6GV2 | pdb_00006gv2

Sulfolobus solfataricus 2-keto-3-deoxygluconate aldolase Y103F,Y130F,A198F variant in complex with L-2-keto, 3-deoxy-galactonate

PDB DOI: https://doi.org/10.2210/pdb6GV2/pdb

Classification: HYDROLASE
Organism(s): Saccharolobus solfataricus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2018-06-20 Released: 2019-07-03
Deposition Author(s): Crennell, S.J., Danson, M.J., Royer, S.
Funding Organization(s): Biotechnology and Biological Sciences Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.212 (Depositor), 0.216 (DCC)
R-Value Work:
0.164 (Depositor), 0.166 (DCC)
R-Value Observed:
0.167 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Sulfolobus solfataricus 2-keto-3-deoxygluconate aldolase Y132V,T157C variant

Crennell, S.J., Danson, M.J., Royer, S.

To be published.

Macromolecule Content

Total Structure Weight: 67.7 kDa
Atom Count: 5,252
Modeled Residue Count: 588
Deposited Residue Count: 590
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase	A, B	294	Saccharolobus solfataricus	Mutation(s): 3 EC: 4.1.2.55
UniProt
Find proteins for O54288 (Saccharolobus solfataricus) Explore O54288 Go to UniProtKB: O54288
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O54288
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SSH Query on SSH Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain C [auth A] MOL2 format, chain I [auth B] MOL2 format, chain C [auth A] mmCIF format, chain I [auth B] mmCIF format, chain C [auth A]	C [auth A], I [auth B]	3-DEOXY-D-ARABINO-HEXONIC ACID C₆ H₁₂ O₆ YGMNHEPVTNXLLS-VAYJURFESA-N		Interactions Focus chain C [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] H [auth A] L [auth B] M [auth B] F [auth A], G [auth A], H [auth A], L [auth B], M [auth B], N [auth B], O [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B]
GXV Query on GXV Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain D [auth A] mmCIF format, chain J [auth B] mmCIF format, chain D [auth A]	D [auth A], J [auth B]	L-glyceraldehyde C₃ H₆ O₃ MNQZXJOMYWMBOU-GSVOUGTGSA-N		Interactions Focus chain D [auth A] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain J [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain E [auth A]	E [auth A], K [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain K [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KPI Query on KPI	A, B	L-PEPTIDE LINKING	C₉ H₁₆ N₂ O₄		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.212 (Depositor), 0.216 (DCC)
R-Value Work: 0.164 (Depositor), 0.166 (DCC)
R-Value Observed: 0.167 (Depositor)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.478	α = 90
b = 103.478	β = 90
c = 245.551	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
BALBES	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2019-07-03

Deposition Author(s):

Crennell, S.J.

Danson, M.J.

Royer, S.

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	--

Revision History (Full details and data files)

Version 1.0: 2019-07-03
Type: Initial release
Version 2.0: 2023-11-29
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary
Version 2.1: 2024-01-17
Changes: Refinement description
Version 2.2: 2024-10-23
Changes: Structure summary

6GV2 | pdb_00006gv2

Sulfolobus solfataricus 2-keto-3-deoxygluconate aldolase Y103F,Y130F,A198F variant in complex with L-2-keto, 3-deoxy-galactonate

Literature

Sulfolobus solfataricus 2-keto-3-deoxygluconate aldolase Y132V,T157C variant

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand