Download MendeleySubstrate complex structure of Xoo1075, a peptide deformylase, from Xanthomonas oryzae pv. oryzae
Ngo, H.P.T., Kim, J.K., Kang, L.W.To be published.
4NT8
Formyl-methionine-alanine complex structure of peptide deformylase from Xanthomoonas oryzae pv. oryzae
- PDB DOI: https://doi.org/10.2210/pdb4NT8/pdb
- Classification: HYDROLASE
- Organism(s): Xanthomonas oryzae pv. oryzae KACC 10331
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2013-12-02 Released: 2014-12-03
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 Å
- R-Value Free: 0.235
- R-Value Work: 0.190
- R-Value Observed: 0.192
Starting Model: experimental
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This is version 1.2 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 |
| Peptide deformylase | 171 | Xanthomonas oryzae pv. oryzae KACC 10331 | Mutation(s): 0 Gene Names: def, XOO1075 EC: 3.5.1.88 |  | |
UniProt | |||||
Find proteins for Q5H3Z2 (Xanthomonas oryzae pv. oryzae (strain KACC10331 / KXO85)) Explore Q5H3Z2 Go to UniProtKB: Q5H3Z2 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q5H3Z2 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 6 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| FME Query on FME | H [auth A] | N-FORMYLMETHIONINE C6 H11 N O3 S PYUSHNKNPOHWEZ-YFKPBYRVSA-N |  | ||
| CD Query on CD | B [auth A], C [auth A], D [auth A] | CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N |  | ||
| GOL Query on GOL | J [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| ALA Query on ALA | I [auth A] | ALANINE C3 H7 N O2 QNAYBMKLOCPYGJ-REOHCLBHSA-N |  | ||
| ACT Query on ACT | E [auth A] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M |  | ||
| NA Query on NA | F [auth A], G [auth A] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| CSD Query on CSD | A | L-PEPTIDE LINKING | C3 H7 N O4 S |  | CYS |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 Å
- R-Value Free: 0.235
- R-Value Work: 0.190
- R-Value Observed: 0.192
- Space Group: P 61 2 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 58.584 | α = 90 |
| b = 58.584 | β = 90 |
| c = 266.188 | γ = 120 |
| Software Name | Purpose |
|---|---|
| HKL-2000 | data collection |
| PHASES | phasing |
| REFMAC | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
Entry History
Deposition Data
- Released Date: 2014-12-03 Deposition Author(s): Ngo, H.P.T., Kim, J.K., Kang, L.W.
Revision History (Full details and data files)
- Version 1.0: 2014-12-03
Type: Initial release - Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description - Version 1.2: 2024-11-06
Changes: Structure summary
