4UXA | pdb_00004uxa

Improved variant of (R)-selective manganese-dependent hydroxynitrile lyase from bacteria

PDB DOI: https://doi.org/10.2210/pdb4UXA/pdb

Classification: LYASE
Organism(s): Granulicella tundricola
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2014-08-21 Released: 2015-01-21
Deposition Author(s): Pavkov-Keller, T., Wiedner, R., Kothbauer, B., Gruber-Khadjawi, M., Schwab, H., Steiner, K., Gruber, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.234 (Depositor), 0.234 (DCC)
R-Value Work:
0.181 (Depositor), 0.186 (DCC)
R-Value Observed:
0.183 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Improving the Properties of Bacterial R-Selective Hydroxynitrile Lyases for Industrial Applications

Wiedner, R., Kothbauer, B., Pavkov-Keller, T., Gruber-Khadjawi, M., Grube, K., Schwab, H., Steiner, K.

(2015) ChemCatChem

DOI: https://doi.org/10.1002/CCTC.201402742

Macromolecule Content

Total Structure Weight: 288.04 kDa
Atom Count: 21,980
Modeled Residue Count: 2,620
Deposited Residue Count: 2,620
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CUPIN 2 CONSERVED BARREL DOMAIN PROTEIN	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T	131	Granulicella tundricola	Mutation(s): 3 EC: 4.1.2.10
UniProt
Find proteins for E8WYN5 (Granulicella tundricola (strain ATCC BAA-1859 / DSM 23138 / MP5ACTX9)) Explore E8WYN5 Go to UniProtKB: E8WYN5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	E8WYN5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain BA [auth H] SDF format, chain CA [auth I] SDF format, chain DA [auth J] SDF format, chain EA [auth K] SDF format, chain FA [auth L] SDF format, chain GA [auth M] SDF format, chain HA [auth N] SDF format, chain IA [auth O] SDF format, chain JA [auth P] SDF format, chain KA [auth Q] SDF format, chain LA [auth R] SDF format, chain MA [auth S] SDF format, chain NA [auth T] SDF format, chain U [auth A] SDF format, chain V [auth B] SDF format, chain W [auth C] SDF format, chain X [auth D] SDF format, chain Y [auth E] SDF format, chain Z [auth F] MOL2 format, chain AA [auth G] MOL2 format, chain BA [auth H] MOL2 format, chain CA [auth I] MOL2 format, chain DA [auth J] MOL2 format, chain EA [auth K] MOL2 format, chain FA [auth L] MOL2 format, chain GA [auth M] MOL2 format, chain HA [auth N] MOL2 format, chain IA [auth O] MOL2 format, chain JA [auth P] MOL2 format, chain KA [auth Q] MOL2 format, chain LA [auth R] MOL2 format, chain MA [auth S] MOL2 format, chain NA [auth T] MOL2 format, chain U [auth A] MOL2 format, chain V [auth B] MOL2 format, chain W [auth C] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth E] MOL2 format, chain Z [auth F] mmCIF format, chain AA [auth G] mmCIF format, chain BA [auth H] mmCIF format, chain CA [auth I] mmCIF format, chain DA [auth J] mmCIF format, chain EA [auth K] mmCIF format, chain FA [auth L] mmCIF format, chain GA [auth M] mmCIF format, chain HA [auth N] mmCIF format, chain IA [auth O] mmCIF format, chain JA [auth P] mmCIF format, chain KA [auth Q] mmCIF format, chain LA [auth R] mmCIF format, chain MA [auth S] mmCIF format, chain NA [auth T] mmCIF format, chain U [auth A] mmCIF format, chain V [auth B] mmCIF format, chain W [auth C] mmCIF format, chain X [auth D] mmCIF format, chain Y [auth E] mmCIF format, chain Z [auth F]	AA [auth G] BA [auth H] CA [auth I] DA [auth J] EA [auth K] AA [auth G], BA [auth H], CA [auth I], DA [auth J], EA [auth K], FA [auth L], GA [auth M], HA [auth N], IA [auth O], JA [auth P], KA [auth Q], LA [auth R], MA [auth S], NA [auth T], U [auth A], V [auth B], W [auth C], X [auth D], Y [auth E], Z [auth F]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain AA [auth G] Focus chain BA [auth H] Focus chain CA [auth I] Focus chain DA [auth J] Focus chain EA [auth K] Focus chain FA [auth L] Focus chain GA [auth M] Focus chain HA [auth N] Focus chain IA [auth O] Focus chain JA [auth P] Focus chain KA [auth Q] Focus chain LA [auth R] Focus chain MA [auth S] Focus chain NA [auth T] Focus chain U [auth A] Focus chain V [auth B] Focus chain W [auth C] Focus chain X [auth D] Focus chain Y [auth E] Focus chain Z [auth F] Interactions & Density Focus chain AA [auth G] Focus chain BA [auth H] Focus chain CA [auth I] Focus chain DA [auth J] Focus chain EA [auth K] Focus chain FA [auth L] Focus chain GA [auth M] Focus chain HA [auth N] Focus chain IA [auth O] Focus chain JA [auth P] Focus chain KA [auth Q] Focus chain LA [auth R] Focus chain MA [auth S] Focus chain NA [auth T] Focus chain U [auth A] Focus chain V [auth B] Focus chain W [auth C] Focus chain X [auth D] Focus chain Y [auth E] Focus chain Z [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.234 (Depositor), 0.234 (DCC)
R-Value Work: 0.181 (Depositor), 0.186 (DCC)
R-Value Observed: 0.183 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.806	α = 90
b = 93.174	β = 111.93
c = 146.671	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2015-01-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-01-21
Type: Initial release
Version 1.1: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Other, Refinement description