7RSK | pdb_00007rsk

The crystal structure from microfluidic crystals of glycosyl hydrolase family 2 (GH2) member from Bacteroides cellulosilyticus

PDB DOI: https://doi.org/10.2210/pdb7RSK/pdb

Classification: HYDROLASE
Organism(s): Bacteroides cellulosilyticus DSM 14838
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-08-11 Released: 2021-08-25
Deposition Author(s): Kim, Y., Nocek, B., Endres, M., Joachimiak, G., Johnson, J., Babnigg, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.220 (Depositor), 0.220 (DCC)
R-Value Work:
0.183 (Depositor), 0.183 (DCC)
R-Value Observed:
0.185 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

The crystal structure from microfluidic crystals of glycosyl hydrolase family 2 (GH2) member from Bacteroides cellulosilyticus

Kim, Y., Nocek, B., Endres, M., Joachimiak, G., Johnson, J., Babnigg, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

To be published.

Macromolecule Content

Total Structure Weight: 176.03 kDa
Atom Count: 12,506
Modeled Residue Count: 1,550
Deposited Residue Count: 1,558
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyl hydrolase family 2, sugar binding domain protein	A, B	779	Bacteroides cellulosilyticus DSM 14838	Mutation(s): 0 Gene Names: BACCELL_00063
UniProt
Find proteins for E2N721 (Bacteroides cellulosilyticus DSM 14838) Explore E2N721 Go to UniProtKB: E2N721
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	E2N721
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.220 (Depositor), 0.220 (DCC)
R-Value Work: 0.183 (Depositor), 0.183 (DCC)
R-Value Observed: 0.185 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.228	α = 90
b = 231.147	β = 109.018
c = 67.558	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MOLREP	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-08-25

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History (Full details and data files)

Version 1.0: 2021-08-25
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Refinement description
Version 1.2: 2023-11-15
Changes: Data collection
Version 1.3: 2024-11-13
Changes: Structure summary

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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.