6SM7 | pdb_00006sm7

Crystal structure of SLA Reductase YihU from E. Coli

PDB DOI: https://doi.org/10.2210/pdb6SM7/pdb

Classification: OXIDOREDUCTASE
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-08-21 Released: 2020-08-12
Deposition Author(s): Sharma, M., Davies, G.J.
Funding Organization(s): Leverhulme Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free:
0.216 (Depositor), 0.222 (DCC)
R-Value Work:
0.180 (Depositor), 0.188 (DCC)
R-Value Observed:
0.182 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6SM7

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

Literature

Dynamic Structural Changes Accompany the Production of Dihydroxypropanesulfonate by Sulfolactaldehyde Reductase

Sharma, M., Abayakoon, P., Lingford, J.P., Epa, R., John, A., Jin, Y., Goddard-Borger, E.D., Davies, G.J., Williams, S.J.

(2020) ACS Catal

DOI: https://doi.org/10.1021/acscatal.9b04427

Macromolecule Content

Total Structure Weight: 129.28 kDa
Atom Count: 9,141
Modeled Residue Count: 1,179
Deposited Residue Count: 1,224
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-sulfolactaldehyde reductase	A, B, C [auth D], D [auth C]	306	Escherichia coli	Mutation(s): 0 Gene Names: yihU, garR_1, garR_2, garR_3, mmsB, A8C65_00150, AML07_00060, APZ14_22310, AUQ13_20575, AUS26_20040... yihU, garR_1, garR_2, garR_3, mmsB, A8C65_00150, AML07_00060, APZ14_22310, AUQ13_20575, AUS26_20040, AW106_21710, BANRA_02548, BANRA_03067, BET08_12475, BHS81_23180, BUE81_09905, BvCms12BK_03464, BvCms2454_03851, BvCmsA75A_01696, BvCmsH15A_04687, BvCmsKSP039_00778, BvCmsNSNP006_03738, BvCmsNSNP036_00183, BvCmsOUP014_01268, BvCmsSINP012_03704, BvCmsSINP036_03005, BvCmsSIP019_01210, BvCmsSIP044_01085, C2U48_13500, C4J69_10130, C5N07_19050, C5P01_22840, CA593_06580, COD30_17900, CV83915_02180, D0X26_17330, D3821_15280, D9I97_17995, D9J11_11940, DIV22_13840, DL800_27080, DNQ41_00720, E2855_04886, E2863_04195, E4Z89_22515, EAI42_02715, EAI52_23825, EC1094V2_4430, EC3234A_72c00280, EC3426_00187, EC95NR1_03333, ED600_18125, EEP23_19010, EKI52_16085, EL75_4302, EL79_4554, EL80_4461, EPS71_08590, EPS97_11270, ERS150876_03348, EXX32_12725, EYD11_22365, FORC28_5901, NCTC10090_02897, NCTC10865_06042, NCTC13462_03726, NCTC8500_05456, NCTC8960_02460, NCTC9037_04932, NCTC9045_05673, NCTC9058_02032, NCTC9062_03294, NCTC9706_02118, RK56_017955, SAMEA3484427_03349, SAMEA3484429_03464, SAMEA3752557_02792, SAMEA3752559_05062, SAMEA3753300_04042, WQ89_24850 EC: 1.1.1.373 (PDB Primary Data), 1.1.1.61 (UniProt)
UniProt
Find proteins for P0A9V8 (Escherichia coli (strain K12)) Explore P0A9V8 Go to UniProtKB: P0A9V8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A9V8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BO3 Query on BO3 Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain H [auth C] SDF format, chain G [auth D] SDF format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain H [auth C] MOL2 format, chain G [auth D] MOL2 format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain H [auth C] mmCIF format, chain G [auth D] mmCIF format, chain E [auth A]	E [auth A], F [auth B], G [auth D], H [auth C]	BORIC ACID B H₃ O₃ KGBXLFKZBHKPEV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth D] Focus chain H [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth D] Focus chain H [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free: 0.216 (Depositor), 0.222 (DCC)
R-Value Work: 0.180 (Depositor), 0.188 (DCC)
R-Value Observed: 0.182 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.447	α = 90
b = 113.784	β = 90
c = 143.229	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
xia2	data reduction
BALBES	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-08-12

Deposition Author(s):

Funding Organization	Location	Grant Number
Leverhulme Trust	United Kingdom	RPG-2017-190

Revision History (Full details and data files)

Version 1.0: 2020-08-12
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description