6U5G

MicroED structure of a FIB-milled CypA Crystal

• PDB DOI: https://doi.org/10.2210/pdb6U5G/pdb
• EM Map EMD-20645: EMDB EMDataResource

• Classification: ISOMERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-08-27 Released: 2020-01-29 
• Deposition Author(s): Wolff, A.M., Martynowycz, M.W., Zhao, W., Gonen, T., Fraser, J.S., Thompson, M.C.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: ELECTRON CRYSTALLOGRAPHY
• Resolution: 2.50 Å
• R-Value Free: 0.224 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 

Starting Model: experimental

Literature

Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals

Wolff, A.M., Young, I.D., Sierra, R.G., Brewster, A.S., Martynowycz, M.W., Nango, E., Sugahara, M., Nakane, T., Ito, K., Aquila, A., Bhowmick, A., Biel, J.T., Carbajo, S., Cohen, A.E., Cortez, S., Gonzalez, A., Hino, T., Im, D., Koralek, J.D., Kubo, M., Lazarou, T.S., Nomura, T., Owada, S., Samelson, A., Tanaka, T., Tanaka, R., Thompson, E.M., van den Bedem, H., Woldeyes, R.A., Yumoto, F., Zhao, W., Tono, K., Boutet, S., Iwata, S., Gonen, T., Sauter, N.K., Fraser, J.S., Thompson, M.C.

(2020) IUCrJ 7: 306-323

• DOI: https://doi.org/10.1107/S205225252000072X

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 18.04 kDa 
• Atom Count: 1,280 
• Modelled Residue Count: 163 
• Deposited Residue Count: 165 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase A	A	165	Homo sapiens	Mutation(s): 0  Gene Names: PPIA, CYPA EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P62937 (Homo sapiens) Explore P62937  Go to UniProtKB:  P62937
PHAROS:  P62937 GTEx:  ENSG00000196262

Experimental Data & Validation

Experimental Data

• Method: ELECTRON CRYSTALLOGRAPHY
• Resolution: 2.50 Å
• R-Value Free: 0.224 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 
• Space Group: P 2₁ 2₁ 2₁
• Diffraction Data: https://doi.org/10.15785/SBGRID/752

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.4	α = 90
b = 53.4	β = 90
c = 87.76	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
XDS	data scaling
XDS	data reduction

EM Software:

Task	Software Package	Version
RECONSTRUCTION	PHENIX	dev2880
MODEL REFINEMENT	PHENIX	1.16-3549

Structure Validation

Currently 6U5G does not have a validation slider image.

Entry History & Funding Information

Deposition Data

• Released Date: 2020-01-29 
Deposition Author(s): Wolff, A.M., Martynowycz, M.W., Zhao, W., Gonen, T., Fraser, J.S., Thompson, M.C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM123159
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM124149
National Science Foundation (NSF, United States)	United States	STC-1231306
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM117126

Revision History  

• Version 1.0: 2020-01-29
  Type: Initial release
  
• Version 1.1: 2020-02-12
  Changes: Database references, Structure summary
• Version 1.2: 2020-03-11
  Changes: Database references
• Version 1.3: 2023-10-11
  Changes: Data collection, Database references, Refinement description