3MYT | pdb_00003myt

Crystal structure of Ketosteroid Isomerase D38HD99N from Pseudomonas testosteroni (tKSI)

PDB DOI: https://doi.org/10.2210/pdb3MYT/pdb

Classification: ISOMERASE
Organism(s): Comamonas testosteroni
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2010-05-11 Released: 2011-11-23
Deposition Author(s): Gonzalez, A., Tsai, Y., Schwans, J., Sunden, F., Herschlag, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.96 Å
R-Value Free:
0.282 (Depositor), 0.280 (DCC)
R-Value Work:
0.223 (Depositor), 0.220 (DCC)
R-Value Observed:
0.226 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of Ketosteroid Isomerase D38HD99N from Pseudomonas Testosteroni (tKSI)

Schwans, J., Sunden, F., Gonzalez, A., Tsai, Y., Herschlag, D.

To be published.

Macromolecule Content

Total Structure Weight: 56.35 kDa
Atom Count: 4,413
Modeled Residue Count: 498
Deposited Residue Count: 500
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Steroid Delta-isomerase	A, B, C, D	125	Comamonas testosteroni	Mutation(s): 2 Gene Names: ksi 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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EQU Query on EQU Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain R [auth C] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain R [auth C] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain R [auth C]	F [auth A], K [auth B], R [auth C]	EQUILENIN C₁₈ H₁₈ O₂ PDRGHUMCVRDZLQ-WMZOPIPTSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Focus chain R [auth C] Interactions & Density Focus chain F [auth A] Focus chain K [auth B] Focus chain R [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain M [auth C] 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 T [auth D] SDF format, chain U [auth D] SDF format, chain V [auth D] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain Y [auth D] SDF format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] 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 T [auth D] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C] 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 T [auth D] mmCIF format, chain U [auth D] mmCIF format, chain V [auth D] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain E [auth A]	E [auth A] H [auth B] I [auth B] J [auth B] M [auth C] E [auth A], H [auth B], I [auth B], J [auth B], M [auth C], N [auth C], O [auth C], P [auth C], Q [auth C], T [auth D], U [auth D], V [auth D], W [auth D], X [auth D], Y [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain S [auth C] SDF format, chain Z [auth D] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain S [auth C] MOL2 format, chain Z [auth D] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain S [auth C] mmCIF format, chain Z [auth D]	G [auth A], L [auth B], S [auth C], Z [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Focus chain S [auth C] Focus chain Z [auth D] Interactions & Density Focus chain G [auth A] Focus chain L [auth B] Focus chain S [auth C] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.96 Å
R-Value Free: 0.282 (Depositor), 0.280 (DCC)
R-Value Work: 0.223 (Depositor), 0.220 (DCC)
R-Value Observed: 0.226 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.274	α = 90
b = 64.274	β = 90
c = 504.199	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
Web-Ice	data collection
XDS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-11-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-11-23
Type: Initial release
Version 1.1: 2017-11-08
Changes: Refinement description
Version 1.2: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description