/σ(I): 16.16
Reflection shellResolution: 1.05→1.08 Å / Num. unique obs: 6791 / CC1/2: 0.075 / CC star: 0.373

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
CrysalisProdata reduction
CrysalisProdata scaling
PHENIXphasing
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.2237 2000 2.48 %
Rwork0.205 --
obs0.2054 80574 87.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.05→22.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1680 0 10 326 2016
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081830
X-RAY DIFFRACTIONf_angle_d1.1322489
X-RAY DIFFRACTIONf_dihedral_angle_d13.129703
X-RAY DIFFRACTIONf_chiral_restr0.093260
X-RAY DIFFRACTIONf_plane_restr0.009336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.05-1.080.40291130.42484425X-RAY DIFFRACTION69
1.08-1.110.42891160.37294590X-RAY DIFFRACTION72
1.11-1.140.31531210.33214768X-RAY DIFFRACTION75
1.14-1.170.29341290.30525027X-RAY DIFFRACTION78
1.17-1.220.26531320.27265194X-RAY DIFFRACTION82
1.22-1.270.26191390.25575471X-RAY DIFFRACTION86
1.27-1.320.29911410.24145565X-RAY DIFFRACTION87
1.32-1.390.24521500.21455882X-RAY DIFFRACTION92
1.39-1.480.23511530.2025959X-RAY DIFFRACTION93
1.48-1.590.21821530.18756047X-RAY DIFFRACTION94
1.59-1.750.20231610.17666288X-RAY DIFFRACTION98
1.75-2.010.2181610.17086370X-RAY DIFFRACTION99
2.01-2.530.18941630.18296400X-RAY DIFFRACTION99
2.53-22.080.18641680.17326588X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
12.885-1.1288-2.63195.12742.57914.1236-0.3315-0.3916-0.24610.41050.34530.08450.33070.2255-0.03450.1020.00270.01910.06820.01510.0623-19.0671-20.25819.9697
24.27170.2468-2.26231.0034-0.18235.6394-0.08030.2973-0.2018-0.14480.02140.13090.1594-0.06410.10870.06920.0039-0.01450.057-0.00570.0785-26.916-15.5425-3.7432
34.1551-1.24293.43811.8273-0.43773.2819-0.1109-0.04290.07850.04460.0959-0.0677-0.1838-0.00180.01150.065-0.01730.01380.06140.00130.0818-14.6312-8.76392.6474
44.8084-3.55543.17366.574-2.69116.2178-0.2117-0.07730.26680.4311-0.1134-0.2357-0.2530.1390.31310.091-0.0244-0.01260.0933-0.01170.0971-7.1821-8.81939.62
52.90250.26191.09622.33673.32625.5247-0.17910.16250.2442-0.72460.272-0.2149-0.69370.2694-0.10050.115-0.0126-0.00780.07670.00770.0987-14.2225-5.918-3.417
68.1936-0.22194.75354.6327-1.57857.90260.07390.5777-0.0338-0.3531-0.0534-0.00710.12130.4358-0.0060.07380.01130.01130.10460.00340.0739-12.0664-16.8288-7.0808
76.4596-1.7281-0.74360.70690.05161.0537-0.04880.1278-0.13110.0304-0.01810.03790.00850.00440.06450.0722-0.00480.00640.04170.00380.0638-19.7937-17.48590.9036
82.05761.6751-0.42662.05760.26041.1367-0.233-0.16530.14040.3050.1285-0.076-0.00750.12410.01260.07410.00860.0030.07090.00270.0511-16.8369-15.9729.2288
97.8366-2.27780.94230.6716-0.12172.03030.05410.0055-0.4273-0.0202-0.02560.00410.0998-0.0215-0.02350.0712-0.00090.00010.0667-0.00030.0797-5.6621-24.03063.695
106.55451.4492-1.82071.8377-0.80373.10670.0547-0.2645-0.06360.0567-0.0353-0.01440.02870.1149-0.02790.06490.00850.00010.0851-0.00280.05880.5383-18.88146.9123
114.6115-2.24382.46931.7677-1.35882.8718-0.03990.02220.0930.01760.05230.0649-0.18470.00090.0130.0649-0.01410.00590.03090.00650.0774-18.8151-9.66341.8973
123.16-0.9277-0.51691.67550.05113.05840.0077-0.08-0.25570.02820.01510.15620.0644-0.0058-0.02370.0637-0.03210.01370.0381-0.01040.0989-26.8169-0.477430.049
133.5241-0.91441.39573.3392-0.1683.1115-0.0903-0.16220.11090.19120.007-0.172-0.07030.13750.05890.0609-0.0160.010.09540.01710.0755-14.20326.803729.4245
144.02-0.9419-0.08060.64640.26470.1671-0.0142-0.2754-0.10170.06930.01970.00950.01560.0453-0.00460.0847-0.00510.00140.09820.01710.0537-15.1819-0.558230.9641
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 9 )
2X-RAY DIFFRACTION2chain 'A' and (resid 10 through 21 )
3X-RAY DIFFRACTION3chain 'A' and (resid 22 through 30 )
4X-RAY DIFFRACTION4chain 'A' and (resid 31 through 43 )
5X-RAY DIFFRACTION5chain 'A' and (resid 44 through 50 )
6X-RAY DIFFRACTION6chain 'A' and (resid 51 through 57 )
7X-RAY DIFFRACTION7chain 'A' and (resid 58 through 71 )
8X-RAY DIFFRACTION8chain 'A' and (resid 72 through 77 )
9X-RAY DIFFRACTION9chain 'A' and (resid 78 through 86 )
10X-RAY DIFFRACTION10chain 'A' and (resid 87 through 97 )
11X-RAY DIFFRACTION11chain 'A' and (resid 98 through 108 )
12X-RAY DIFFRACTION12chain 'B' and (resid 1 through 21 )
13X-RAY DIFFRACTION13chain 'B' and (resid 22 through 57 )
14X-RAY DIFFRACTION14chain 'B' and (resid 58 through 108 )

+
About Yorodumi

-
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

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

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

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
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

Read more