6R62 | pdb_00006r62

Crystal structure of a class II pyruvate aldolase from Sphingomonas wittichii RW1 in complex with hydroxypyruvate

PDB DOI: https://doi.org/10.2210/pdb6R62/pdb

Classification: LYASE
Organism(s): Rhizorhabdus wittichii RW1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-03-26 Released: 2019-05-29
Deposition Author(s): Marsden, S.R., Mestrom, L., Hagedoorn, P.L., Bento, I., McMillan, D.G.G., Hanefeld, U.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.185 (Depositor), 0.191 (DCC)
R-Value Work:
0.164 (Depositor), 0.168 (DCC)
R-Value Observed:
0.165 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 6R62

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

Literature

CH-Pi Interactions Promote the Conversion of Hydroxypyruvate in a Class II Pyruvate Aldolase

Marsden, S.R., Mestrom, L., Bento, I., Hagedoorn, P.L., McMillan, D.G.G., Hanefeld, U.

(2019) Adv Synth Catal

DOI: https://doi.org/10.1002/adsc.201900205

Macromolecule Content

Total Structure Weight: 27.34 kDa
Atom Count: 2,305
Modeled Residue Count: 252
Deposited Residue Count: 252
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HpcH/HpaI aldolase	A	252	Rhizorhabdus wittichii RW1	Mutation(s): 0 Gene Names: Swit_5035 EC: 4.1.2
UniProt
Find proteins for A0A9J9HGY6 (Rhizorhabdus wittichii (strain DSM 6014 / CCUG 31198 / JCM 15750 / NBRC 105917 / EY 4224 / RW1)) Explore A0A9J9HGY6 Go to UniProtKB: A0A9J9HGY6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A9J9HGY6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3PY Query on 3PY Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	3-HYDROXYPYRUVIC ACID C₃ H₄ O₄ HHDDCCUIIUWNGJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
BR Query on BR Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]
ACT Query on ACT 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]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A], I [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.185 (Depositor), 0.191 (DCC)
R-Value Work: 0.164 (Depositor), 0.168 (DCC)
R-Value Observed: 0.165 (Depositor)

Space Group: P 4₂ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.569	α = 90
b = 116.569	β = 90
c = 116.569	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

Deposition Data

Released Date: 2019-05-29

Deposition Author(s):

Hagedoorn, P.L.

McMillan, D.G.G.

Revision History (Full details and data files)

Version 1.0: 2019-05-29
Type: Initial release
Version 1.1: 2024-05-15
Changes: Data collection, Database references, Derived calculations

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.