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- Biological Assembly 1 (CIF - gz)
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2G4O | pdb_00002g4o
anomalous substructure of 3-ISOPROPYLMALATE DEHYDROGENASE
- PDB DOI: https://doi.org/10.2210/pdb2G4O/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Mycobacterium tuberculosis
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2006-02-22 Released: 2007-02-20
- Deposition Author(s): Mueller-Dieckmann, C., Weiss, M.S.
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.260 (Depositor)
- R-Value Work: 0.209 (Depositor), 0.210 (DCC)
- R-Value Observed: 0.210 (Depositor)
wwPDB Validation 3D Report Full Report
- 👁 Image
Download Mendeley
On the routine use of soft X-rays in macromolecular crystallography. Part IV. Efficient determination of anomalous substructures in biomacromolecules using longer X-ray wavelengths.
Mueller-Dieckmann, C., Panjikar, S., Schmidt, A., Mueller, S., Kuper, J., Geerlof, A., Wilmanns, M., Singh, R.K., Tucker, P.A., Weiss, M.S.(2007) Acta Crystallogr D Biol Crystallogr 63: 366-380
- PubMed: 17327674 Search on PubMed
- DOI: https://doi.org/10.1107/S0907444906055624
- Primary Citation Related Structures:
2G4H, 2G4I, 2G4J, 2G4K, 2G4L, 2G4M, 2G4N, 2G4O, 2G4P, 2G4Q, 2G4R, 2G4S, 2G4T, 2G4U, 2G4V, 2G4W, 2G4X, 2G4Y, 2G4Z, 2G51, 2G52, 2G55, 2ILL - PubMed Abstract:
23 different crystal forms of 19 different biological macromolecules were examined with respect to their anomalously scattering substructures using diffraction data collected at a wavelength of 2.0 A (6.2 keV). In more than 90% of the cases the substructure was found to contain more than just the protein S atoms. The data presented suggest that chloride, sulfate, phosphate or metal ions from the buffer or even from the purification protocol are frequently bound to the protein molecule and that these ions are often overlooked, especially if they are not bound at full occupancy. Thus, in order to fully describe the macromolecule under study, it seems desirable that any structure determination be complemented with a long-wavelength data set.
- EMBL Hamburg Outstation, c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany.
Organizational Affiliation:
Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report | Ligand Interaction (SO4)
Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report | Ligand Interaction (SO4)
Global Symmetry: Cyclic - C2 (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2
Find Similar Assemblies
Biological assembly 1 assigned by authors and generated by PISA (software)
Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report | Ligand Interaction (SO4)
Global Symmetry: Cyclic - C2 (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2
Find Similar Assemblies
Biological assembly 2 assigned by authors and generated by PISA (software)
Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report | Ligand Interaction (SO4)
Global Symmetry: Dihedral - D2 (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4
Find Similar Assemblies
Biological assembly 3 generated by PISA (software)
Macromolecule Content
- Total Structure Weight: 142.15 kDa
- Atom Count: 10,587
- Modeled Residue Count: 1,348
- Deposited Residue Count: 1,348
- Unique protein chains: 1
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| 3-isopropylmalate dehydrogenase | 337 | Mycobacterium tuberculosis | Mutation(s): 0 Gene Names: leuB EC: 1.1.1.85 | 👁 Image | |
UniProt | |||||
Find proteins for P9WKK9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WKK9 Go to UniProtKB: P9WKK9 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P9WKK9 | ||||
Sequence AnnotationsExpand | |||||
| |||||
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| SO4 Query on SO4 Download Ideal Coordinates CCD File | E [auth A], K [auth D] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L | 👁 Image | ||
| CL Query on CL Download Ideal Coordinates CCD File
| F [auth A] G [auth A] H [auth A] I [auth B] J [auth C] F [auth A], G [auth A], H [auth A], I [auth B], J [auth C], L [auth D] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M | 👁 Image | ||
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.260 (Depositor)
- R-Value Work: 0.209 (Depositor), 0.210 (DCC)
- R-Value Observed: 0.210 (Depositor)
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 78.57 | α = 90 |
| b = 98.58 | β = 90 |
| c = 184.03 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| DENZO | data reduction |
| CCP4 | data scaling |
| FFT | phasing |
Deposition Data
- Released Date: 2007-02-20 Deposition Author(s): Mueller-Dieckmann, C., Weiss, M.S.
Revision History (Full details and data files)
- Version 1.0: 2007-02-20
Type: Initial release - Version 1.1: 2008-05-01
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance - Version 1.3: 2024-02-14
Changes: Data collection, Database references, Derived calculations
