5DKM | pdb_00005dkm

S. erythraea trypsin Michaelis-Menten complex

PDB DOI: https://doi.org/10.2210/pdb5DKM/pdb

Classification: HYDROLASE
Organism(s): Saccharopolyspora erythraea
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-09-03 Released: 2017-03-08
Deposition Author(s): Blankenship, E., Lodowski, D.T.
Funding Organization(s): National Institutes of Health/National Eye Institute (NIH/NEI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 0.92 Å
R-Value Free:
0.130 (Depositor), 0.134 (DCC)
R-Value Work:
0.119 (Depositor), 0.123 (DCC)
R-Value Observed:
0.120 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5DKM

This is version 1.5 of the entry. See complete history.

Literature

High resolution structures of S. erythraeus trypsin throughout the catalytic cycle

Blankenship, E., Lodowski, D.T.

To be published.

Macromolecule Content

Total Structure Weight: 23.66 kDa
Atom Count: 2,220
Modeled Residue Count: 230
Deposited Residue Count: 230
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Trypsin	A	230	Saccharopolyspora erythraea	Mutation(s): 0 EC: 3.4.21.4
UniProt
Find proteins for Q54137 (Saccharopolyspora erythraea) Explore Q54137 Go to UniProtKB: Q54137
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q54137
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 0.92 Å
R-Value Free: 0.130 (Depositor), 0.134 (DCC)
R-Value Work: 0.119 (Depositor), 0.123 (DCC)
R-Value Observed: 0.120 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.072	α = 90
b = 47.441	β = 106.1
c = 53.471	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
Coot	model building
XDS	data scaling
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2017-03-08

Deposition Author(s):

Blankenship, E.

Funding Organization	Location	Grant Number
National Institutes of Health/National Eye Institute (NIH/NEI)	United States	EY019718

Revision History (Full details and data files)

Version 1.0: 2017-03-08
Type: Initial release
Version 1.1: 2017-09-13
Changes: Author supporting evidence
Version 1.2: 2017-11-22
Changes: Refinement description
Version 1.3: 2019-12-11
Changes: Author supporting evidence
Version 1.4: 2023-09-27
Changes: Data collection, Database references, Refinement description
Version 1.5: 2024-10-09
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.