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- PDB-1pya: REFINED STRUCTURE OF THE PYRUVOYL-DEPENDENT HISTIDINE DECARBOXYLA... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1pya | |||||||||
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Title | REFINED STRUCTURE OF THE PYRUVOYL-DEPENDENT HISTIDINE DECARBOXYLASE FROM LACTOBACILLUS 30A | |||||||||
![]() | (PYRUVOYL-DEPENDENT HISTIDINE DECARBOXYLASE (L-HISTIDINE CARBOXYLASE)) x 2 | |||||||||
![]() | CARBOXY-LYASE | |||||||||
Function / homology | ![]() histidine decarboxylase / histidine decarboxylase activity / L-histidine metabolic process / amino acid metabolic process Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() | |||||||||
![]() | Gallagher, T. / Rozwarski, D.A. / Ernst, S.R. / Hackert, M.L. | |||||||||
![]() | ![]() Title: Refined structure of the pyruvoyl-dependent histidine decarboxylase from Lactobacillus 30a. Authors: Gallagher, T. / Rozwarski, D.A. / Ernst, S.R. / Hackert, M.L. #1: ![]() Title: Pyruvoyl-Dependent Histidine Decarboxylase: Active Site Structure and Mechanistic Analysis Authors: Gallagher, T. / Snell, E.E. / Hackert, M.L. #2: ![]() Title: Structure Determination of Histidine Decarboxylase from Lactobacillus 30A at 3.0 Angstroms Resolution Authors: Parks, E.H. / Ernst, S.R. / Hamlin, R. / Xuong, N.H. / Hackert, M.L. #3: ![]() Title: The Molecular Symmetry of Histidine Decarboxylase and Prohistidine Decarboxylase by Rotation Function Analysis Authors: Parks, E.H. / Clinger, K. / Hackert, M.L. #4: ![]() Title: Crystallization and Subunit Structure of Histidine Decarboxylase from Lactobacillus 30A Authors: Hackert, M.L. / Meador, W.E. / Oliver, R.M. / Salmon, J.B. / Rescei, P.A. / Snell, E.E. | |||||||||
History |
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Remark 650 | HELIX ISOLATED TURNS OF A 3-10 HELIX OCCUR AT RESIDUES 98 - 102 AND 266 - 270. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 246 KB | Display | ![]() |
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PDB format | ![]() | 200.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Details | TWO TRIMERS RELATED BY A CRYSTALLOGRAPHIC TWO-FOLD SYMMETRY AXIS GENERATE THE HEXAMER. THE TRANSFORMATION PRESENTED AS *MTRIX 1* BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAINS *A* AND *B* WHEN APPLIED TO CHAINS *C* AND *D*, RESPECTIVELY. THE TRANSFORMATION PRESENTED AS *MTRIX 2* BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAINS *A* AND *B* WHEN APPLIED TO CHAINS *E* AND *F*, RESPECTIVELY. |
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Components
#1: Protein | Mass: 8850.832 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() #2: Protein | Mass: 25285.375 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.21 Å3/Da / Density % sol: 61.71 % | |||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 4.8 / Method: unknown | |||||||||||||||||||||||||
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 |
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Processing
Software |
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Refinement | Rfactor Rwork: 0.15 / Rfactor obs: 0.15 / Highest resolution: 2.5 Å Details: THE SEGMENT NUMBERS ARE AS FOLLOWS: (1,3,5 = BETA SUBUNITS) (2,4,6 = ALPHA SUBUNITS), (7,8,9 = PVL MOIETIES WITH 7-2 REPRESENTING THE PVL GROUP COVALENTLY ATTACHED TO THE BEGINNING OF AN ...Details: THE SEGMENT NUMBERS ARE AS FOLLOWS: (1,3,5 = BETA SUBUNITS) (2,4,6 = ALPHA SUBUNITS), (7,8,9 = PVL MOIETIES WITH 7-2 REPRESENTING THE PVL GROUP COVALENTLY ATTACHED TO THE BEGINNING OF AN ALPHA SUBUNIT OR SEGMENT 2). THE SEGMENT NUMBERS FOR THE THREE *AB* SUBUNITS ARE: 1, 7 - 2; 3, 8 - 4; AND 5, 9 - 6. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.5 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 5 Å / Num. reflection obs: 39926 / Rfactor obs: 0.15 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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