7DKI | pdb_00007dki

Silk worm FKBP, isoform-1

• PDB DOI: https://doi.org/10.2210/pdb7DKI/pdb

• Classification: ISOMERASE
• Organism(s): Bombyx mori
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-11-24 Released: 2022-02-23 
• Deposition Author(s): Yuchi, Z., Nayak, B.C.
• Funding Organization(s): National Natural Science Foundation of China (NSFC), Ministry of Science and Technology (MoST, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.198 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Starting Model: experimental

Literature

Silk worm FKBP, isoform-1

Yuchi, Z., Nayak, B.C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 24.14 kDa 
• Atom Count: 1,840 
• Modeled Residue Count: 214 
• Deposited Residue Count: 220 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidylprolyl isomerase	A, B	110	Bombyx mori	Mutation(s): 0  Gene Names: 732917 EC: 5.2.1.8
UniProt
Find proteins for Q1HQ55 (Bombyx mori) Explore Q1HQ55  Go to UniProtKB:  Q1HQ55

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.198 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.409	α = 90
b = 52.409	β = 90
c = 77.109	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHENIX	model building
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-02-23 
Deposition Author(s): Yuchi, Z., Nayak, B.C.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31972287
Ministry of Science and Technology (MoST, China)	China	2017YFD0201400, 2017YFD0201403
National Natural Science Foundation of China (NSFC)	China	2019B2-0017

Revision History  

• Version 1.0: 2022-02-23
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description