3DJB | pdb_00003djb

Crystal structure of a HD-superfamily hydrolase (BT9727_1981) from Bacillus thuringiensis, Northeast Structural Genomics Consortium Target BuR114

PDB DOI: https://doi.org/10.2210/pdb3DJB/pdb

Classification: HYDROLASE
Organism(s): [Bacillus thuringiensis] serovar konkukian
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2008-06-23 Released: 2008-08-19
Deposition Author(s): Forouhar, F., Su, M., Seetharaman, J., Vorobiev, S.M., Janjua, H., Fang, Y., Xiao, R., Cunningham, K., Maglaqui, M., Owen, L.A., Wang, D., Baran, M.C., Liu, J., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.291 (Depositor), 0.306 (DCC)
R-Value Work:
0.246 (Depositor), 0.255 (DCC)
R-Value Observed:
0.246 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3DJB

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

Literature

Crystal structure of a HD-superfamily hydrolase (BT9727_1981) from Bacillus thuringiensis, Northeast Structural Genomics Consortium Target BuR114

Forouhar, F., Su, M., Seetharaman, J., Vorobiev, S.M., Janjua, H., Fang, Y., Xiao, R., Cunningham, K., Maglaqui, M., Owen, L.A., Wang, D., Baran, M.C., Liu, J., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 52.89 kDa
Atom Count: 3,060
Modeled Residue Count: 376
Deposited Residue Count: 446
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hydrolase, HD family	A, B	223	[Bacillus thuringiensis] serovar konkukian	Mutation(s): 3 Gene Names: BT9727_1981
UniProt
Find proteins for Q6HJG6 (Bacillus thuringiensis subsp. konkukian (strain 97-27)) Explore Q6HJG6 Go to UniProtKB: Q6HJG6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6HJG6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

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: 2.90 Å
R-Value Free: 0.291 (Depositor), 0.306 (DCC)
R-Value Work: 0.246 (Depositor), 0.255 (DCC)
R-Value Observed: 0.246 (Depositor)

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.273	α = 90
b = 66.273	β = 90
c = 101.736	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-08-19

Deposition Author(s):

Seetharaman, J.

Montelione, G.T.

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2008-08-19
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2021-10-20
Changes: Database references, Derived calculations
Version 1.3: 2024-11-06
Changes: Data collection, 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.