6UAE | pdb_00006uae

Ketosteroid isomerase (C. testosteroni) with truncated & designed loop for precise positioning of a catalytic E38

PDB DOI: https://doi.org/10.2210/pdb6UAE/pdb

Classification: ISOMERASE
Organism(s): Comamonas testosteroni
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-09-10 Released: 2020-09-16
Deposition Author(s): Krivacic, C., Kundert, K., Thompson, M.C., Fraser, J.S., Kortemme, T.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free:
0.212 (Depositor), 0.210 (DCC)
R-Value Work:
0.175 (Depositor), 0.180 (DCC)
R-Value Observed:
0.177 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Ketosteroid isomerase (C. testosteroni) with truncated & designed loop for precise positioning of a catalytic E38

Krivacic, C., Kundert, K., Thompson, M.C., Fraser, J.S., Kortemme, T.

To be published.

Macromolecule Content

Total Structure Weight: 58.52 kDa
Atom Count: 4,659
Modelled Residue Count: 495
Deposited Residue Count: 508
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ketosteroid isomerase with designed loop	A, B, C, D	127	Comamonas testosteroni	Mutation(s): 0 EC: 5.3.3.1
UniProt
Find proteins for P00947 (Comamonas testosteroni) Explore P00947 Go to UniProtKB: P00947
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00947
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DXC Query on DXC Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain S [auth C] SDF format, chain V [auth D] MOL2 format, chain I [auth A] MOL2 format, chain S [auth C] MOL2 format, chain V [auth D] mmCIF format, chain I [auth A] mmCIF format, chain S [auth C] mmCIF format, chain V [auth D]	I [auth A], S [auth C], V [auth D]	(3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID C₂₄ H₄₀ O₄ KXGVEGMKQFWNSR-LLQZFEROSA-N		Interactions Focus chain I [auth A] Focus chain S [auth C] Focus chain V [auth D] Interactions & Density Focus chain I [auth A] Focus chain S [auth C] Focus chain V [auth D]
EQU Query on EQU Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain T [auth C] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain T [auth C] mmCIF format, chain J [auth A] mmCIF format, chain M [auth B] mmCIF format, chain T [auth C]	J [auth A], M [auth B], T [auth C]	EQUILENIN C₁₈ H₁₈ O₂ PDRGHUMCVRDZLQ-WMZOPIPTSA-N		Interactions Focus chain J [auth A] Focus chain M [auth B] Focus chain T [auth C] Interactions & Density Focus chain J [auth A] Focus chain M [auth B] Focus chain T [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain U [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain U [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain U [auth D]	E [auth A] F [auth A] G [auth A] H [auth A] K [auth B] E [auth A], F [auth A], G [auth A], H [auth A], K [auth B], L [auth B], N [auth C], O [auth C], P [auth C], Q [auth C], R [auth C], U [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain U [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain U [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free: 0.212 (Depositor), 0.210 (DCC)
R-Value Work: 0.175 (Depositor), 0.180 (DCC)
R-Value Observed: 0.177 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.012	α = 90
b = 209.997	β = 90
c = 39.639	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
DIALS	data reduction
pointless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-09-16

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01-GM110089
National Science Foundation (NSF, United States)	United States	DBI-1564692