[English] 日本語
Yorodumi- PDB-6bal: 2.1 Angstrom Resolution Crystal Structure of Malate Dehydrogenase... -
+
Open data
-
Basic information
| Entry | Database: PDB / ID: 6bal | ||||||
|---|---|---|---|---|---|---|---|
| Title | 2.1 Angstrom Resolution Crystal Structure of Malate Dehydrogenase from Haemophilus influenzae in Complex with L-Malate | ||||||
Components | Malate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Malate Dehydrogenase / L-Malate | ||||||
| Function / homology | Function and homology information(S)-malate dehydrogenase (NAD+, oxaloacetate-forming) / L-malate dehydrogenase (NAD+) activity / malate metabolic process / tricarboxylic acid cycle / cytoplasm Similarity search - Function | ||||||
| Biological species | Haemophilus influenzae (bacteria) | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Minasov, G. / Wawrzak, Z. / Skarina, T. / Grimshaw, S. / Satchell, K.J.F. / Savchenko, A. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: Microbiol Resour Announc / Year: 2025Title: Structural genomics of bacterial drug targets: Application of a high-throughput pipeline to solve 58 protein structures from pathogenic and related bacteria. Authors: Inniss, N.L. / Minasov, G. / Chang, C. / Tan, K. / Kim, Y. / Maltseva, N. / Stogios, P. / Filippova, E. / Michalska, K. / Osipiuk, J. / Jaroszewki, L. / Godzik, A. / Savchenko, A. / ...Authors: Inniss, N.L. / Minasov, G. / Chang, C. / Tan, K. / Kim, Y. / Maltseva, N. / Stogios, P. / Filippova, E. / Michalska, K. / Osipiuk, J. / Jaroszewki, L. / Godzik, A. / Savchenko, A. / Joachimiak, A. / Anderson, W.F. / Satchell, K.J.F. | ||||||
| History |
|
-
Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
|---|
-
Downloads & links
-
Download
| PDBx/mmCIF format | 6bal.cif.gz | 924.1 KB | Display | PDBx/mmCIF format |
|---|---|---|---|---|
| PDB format | pdb6bal.ent.gz | 770.6 KB | Display | PDB format |
| PDBx/mmJSON format | 6bal.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ba/6bal ftp://data.pdbj.org/pub/pdb/validation_reports/ba/6bal | HTTPS FTP |
|---|
-Related structure data
| Related structure data | ![]() 5tr3C ![]() 5tv2C ![]() 5ty0C ![]() 5u1oC ![]() 5u2gC ![]() 5u47C ![]() 5ue1C ![]() 5umeC ![]() 5us8C ![]() 5uswC ![]() 5usxC ![]() 5utxC ![]() 5uu6C ![]() 5uwyC ![]() 5ux9C ![]() 5v36C ![]() 5vdnC ![]() 5vfbC ![]() 5vh6C ![]() 5wi5C ![]() 5wp0C ![]() 6aonC ![]() 6aooC ![]() 6awaC ![]() 6aziC ![]() 6b4oC ![]() 6b5fC ![]() 6b8dC ![]() 6bk7C ![]() 6blbC ![]() 6bq9C ![]() 6bz0C ![]() 6c8qC ![]() 6cmzC ![]() 6cn1C ![]() 6czpC ![]() 6e5yC ![]() 6muqC ![]() 6n0iC ![]() 6n7fC ![]() 6nfpC ![]() 6nkjC ![]() 6po4C ![]() 6pu9C ![]() 6puaC ![]() 6pxaC ![]() 6w2zC ![]() 9bznC ![]() 9bzqC ![]() 9bzrC ![]() 3hhpS C: citing same article ( S: Starting model for refinement |
|---|---|
| Similar structure data | |
| Other databases |
-
Links
-
Assembly
| Deposited unit | ![]()
| ||||||||
|---|---|---|---|---|---|---|---|---|---|
| 1 | ![]()
| ||||||||
| 2 | ![]()
| ||||||||
| 3 | ![]()
| ||||||||
| 4 | ![]()
| ||||||||
| Unit cell |
|
-
Components
| #1: Protein | Mass: 35318.438 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) (bacteria)Strain: ATCC 51907 / DSM 11121 / KW20 / Rd / Gene: mdh, HI_1210 / Plasmid: pMCSG53 / Production host: ![]() References: UniProt: P44427, (S)-malate dehydrogenase (NAD+, oxaloacetate-forming) #2: Chemical | ChemComp-LMR / ( | #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | Has protein modification | N | |
|---|
-Experimental details
-Experiment
| Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
|---|
-
Sample preparation
| Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.3 % |
|---|---|
| Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Protein: 20.0 mg/ml, 0.3M Sodium chloride, 0.01M HEPES pH 7.5; Screen: 0.2M Ammonium formate, 20% (w/v) PEG3350, 0.25mM DL-Malic acid; Cryo: paratone. |
-Data collection
| Diffraction | Mean temperature: 100 K |
|---|---|
| Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
| Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 20, 2017 / Details: C(111) |
| Radiation | Monochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
| Reflection | Resolution: 2.1→30 Å / Num. obs: 126522 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 28.3 Å2 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.054 / Rrim(I) all: 0.108 / Rsym value: 0.093 / Χ2: 1.021 / Net I/σ(I): 13.4 |
| Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.662 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 6257 / CC1/2: 0.665 / Rpim(I) all: 0.392 / Rrim(I) all: 0.77 / Rsym value: 0.662 / Χ2: 1.019 / % possible all: 97.2 |
-
Processing
| Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting model: 3HHP Resolution: 2.1→29.75 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.941 / SU B: 11.591 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.253 / ESU R Free: 0.191 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Displacement parameters | Biso mean: 35.765 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refinement step | Cycle: 1 / Resolution: 2.1→29.75 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refine LS restraints |
|
Movie
Controller
About Yorodumi



Haemophilus influenzae (bacteria)
X-RAY DIFFRACTION
Citation




























































PDBj











