3HXK | pdb_00003hxk

Crystal Structure of a sugar hydrolase (YeeB) from Lactococcus lactis, Northeast Structural Genomics Consortium Target KR108

PDB DOI: https://doi.org/10.2210/pdb3HXK/pdb

Classification: HYDROLASE
Organism(s): Lactococcus lactis subsp. lactis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2009-06-20 Released: 2009-07-07
Deposition Author(s): Forouhar, F., Su, M., Seetharaman, J., Mao, M., Xiao, R., Ciccosanti, C., Foote, E.L., Maglaqui, M., Zhao, L., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free:
0.296 (Depositor), 0.310 (DCC)
R-Value Work:
0.256 (Depositor), 0.273 (DCC)
R-Value Observed:
0.257 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal Structure of a sugar hydrolase (YeeB) from Lactococcus lactis, Northeast Structural Genomics Consortium Target KR108

Forouhar, F., Su, M., Seetharaman, J., Mao, M., Xiao, R., Ciccosanti, C., Foote, E.L., Maglaqui, M., Zhao, L., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 128.1 kDa
Atom Count: 8,141
Modeled Residue Count: 1,000
Deposited Residue Count: 1,104
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sugar hydrolase	A, B, C, D	276	Lactococcus lactis subsp. lactis	Mutation(s): 0 Gene Names: L427, L42784, LL0430, yeeB
UniProt
Find proteins for Q9CID4 (Lactococcus lactis subsp. lactis (strain IL1403)) Explore Q9CID4 Go to UniProtKB: Q9CID4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9CID4
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.296 (Depositor), 0.310 (DCC)
R-Value Work: 0.256 (Depositor), 0.273 (DCC)
R-Value Observed: 0.257 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.391	α = 90
b = 150.425	β = 90
c = 218.859	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
SnB	phasing
REFMAC	refinement

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-07-07

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2009-07-07
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2024-10-30
Changes: Data collection, Database references, Structure summary