5EY5 | pdb_00005ey5

LBCATS

PDB DOI: https://doi.org/10.2210/pdb5EY5/pdb

Classification: LYASE
Organism(s): synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-11-24 Released: 2016-04-27
Deposition Author(s): Busch, F., Rajendran, C., Schlee, S., Heyn, K., Merkl, R., Sterner, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free:
0.232 (Depositor), 0.231 (DCC)
R-Value Work:
0.178 (Depositor), 0.183 (DCC)
R-Value Observed:
0.181 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

LBCATS

Merkl, R., Schlee, S., Heyn, K.

To be published.

Macromolecule Content

Total Structure Weight: 148.09 kDa
Atom Count: 9,967
Modeled Residue Count: 1,272
Deposited Residue Count: 1,344
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LBCATS-a	A, C	273	synthetic construct	Mutation(s): 0

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
LBCA-b	B, D	399	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP Query on PLP Download:Ideal Coordinates CCD File SDF format, chain I [auth D] SDF format, chain F [auth B] MOL2 format, chain I [auth D] MOL2 format, chain F [auth B] mmCIF format, chain I [auth D] mmCIF format, chain F [auth B]	F [auth B], I [auth D]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Focus chain I [auth D] Interactions & Density Focus chain F [auth B] Focus chain I [auth D]
G3P Query on G3P Download:Ideal Coordinates CCD File SDF format, chain H [auth C] SDF format, chain E [auth A] MOL2 format, chain H [auth C] MOL2 format, chain E [auth A] mmCIF format, chain H [auth C] mmCIF format, chain E [auth A]	E [auth A], H [auth C]	SN-GLYCEROL-3-PHOSPHATE C₃ H₉ O₆ P AWUCVROLDVIAJX-GSVOUGTGSA-N		Interactions Focus chain E [auth A] Focus chain H [auth C] Interactions & Density Focus chain E [auth A] Focus chain H [auth C]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain J [auth D] SDF format, chain G [auth B] MOL2 format, chain K [auth D] MOL2 format, chain J [auth D] MOL2 format, chain G [auth B] mmCIF format, chain K [auth D] mmCIF format, chain J [auth D] mmCIF format, chain G [auth B]	G [auth B], J [auth D], K [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain J [auth D] Focus chain K [auth D] Interactions & Density Focus chain G [auth B] Focus chain J [auth D] Focus chain K [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free: 0.232 (Depositor), 0.231 (DCC)
R-Value Work: 0.178 (Depositor), 0.183 (DCC)
R-Value Observed: 0.181 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.963	α = 90
b = 162.996	β = 93.78
c = 78.058	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-04-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-04-27
Type: Initial release
Version 1.1: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description