[English] 日本語
Yorodumi
- PDB-8z38: FK506 binding protein 1B (including FK506) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8z38
TitleFK506 binding protein 1B (including FK506)
Componentspeptidylprolyl isomerase
KeywordsPROTEIN BINDING / FK506 / FK506 binding protein 1B
Function / homology: / 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 / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / 6-CARBOXYPIPERIDINE / peptidylprolyl isomerase
Function and homology information
Biological speciesPyricularia oryzae (rice blast fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsLiu, X.H. / Zhao, W.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)2023YFD1400202-3 China
CitationJournal: To Be Published
Title: High-resolution cocrystallized crystal structures of FK506 and FK506-binding proteins
Authors: Liu, X.H. / Zhao, W.H.
History
DepositionApr 14, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: peptidylprolyl isomerase
B: peptidylprolyl isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1043
Polymers23,9752
Non-polymers1291
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-9 kcal/mol
Surface area10520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.157, 59.382, 67.246
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein peptidylprolyl isomerase / FK506 binding protein 1B(including FK506)


Mass: 11987.425 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyricularia oryzae (rice blast fungus) / Gene: PoMZ_03707 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4P7N8E2, peptidylprolyl isomerase
#2: Chemical ChemComp-CPI / 6-CARBOXYPIPERIDINE


Type: D-peptide linking / Mass: 129.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.45 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES pH 7.5, 1.4 M tri-Sodium Citrate dihydrate or 2.1 M DL-Malic Acid pH 7.0.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Sep 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.17→42.65 Å / Num. obs: 10844 / % possible obs: 88.93 % / Redundancy: 5.6 % / Biso Wilson estimate: 26.41 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.1712 / Rpim(I) all: 0.07119 / Rrim(I) all: 0.1866 / Net I/σ(I): 6.74
Reflection shellResolution: 2.17→2.248 Å / Rmerge(I) obs: 0.7258 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1114 / CC1/2: 0.758 / Rpim(I) all: 0.3117 / Rrim(I) all: 0.7951

-
Processing

Software
NameVersionClassification
HKL-30007.21data scaling
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
HKL-30007.21data reduction
PHASER2.7.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.17→42.65 Å / SU ML: 0.2501 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.2621
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2586 522 4.82 %
Rwork0.1984 10319 -
obs0.2014 10841 88.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.64 Å2
Refinement stepCycle: LAST / Resolution: 2.17→42.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1680 0 9 76 1765
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00631721
X-RAY DIFFRACTIONf_angle_d0.82812329
X-RAY DIFFRACTIONf_chiral_restr0.0548258
X-RAY DIFFRACTIONf_plane_restr0.0058306
X-RAY DIFFRACTIONf_dihedral_angle_d13.2814631
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.17-2.390.29881240.23832636X-RAY DIFFRACTION92.31
2.39-2.730.34211210.25382619X-RAY DIFFRACTION91.55
2.73-3.440.25011390.20132485X-RAY DIFFRACTION86.43
3.44-42.650.22521380.16522579X-RAY DIFFRACTION85.76

+
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