5MIG
The study of the X-ray induced enzymatic reduction of molecular oxygen to water for laccase from Steccherinum murashkinskyi.The 16-th structure of the series with total exposition time 453 min. The crystal was quick refreezing before this data collection.
- PDB DOI: https://doi.org/10.2210/pdb5MIG/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Steccherinum murashkinskyi
- Mutation(s): No 
- Deposited: 2016-11-28 Released: 2017-05-10 
- Funding Organization(s): RFBR
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.35 Å
- R-Value Free: 0.162 
- R-Value Work: 0.141 
- R-Value Observed: 0.142 
wwPDB Validation   3D Report Full Report
This is version 2.1 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 |
Laccase 2 | 546 | Steccherinum murashkinskyi | Mutation(s): 0  EC: 1.10.3.2 | ||
UniProt | |||||
Find proteins for I1VE66 (Steccherinum murashkinskyi) Explore I1VE66  Go to UniProtKB:  I1VE66 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | I1VE66 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 3 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
CIT Query on CIT | H [auth A] | CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N | |||
CU Query on CU | D [auth A], E [auth A], F [auth A], G [auth A] | COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N | |||
NA Query on NA | I [auth A] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.35 Å
- R-Value Free: 0.162 
- R-Value Work: 0.141 
- R-Value Observed: 0.142 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 56.268 | α = 90 |
b = 84.415 | β = 90 |
c = 112.384 | γ = 90 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
XSCALE | data reduction |
XSCALE | data scaling |
MOLREP | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2017-05-10  Deposition Author(s): Polyakov, K.M., Gavryushov, S., Fedorova, T.V., Glazunova, O.A., Popov, A.N.
Funding Organization | Location | Grant Number |
---|---|---|
RFBR | Russian Federation | 16-04-0052 |
Revision History (Full details and data files)
- Version 1.0: 2017-05-10
Type: Initial release - Version 1.1: 2017-05-24
Changes: Database references - Version 1.2: 2019-07-17
Changes: Data collection - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2024-01-17
Changes: Data collection, Database references, Refinement description, Structure summary