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- PDB-1lth: T AND R STATES IN THE CRYSTALS OF BACTERIAL L-LACTATE DEHYDROGENA... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1lth | ||||||
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Title | T AND R STATES IN THE CRYSTALS OF BACTERIAL L-LACTATE DEHYDROGENASE REVEAL THE MECHANISM FOR ALLOSTERIC CONTROL | ||||||
![]() | L-LACTATE DEHYDROGENASE (T- AND R- STATE TETRAMER COMPLEX) | ||||||
![]() | OXIDOREDUCTASE / CHOH(D)-NAD(A) / ALLOSTERIC ENZYME | ||||||
Function / homology | ![]() L-lactate dehydrogenase / lactate metabolic process / L-lactate dehydrogenase activity / glycolytic process / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Iwata, S. / Ohta, T. | ||||||
![]() | ![]() Title: T and R states in the crystals of bacterial L-lactate dehydrogenase reveal the mechanism for allosteric control. Authors: Iwata, S. / Kamata, K. / Yoshida, S. / Minowa, T. / Ohta, T. #1: ![]() Title: A Regular 1:1 Complex of Two Allosteric States in the Single Crystal of L-Lactate Dehydrogenase from Bifidobacterium Longum Authors: Iwata, S. / Yoshida, S. / Ohta, T. #2: ![]() Title: Molecular Basis of Allosteric Activation of Bacterial L-Lactate Dehydrogenase Authors: Iwata, S. / Ohta, T. #3: ![]() Title: Mechanism of Allosteric Transition of Bacterial L-Lactate Dehydrogenase Authors: Ohta, T. / Minowa, T. / Yokota, K. / Iwata, S. #4: ![]() Title: Crystallization of and Preliminary Crystallographic Data for Allosteric L-Lactate Dehydrogenase from Bifidobacterium Longum Authors: Iwata, S. / Minowa, T. / Mikani, B. / Morita, Y. / Ohta, T. #5: ![]() Title: Sequence and Characteristics of the Bifidobacterium Longum Gene Encoding L-Lactate Dehydrogenase and the Primary Structure of the Enzyme: A New Feature of the Allosteric Site Authors: Minowa, T. / Iwata, S. / Sakai, H. / Masaki, H. / Ohta, T. #6: ![]() Title: Amino Acid Residues in the Allosteric Site of L-Lactate Dehydrogenase from Bifidobacterium Longum Authors: Iwata, S. / Minowa, T. / Sakai, H. / Ohta, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 138.7 KB | Display | ![]() |
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PDB format | ![]() | 109.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 30.9 KB | Display | |
Data in CIF | ![]() | 43.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO T 126 / 2: CIS PROLINE - PRO R 126 | ||||||||
Details | THIS CRYSTAL STRUCTURE REFERENCES THE REGULAR 1:1 COMPLEX OF T-STATE (LOW AFFINITY TO SUBSTRATE) AND R-STATE (HIGH AFFINITY TO SUBSTRATE) TETRAMERS OF L-LACTATE DEHYDROGENASE FROM BIFIDOBACTERIUM LONGUM. THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT CONTAINS ONE T-STATE SUBUNIT AND ONE R-STATE SUBUNIT ASSIGNED CHAIN IDENTIFIERS "T" AND "R", RESPECTIVELY. SYMMETRY THE CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS PRESENTED BELOW GENERATE THE SUBUNITS OF THE POLYMERIC MOLECULE. APPLIED TO RESIDUES: T 6 .. T 321 FORMATION OF THE P-AXIS RELATED SUBUNIT OF THE T-STATE TETRAMER SYMMETRY1 1 1.000000 0.000000 0.000000 0.00000 SYMMETRY2 1 0.000000 -1.000000 0.000000 0.00000 SYMMETRY3 1 0.000000 0.000000 -1.000000 0.00000 APPLIED TO RESIDUES: T 6 .. T 321 FORMATION OF THE Q-AXIS RELATED SUBUNIT OF THE T-STATE TETRAMER SYMMETRY1 2 -1.000000 0.000000 0.000000 0.00000 SYMMETRY2 2 0.000000 1.000000 0.000000 0.00000 SYMMETRY3 2 0.000000 0.000000 -1.000000 0.00000 APPLIED TO RESIDUES: T 6 .. T 321 FORMATION OF THE R-AXIS RELATED SUBUNIT OF THE T-STATE TETRAMER SYMMETRY1 3 -1.000000 0.000000 0.000000 0.00000 SYMMETRY2 3 0.000000 -1.000000 0.000000 0.00000 SYMMETRY3 3 0.000000 0.000000 1.000000 0.00000 APPLIED TO RESIDUES: R 6 .. R 322 FORMATION OF THE P-AXIS RELATED SUBUNIT OF THE R-STATE TETRAMER SYMMETRY1 4 1.000000 0.000000 0.000000 0.00000 SYMMETRY2 4 0.000000 -1.000000 0.000000 147.92900 SYMMETRY3 4 0.000000 0.000000 -1.000000 35.46099 APPLIED TO RESIDUES: R 6 .. R 322 FORMATION OF THE Q-AXIS RELATED SUBUNIT OF THE R-STATE TETRAMER SYMMETRY1 5 -1.000000 0.000000 0.000000 74.18398 SYMMETRY2 5 0.000000 1.000000 0.000000 0.00000 SYMMETRY3 5 0.000000 0.000000 -1.000000 35.46099 APPLIED TO RESIDUES: R 6 .. R 322 FORMATION OF THE R-AXIS RELATED SUBUNIT OF THE R-STATE TETRAMER SYMMETRY1 6 -1.000000 0.000000 0.000000 74.18398 SYMMETRY2 6 0.000000 -1.000000 0.000000 147.92900 SYMMETRY3 6 0.000000 0.000000 1.000000 0.00000 |
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Components
#1: Protein | Mass: 34128.777 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Species: Bifidobacterium longum / Strain: subsp. longum / Gene: BIFIDOBACTERIUM LONGUM LDH GENE / Plasmid: PUBM9 (A DERIVATIVE OF PUC119) / Production host: ![]() ![]() References: UniProt: P19869, UniProt: E8ME30*PLUS, L-lactate dehydrogenase #2: Sugar | #3: Chemical | #4: Chemical | ChemComp-OXM / | #5: Water | ChemComp-HOH / | Compound details | THE T-STATE TETRAMERS, THAT BIND NADH AND FBP, ARE CENTERED AT THE ORIGIN AND ITS EQUIVALENTS. THE ...THE T-STATE TETRAMERS, THAT BIND NADH AND FBP, ARE CENTERED AT THE ORIGIN AND ITS EQUIVALENT | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.89 % | |||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 10 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.5→100 Å / Num. obs: 24341 / % possible obs: 89.1 % / Observed criterion σ(I): 1 |
Reflection | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 100 Å / % possible obs: 97.6 % / Num. measured all: 115542 / Rmerge(I) obs: 0.055 |
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Processing
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Refinement | Resolution: 2.5→10 Å / σ(F): 2
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Displacement parameters | Biso mean: 23.79 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→10 Å
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Refine LS restraints |
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