6PHE | pdb_00006phe

Crystal structure of Methylglyoxal synthase from Elizabethkingia anophelis NUHP1

PDB DOI: https://doi.org/10.2210/pdb6PHE/pdb

Classification: LYASE
Organism(s): Elizabethkingia anophelis NUHP1
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2019-06-25 Released: 2019-07-24
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.184 (Depositor), 0.180 (DCC)
R-Value Work:
0.147 (Depositor), 0.150 (DCC)
R-Value Observed:
0.148 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of Methylglyoxal synthase from Elizabethkingia anophelis NUHP1

Abendroth, J., Fox III, D., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 221.05 kDa
Atom Count: 16,022
Modeled Residue Count: 1,817
Deposited Residue Count: 1,932
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methylglyoxal synthase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	161	Elizabethkingia anophelis NUHP1	Mutation(s): 0 Gene Names: mgsA, BD94_2272 EC: 4.2.3.3
UniProt
Find proteins for A0A077EEZ5 (Elizabethkingia anophelis NUHP1) Explore A0A077EEZ5 Go to UniProtKB: A0A077EEZ5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A077EEZ5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain S [auth E] SDF format, chain P [auth C] MOL2 format, chain S [auth E] MOL2 format, chain P [auth C] mmCIF format, chain S [auth E] mmCIF format, chain P [auth C]	P [auth C], S [auth E]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain P [auth C] Focus chain S [auth E] Interactions & Density Focus chain P [auth C] Focus chain S [auth E]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain Z [auth L] SDF format, chain Y [auth K] SDF format, chain X [auth J] SDF format, chain W [auth I] SDF format, chain V [auth H] SDF format, chain U [auth G] SDF format, chain T [auth F] SDF format, chain R [auth E] SDF format, chain Q [auth D] SDF format, chain O [auth C] SDF format, chain N [auth B] SDF format, chain M [auth A] MOL2 format, chain Z [auth L] MOL2 format, chain Y [auth K] MOL2 format, chain X [auth J] MOL2 format, chain W [auth I] MOL2 format, chain V [auth H] MOL2 format, chain U [auth G] MOL2 format, chain T [auth F] MOL2 format, chain R [auth E] MOL2 format, chain Q [auth D] MOL2 format, chain O [auth C] MOL2 format, chain N [auth B] MOL2 format, chain M [auth A] mmCIF format, chain Z [auth L] mmCIF format, chain Y [auth K] mmCIF format, chain X [auth J] mmCIF format, chain W [auth I] mmCIF format, chain V [auth H] mmCIF format, chain U [auth G] mmCIF format, chain T [auth F] mmCIF format, chain R [auth E] mmCIF format, chain Q [auth D] mmCIF format, chain O [auth C] mmCIF format, chain N [auth B] mmCIF format, chain M [auth A]	M [auth A] N [auth B] O [auth C] Q [auth D] R [auth E] M [auth A], N [auth B], O [auth C], Q [auth D], R [auth E], T [auth F], U [auth G], V [auth H], W [auth I], X [auth J], Y [auth K], Z [auth L]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain R [auth E] Focus chain T [auth F] Focus chain U [auth G] Focus chain V [auth H] Focus chain W [auth I] Focus chain X [auth J] Focus chain Y [auth K] Focus chain Z [auth L] Interactions & Density Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain R [auth E] Focus chain T [auth F] Focus chain U [auth G] Focus chain V [auth H] Focus chain W [auth I] Focus chain X [auth J] Focus chain Y [auth K] Focus chain Z [auth L]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.184 (Depositor), 0.180 (DCC)
R-Value Work: 0.147 (Depositor), 0.150 (DCC)
R-Value Observed: 0.148 (Depositor)

Diffraction Data: https://doi.org/10.18430/m36phe

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 167.59	α = 90
b = 167.59	β = 90
c = 159.9	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MOLREP	phasing
PHASER	phasing
Coot	model building

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2019-07-24

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2019-07-24
Type: Initial release
Version 1.1: 2023-10-11
Changes: Advisory, Data collection, Database references, Refinement description