6KDC | pdb_00006kdc

crystal structure of Fpglu1 from fervidobacterium pennivoraus

PDB DOI: https://doi.org/10.2210/pdb6KDC/pdb

Classification: HYDROLASE
Organism(s): Fervidobacterium pennivorans DSM 9078
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-07-02 Released: 2020-07-08
Deposition Author(s): Yu, S., LiuQing, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.180 (Depositor), 0.182 (DCC)
R-Value Work:
0.154 (Depositor), 0.157 (DCC)

wwPDB Validation 3D Report Full Report

Validation slider image for 6KDC

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

Literature

crystal structure of fpglu1

Yu, S.

To be published.

Macromolecule Content

Total Structure Weight: 55.27 kDa
Atom Count: 4,196
Modeled Residue Count: 465
Deposited Residue Count: 465
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-glucosidase/6-phospho-beta-glucosidase/beta-galactosidase	A	465	Fervidobacterium pennivorans DSM 9078	Mutation(s): 0 Gene Names: Ferpe_1843
UniProt
Find proteins for H9UEF1 (Fervidobacterium pennivorans (strain DSM 9078 / Ven5)) Explore H9UEF1 Go to UniProtKB: H9UEF1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	H9UEF1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]
CO Query on CO Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.180 (Depositor), 0.182 (DCC)
R-Value Work: 0.154 (Depositor), 0.157 (DCC)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.04	α = 90
b = 101.397	β = 90
c = 170.542	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2020-07-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-07-08
Type: Initial release
Version 1.1: 2024-03-27
Changes: Data collection, Database references

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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.