4H7L
Crystal structure of Plim_4148 protein from Planctomyces limnophilus
- PDB DOI: https://doi.org/10.2210/pdb4H7L/pdb
- Classification: Structural Genomics, Unknown Function
- Organism(s): Planctopirus limnophila DSM 3776
- Expression System: Escherichia coli
- Mutation(s): No 
- Deposited: 2012-09-20 Released: 2013-01-02 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.45 Å
- R-Value Free: 0.226 
- R-Value Work: 0.177 
- R-Value Observed: 0.180 
wwPDB Validation   3D Report Full Report
This is version 1.0 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 |
uncharacterized protein | 157 | Planctopirus limnophila DSM 3776 | Mutation(s): 0  Gene Names: Plim_4148 | ||
UniProt | |||||
Find proteins for D5SZ58 (Planctopirus limnophila (strain ATCC 43296 / DSM 3776 / IFAM 1008 / Mu 290)) Explore D5SZ58  Go to UniProtKB:  D5SZ58 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | D5SZ58 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
CU Query on CU | C [auth A], D [auth B] | COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N |
Modified Residues 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Type | Formula | 2D Diagram | Parent |
MSE Query on MSE | A, B | L-PEPTIDE LINKING | C5 H11 N O2 Se | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.45 Å
- R-Value Free: 0.226 
- R-Value Work: 0.177 
- R-Value Observed: 0.180 
- Space Group: P 31 2 1
- Diffraction Data: https://doi.org/10.18430/M34H7L
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 67.091 | α = 90 |
b = 67.091 | β = 90 |
c = 109.874 | γ = 120 |
Software Name | Purpose |
---|---|
SBC-Collect | data collection |
SHELX | model building |
MLPHARE | phasing |
DM | model building |
BUCCANEER | model building |
ARP/wARP | model building |
Coot | model building |
PHENIX | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
SHELX | phasing |
DM | phasing |
BUCCANEER | phasing |
Entry History 
Deposition Data
- Released Date: 2013-01-02  Deposition Author(s): Michalska, K., Bigelow, L., Bruno, C.J.P., Moser, C., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
Revision History (Full details and data files)
- Version 1.0: 2013-01-02
Type: Initial release