3E8V | pdb_00003e8v

Crystal structure of a possible transglutaminase-family protein proteolytic fragment from Bacteroides fragilis

PDB DOI: https://doi.org/10.2210/pdb3E8V/pdb

Classification: structural genomics, unknown function
Organism(s): Bacteroides fragilis NCTC 9343
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-08-20 Released: 2008-09-02
Deposition Author(s): Bonanno, J.B., Rutter, M., Bain, K.T., Hu, S., Romero, R., Smith, D., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.243 (Depositor), 0.239 (DCC)
R-Value Work:
0.225 (Depositor), 0.219 (DCC)
R-Value Observed:
0.226 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of a possible transglutaminase-family protein proteolytic fragment from Bacteroides fragilis

Bonanno, J.B., Rutter, M., Bain, K.T., Hu, S., Romero, R., Smith, D., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 8.92 kDa
Atom Count: 606
Modeled Residue Count: 82
Deposited Residue Count: 82
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Possible transglutaminase-family protein	A	82	Bacteroides fragilis NCTC 9343	Mutation(s): 0 Gene Names: BF1045
UniProt
Find proteins for Q5LGG0 (Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / CCUG 4856 / JCM 11019 / LMG 10263 / NCTC 9343 / Onslow / VPI 2553 / EN-2)) Explore Q5LGG0 Go to UniProtKB: Q5LGG0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5LGG0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UNL Query on UNL Download:Ideal Coordinates CCD File	B [auth A]	Unknown ligand		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.243 (Depositor), 0.239 (DCC)
R-Value Work: 0.225 (Depositor), 0.219 (DCC)
R-Value Observed: 0.226 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.006	α = 90
b = 82.006	β = 90
c = 32.367	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXCD	phasing
SHELXE	model building

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-09-02

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2008-09-02
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2018-11-14
Changes: Data collection, Structure summary
Version 1.4: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
Version 1.5: 2024-02-21
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.