[English] 日本語
Yorodumi
- PDB-4msp: Crystal structure of human peptidyl-prolyl cis-trans isomerase FK... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4msp
TitleCrystal structure of human peptidyl-prolyl cis-trans isomerase FKBP22 (aka FKBP14) containing two EF-hand motifs
ComponentsPeptidyl-prolyl cis-trans isomerase FKBP14
KeywordsISOMERASE / FKBP-type domain / EF-hand motif / peptidyl-prolyl cis-trans isomerase / calcium binding / Endoplasmic reticulum
Function / homology
Function and homology information


XBP1(S) activates chaperone genes / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / endoplasmic reticulum lumen / calcium ion binding
Similarity search - Function
Endoplasmic reticulum targeting sequence. / Chitinase A; domain 3 - #40 / Chitinase A; domain 3 / 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 / EF-hand / Recoverin; domain 1 / EF-hand domain pair ...Endoplasmic reticulum targeting sequence. / Chitinase A; domain 3 - #40 / Chitinase A; domain 3 / 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 / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
S-1,2-PROPANEDIOL / Peptidyl-prolyl cis-trans isomerase FKBP14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD, MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBoudko, S.P. / Ishikawa, Y. / Bachinger, H.P.
CitationJournal: Protein Sci. / Year: 2014
Title: Structure of human peptidyl-prolyl cis-trans isomerase FKBP22 containing two EF-hand motifs.
Authors: Boudko, S.P. / Ishikawa, Y. / Nix, J. / Chapman, M.S. / Bachinger, H.P.
History
DepositionSep 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase FKBP14
B: Peptidyl-prolyl cis-trans isomerase FKBP14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,05217
Polymers45,7662
Non-polymers1,28615
Water5,044280
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6930 Å2
ΔGint-55 kcal/mol
Surface area20010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.430, 101.200, 58.970
Angle α, β, γ (deg.)90.00, 100.01, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Peptidyl-prolyl cis-trans isomerase FKBP14 / PPIase FKBP14 / 22 kDa FK506-binding protein / 22 kDa FKBP / FKBP-22 / FK506-binding protein 14 / ...PPIase FKBP14 / 22 kDa FK506-binding protein / 22 kDa FKBP / FKBP-22 / FK506-binding protein 14 / FKBP-14 / Rotamase


Mass: 22882.996 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP14, FKBP22, UNQ322/PRO381 / Plasmid: pET30a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9NWM8, peptidylprolyl isomerase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical
ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.41 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 25% 1,2-propanediol, 12% PEG 20000, 0.1M MES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Feb 22, 2012
Details: Rosenbaum-Rock monochromator 1: high-resolution double-crystal sagittal focusing, Rosenbaum-Rock monochromator 2: double crystal, Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→23.2 Å / Num. all: 33197 / Num. obs: 33131 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 12.9
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 4.2 / Num. unique all: 4813 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
JBluIce-EPICSdata collection
Blu-Icedata collection
AMoREphasing
PHENIX(phenix.refine: 1.8_1069)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD, MOLECULAR REPLACEMENT / Resolution: 1.9→23.194 Å / SU ML: 0.15 / σ(F): 1.4 / Phase error: 19.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1998 1643 4.96 %RANDOM
Rwork0.1575 ---
obs0.1597 33108 99.9 %-
all-33111 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→23.194 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3057 0 69 280 3406
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063215
X-RAY DIFFRACTIONf_angle_d1.0554305
X-RAY DIFFRACTIONf_dihedral_angle_d13.8171219
X-RAY DIFFRACTIONf_chiral_restr0.078445
X-RAY DIFFRACTIONf_plane_restr0.004561
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.95590.25031300.19452620X-RAY DIFFRACTION100
1.9559-2.0190.21441410.17362633X-RAY DIFFRACTION100
2.019-2.09110.18861250.16392583X-RAY DIFFRACTION100
2.0911-2.17470.21021330.15652617X-RAY DIFFRACTION100
2.1747-2.27360.2481260.15962645X-RAY DIFFRACTION100
2.2736-2.39340.20251460.14872603X-RAY DIFFRACTION100
2.3934-2.54320.21671380.15962618X-RAY DIFFRACTION100
2.5432-2.73920.20241360.16262600X-RAY DIFFRACTION100
2.7392-3.01440.19041390.16542644X-RAY DIFFRACTION100
3.0144-3.44930.2021580.14632575X-RAY DIFFRACTION100
3.4493-4.34110.17141460.1362639X-RAY DIFFRACTION100
4.3411-23.19610.20251250.17092688X-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)
11.8441-0.03950.26982.47030.22361.47060.0880.3425-0.1503-0.48710.03850.06090.06650.1674-0.06570.23580.029-0.00910.2037-0.0370.15371.1110.049621.8661
21.8250.6785-0.05083.50660.92862.7544-0.02460.17470.176-0.08940.0683-0.14110.1024-0.0871-0.04240.16660.0060.02190.17520.03770.215822.2136-22.931319.9434
31.2264-0.1875-0.36433.20440.19831.58120.0155-0.3649-0.04440.38430.0093-0.00850.2908-0.0856-0.01550.2969-0.0101-0.01960.37090.00060.226516.9033-7.094244.6134
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resseq 2:118
2X-RAY DIFFRACTION2chain B and resseq 3:118
3X-RAY DIFFRACTION3(chain A and resseq 119:190) or (chain B and resseq 119:191)

+
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://pdbjlvh1.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