6HBS | pdb_00006hbs

Structure of PLP internal aldimine form of Sphingopyxis sp. MTA144 FumI protein

PDB DOI: https://doi.org/10.2210/pdb6HBS/pdb

Classification: TRANSFERASE
Organism(s): Sphingopyxis macrogoltabida
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-08-13 Released: 2019-08-28
Deposition Author(s): Campopiano, D.J., Serpico, A., Marles-Wright, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.202 (Depositor), 0.198 (DCC)
R-Value Work:
0.169 (Depositor), 0.171 (DCC)
R-Value Observed:
0.171 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of PLP internal aldimine form of Sphingopyxis sp. MTA144 FumI protein

Campopiano, D.J., Serpico, A., Marles-Wright, J.

To be published.

Macromolecule Content

Total Structure Weight: 97.21 kDa
Atom Count: 7,025
Modeled Residue Count: 826
Deposited Residue Count: 880
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminopentol aminotransferase	A, B	440	Sphingopyxis macrogoltabida	Mutation(s): 0 Gene Names: fumI EC: 2.6.1
UniProt
Find proteins for D2D3B2 (Sphingopyxis macrogoltabida) Explore D2D3B2 Go to UniProtKB: D2D3B2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D2D3B2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP (Subject of Investigation/LOI) Query on PLP Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.202 (Depositor), 0.198 (DCC)
R-Value Work: 0.169 (Depositor), 0.171 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.18	α = 90
b = 104.419	β = 109.26
c = 65.25	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2019-08-28

Deposition Author(s):

Campopiano, D.J.

Serpico, A.

Marles-Wright, J.

Revision History (Full details and data files)

Version 1.0: 2019-08-28
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description

6HBS | pdb_00006hbs

Structure of PLP internal aldimine form of Sphingopyxis sp. MTA144 FumI protein

Literature

Structure of PLP internal aldimine form of Sphingopyxis sp. MTA144 FumI protein

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Entry History

Deposition Data

Revision History (Full details and data files)