Download MendeleyStructural basis for substrate binding and catalysis of branching enzyme from Cyanothece sp. ATCC 51142
Hayashi, M., Suzuki, R., Colleoni, C., Ball, S.G., Fujita, N., Suzuki, E.To be published.
5GQY | pdb_00005gqy
Crystal structure of branching enzyme from Cyanothece sp. ATCC 51142 in complex with maltoheptaose
- PDB DOI: https://doi.org/10.2210/pdb5GQY/pdb
- Classification: TRANSFERASE
- Organism(s): Crocosphaera subtropica ATCC 51142
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2016-08-08 Released: 2017-08-16
- Funding Organization(s): Shimadzu Science Foundation, JSPS KAKENHI
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.180 (Depositor), 0.190 (DCC)
- R-Value Work: 0.155 (Depositor), 0.170 (DCC)
- R-Value Observed: 0.156 (Depositor)
Starting Model: experimental
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wwPDB Validation 3D Report Full Report
This is version 2.1 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| 1,4-alpha-glucan branching enzyme GlgB | 793 | Crocosphaera subtropica ATCC 51142 | Mutation(s): 0 Gene Names: glgB, glgB1, cce_2248 EC: 2.4.1.18 |  | |
UniProt | |||||
Find proteins for B1WPM8 (Crocosphaera subtropica (strain ATCC 51142 / BH68)) Explore B1WPM8 Go to UniProtKB: B1WPM8 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | B1WPM8 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Oligosaccharides
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
| alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose | B, E, G | 4 |  | N/A | |
Glycosylation Resources | |||||
GlyTouCan: G87171PZ GlyCosmos: G87171PZ GlyGen: G87171PZ | |||||
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
| alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose | C, H | 3 |  | N/A | |
Glycosylation Resources | |||||
GlyTouCan: G96370VA GlyCosmos: G96370VA GlyGen: G96370VA | |||||
Entity ID: 4 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
| alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose | D, F | 7 |  | N/A | |
Glycosylation Resources | |||||
GlyTouCan: G41288IQ GlyCosmos: G41288IQ GlyGen: G41288IQ | |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| GOL Query on GOL | I [auth A], J [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| MG Query on MG | K [auth A], L [auth A], M [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Biologically Interesting Molecules (External Reference) 2 Unique
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
| PRD_900010 Query on PRD_900010 | B, E, G | alpha-maltotetraose | Oligosaccharide / Substrate analog |  | |
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
| PRD_900009 Query on PRD_900009 | C, H | alpha-maltotriose | Oligosaccharide / Nutrient |  | |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.180 (Depositor), 0.190 (DCC)
- R-Value Work: 0.155 (Depositor), 0.170 (DCC)
- R-Value Observed: 0.156 (Depositor)
Space Group: P 41 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 134.01 | α = 90 |
| b = 134.01 | β = 90 |
| c = 184.28 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| MOLREP | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2017-08-16 Deposition Author(s): Suzuki, R., Suzuki, E.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Shimadzu Science Foundation | Japan | 120003 |
| JSPS KAKENHI | Japan | 15K18685 |
| JSPS KAKENHI | Japan | 25440193 |
Revision History (Full details and data files)
- Version 1.0: 2017-08-16
Type: Initial release - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
