5JOS | pdb_00005jos

Crystal structure of an ancestral cyclohexadienyl dehydratase, AncCDT-3(P188L).

PDB DOI: https://doi.org/10.2210/pdb5JOS/pdb

Classification: LYASE
Organism(s): synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-05-03 Released: 2017-05-03
Deposition Author(s): Clifton, B.E., Carr, P.D., Jackson, C.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.207 (Depositor), 0.208 (DCC)
R-Value Work:
0.176 (Depositor), 0.185 (DCC)
R-Value Observed:
0.177 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

To be published

Clifton, B.E., Kaczmarski, J.A., Carr, P.D., Jackson, C.J.

To be published.

Macromolecule Content

Total Structure Weight: 28.55 kDa
Atom Count: 2,025
Modeled Residue Count: 241
Deposited Residue Count: 247
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclohexadienyl dehydratase	A	247	synthetic construct	Mutation(s): 0 EC: 4.2.1.51 (PDB Primary Data), 4.2.1.91 (PDB Primary Data)

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
BEZ Query on BEZ Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	BENZOIC ACID C₇ H₆ O₂ WPYMKLBDIGXBTP-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.207 (Depositor), 0.208 (DCC)
R-Value Work: 0.176 (Depositor), 0.185 (DCC)
R-Value Observed: 0.177 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.37	α = 90
b = 90.37	β = 90
c = 101.81	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2017-05-03

Deposition Author(s):

Clifton, B.E.

Carr, P.D.

Jackson, C.J.

Revision History (Full details and data files)

Version 1.0: 2017-05-03
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-11-13
Changes: Structure summary