4H04
Lacto-N-biosidase from Bifidobacterium bifidum
- PDB DOI: https://doi.org/10.2210/pdb4H04/pdb
- Classification: HYDROLASE
- Organism(s): Bifidobacterium bifidum JCM 1254
- Expression System: Escherichia coli
- Mutation(s): No 
- Deposited: 2012-09-07 Released: 2013-03-20 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.191 
- R-Value Work: 0.155 
- R-Value Observed: 0.157 
wwPDB Validation   3D Report Full Report
This is version 2.0 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Lacto-N-biosidase | 644 | Bifidobacterium bifidum JCM 1254 | Mutation(s): 0  Gene Names: lnbB EC: 3.2.1.140 | ||
UniProt | |||||
Find proteins for B3TLD6 (Bifidobacterium bifidum (strain DSM 20082 / JCM 1254 / BCRC 11844 / KCTC 3440 / E319f (Variant a))) Explore B3TLD6  Go to UniProtKB:  B3TLD6 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | B3TLD6 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
SO4 Query on SO4 | E [auth A] F [auth A] G [auth A] H [auth A] I [auth B] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.191 
- R-Value Work: 0.155 
- R-Value Observed: 0.157 
- Space Group: P 21 21 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 116.815 | α = 90 |
b = 131.033 | β = 90 |
c = 104.409 | γ = 90 |
Software Name | Purpose |
---|---|
ADSC | data collection |
SOLVE | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
Entry History 
Deposition Data
- Released Date: 2013-03-20  Deposition Author(s): Ito, T., Katayama, T., Wada, J., Suzuki, R., Ashida, H., Wakagi, T., Yamamoto, K., Fushinobu, S.
Revision History (Full details and data files)
- Version 1.0: 2013-03-20
Type: Initial release - Version 1.1: 2013-07-10
Changes: Database references - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary