6Y8G | pdb_00006y8g

selenomethionine derivative of ferulic acid esterase (FAE)

PDB DOI: https://doi.org/10.2210/pdb6Y8G/pdb

Classification: HYDROLASE
Organism(s): Acetivibrio thermocellus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-03-04 Released: 2020-05-20
Deposition Author(s): von Stetten, D., Mueller-Dieckmann, C., Carpentier, P., Flot, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.200 (Depositor), 0.187 (DCC)
R-Value Work:
0.175 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

ID30A-3 (MASSIF-3) - a beamline for macromolecular crystallography at the ESRF with a small intense beam.

von Stetten, D., Carpentier, P., Flot, D., Beteva, A., Caserotto, H., Dobias, F., Guijarro, M., Giraud, T., Lentini, M., McSweeney, S., Royant, A., Petitdemange, S., Sinoir, J., Surr, J., Svensson, O., Theveneau, P., Leonard, G.A., Mueller-Dieckmann, C.

(2020) J Synchrotron Radiat 27: 844-851

PubMed: 32381789 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S1600577520004002
Primary Citation Related Structures:
6SWV, 6Y8G

PubMed Abstract:
ID30A-3 (or MASSIF-3) is a mini-focus (beam size 18 µm × 14 µm) highly intense (2.0 × 10 ¹³ photons s ^-1), fixed-energy (12.81 keV) beamline for macromolecular crystallography (MX) experiments at the European Synchrotron Radiation Facility (ESRF). MASSIF-3 is one of two fixed-energy beamlines sited on the first branch of the canted undulator setup on the ESRF ID30 port and is equipped with a MD2 micro-diffractometer, a Flex HCD sample changer, and an Eiger X 4M fast hybrid photon-counting detector. MASSIF-3 is recommended for collecting diffraction data from single small crystals (≤15 µm in one dimension) or for experiments using serial methods. The end-station has been in full user operation since December 2014, and here its current characteristics and capabilities are described.

Organizational Affiliation

European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France.

Macromolecule Content

Total Structure Weight: 69.52 kDa
Atom Count: 5,040
Modeled Residue Count: 564
Deposited Residue Count: 594
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endo-1,4-beta-xylanase Y	A [auth AAA], B [auth BBB]	297	Acetivibrio thermocellus	Mutation(s): 0 Gene Names: xynY EC: 3.2.1.8
UniProt
Find proteins for P51584 (Acetivibrio thermocellus) Explore P51584 Go to UniProtKB: P51584
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P51584
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CD Query on CD Download:Ideal Coordinates CCD File SDF format, chain I [auth BBB] SDF format, chain J [auth BBB] SDF format, chain H [auth BBB] SDF format, chain G [auth BBB] SDF format, chain F [auth BBB] SDF format, chain E [auth AAA] SDF format, chain D [auth AAA] SDF format, chain C [auth AAA] MOL2 format, chain I [auth BBB] MOL2 format, chain J [auth BBB] MOL2 format, chain H [auth BBB] MOL2 format, chain G [auth BBB] MOL2 format, chain F [auth BBB] MOL2 format, chain E [auth AAA] MOL2 format, chain D [auth AAA] MOL2 format, chain C [auth AAA] mmCIF format, chain I [auth BBB] mmCIF format, chain J [auth BBB] mmCIF format, chain H [auth BBB] mmCIF format, chain G [auth BBB] mmCIF format, chain F [auth BBB] mmCIF format, chain E [auth AAA] mmCIF format, chain D [auth AAA] mmCIF format, chain C [auth AAA]	C [auth AAA] D [auth AAA] E [auth AAA] F [auth BBB] G [auth BBB] C [auth AAA], D [auth AAA], E [auth AAA], F [auth BBB], G [auth BBB], H [auth BBB], I [auth BBB], J [auth BBB]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain C [auth AAA] Focus chain D [auth AAA] Focus chain E [auth AAA] Focus chain F [auth BBB] Focus chain G [auth BBB] Focus chain H [auth BBB] Focus chain I [auth BBB] Focus chain J [auth BBB] Interactions & Density Focus chain C [auth AAA] Focus chain D [auth AAA] Focus chain E [auth AAA] Focus chain F [auth BBB] Focus chain G [auth BBB] Focus chain H [auth BBB] Focus chain I [auth BBB] Focus chain J [auth BBB]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain K [auth BBB] MOL2 format, chain K [auth BBB] mmCIF format, chain K [auth BBB]	K [auth BBB]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth BBB] Interactions & Density Focus chain K [auth BBB]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A [auth AAA], B [auth BBB]	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET
SEP Query on SEP	A [auth AAA], B [auth BBB]	L-PEPTIDE LINKING	C₃ H₈ N O₆ P		SER

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.200 (Depositor), 0.187 (DCC)
R-Value Work: 0.175 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.519	α = 90
b = 108.373	β = 90
c = 112.949	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2020-05-20

Deposition Author(s):

von Stetten, D.

Mueller-Dieckmann, C.

Carpentier, P.

Flot, D.

Revision History (Full details and data files)

Version 1.0: 2020-05-20
Type: Initial release
Version 1.1: 2020-06-03
Changes: Advisory
Version 1.2: 2023-03-01
Changes: Advisory, Database references, Derived calculations
Version 1.3: 2024-10-16
Changes: Data collection, Structure summary