2NTB
Crystal structure of pectin methylesterase in complex with hexasaccharide V
- PDB DOI: https://doi.org/10.2210/pdb2NTB/pdb
- Classification: HYDROLASE
- Organism(s): Dickeya dadantii 3937
- Expression System: Escherichia coli
- Mutation(s): No 
- Deposited: 2006-11-07 Released: 2007-09-18 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.244 
- R-Value Work: 0.205 
- R-Value Observed: 0.207 
wwPDB Validation   3D Report Full Report
This is version 3.1 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 |
Pectinesterase A | 342 | Dickeya dadantii 3937 | Mutation(s): 0  Gene Names: pemA, pem EC: 3.1.1.11 | ||
UniProt | |||||
Find proteins for P0C1A9 (Dickeya dadantii (strain 3937)) Explore P0C1A9  Go to UniProtKB:  P0C1A9 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P0C1A9 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid | C, D | 6 | N/A | ||
Glycosylation Resources | |||||
GlyTouCan:  G02254EM GlyCosmos:  G02254EM |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.244 
- R-Value Work: 0.205 
- R-Value Observed: 0.207 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 51.094 | α = 90 |
b = 85.33 | β = 93.55 |
c = 97.803 | γ = 90 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
ADSC | data collection |
MOSFLM | data reduction |
SCALA | data scaling |
REFMAC | phasing |
Entry History 
Deposition Data
- Released Date: 2007-09-18  Deposition Author(s): Fries, M., Brocklehurst, K., Shevchik, V.E., Pickersgill, R.W.
Revision History (Full details and data files)
- Version 1.0: 2007-09-18
Type: Initial release - Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance - Version 2.0: 2020-05-13
Changes: Advisory, Atomic model, Data collection, Derived calculations - Version 3.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 3.1: 2023-08-30
Changes: Data collection, Database references, Refinement description, Structure summary