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- PDB-5rla: ALTERING THE BINUCLEAR MANGANESE CLUSTER OF ARGINASE DIMINISHES T... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5rla | ||||||
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Title | ALTERING THE BINUCLEAR MANGANESE CLUSTER OF ARGINASE DIMINISHES THERMOSTABILITY AND CATALYTIC FUNCTION | ||||||
![]() | ARGINASE![]() | ||||||
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Function / homology | ![]() regulation of L-arginine import across plasma membrane / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Scolnick, L.R. / Kanyo, Z.F. / Christianson, D.W. | ||||||
![]() | ![]() Title: Altering the binuclear manganese cluster of arginase diminishes thermostability and catalytic function. Authors: Scolnick, L.R. / Kanyo, Z.F. / Cavalli, R.C. / Ash, D.E. / Christianson, D.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 185 KB | Display | ![]() |
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PDB format | ![]() | 147.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related 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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Components
#1: Protein | ![]() Mass: 34995.051 Da / Num. of mol.: 3 / Mutation: H101N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 53 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow![]() | pH: 8.5 Details: 12 - 18% PEG 8000, 50 MM BICINE PH = 8.5, 0.05% AZIDE, 1 MM MNCL2 SOAKED FOR 1 WEEK IN 15MM EDTA + DPA | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 48 % | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Jan 1, 1995 / Details: YALE |
Radiation | Monochromator: YALE MIRRORS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.7→20 Å / Num. obs: 37872 / % possible obs: 91.8 % / Observed criterion σ(I): 2 / Redundancy: 1.6 % / Biso Wilson estimate: 34.2 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 2.7→2.77 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 1.5 / Rsym value: 0.45 / % possible all: 94.9 |
Reflection | *PLUS Num. obs: 23414 / Num. measured all: 37872 |
Reflection shell | *PLUS % possible obs: 94.9 % |
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Processing
Software |
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Refinement | Method to determine structure![]() ![]() Starting model: RAT LIVER ARGINASE Resolution: 2.74→15 Å / Rfactor Rfree error: 0.0004 / Data cutoff high absF: 10000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT CORRECTION USED
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Refine analyze | Luzzati d res low obs: 12 Å / Luzzati sigma a obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.74→15 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.74→2.86 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 22421 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.4 |