- PDB-4add: Structural and functional study of succinyl-ornithine transaminas... -
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ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4add
Title
Structural and functional study of succinyl-ornithine transaminase from E. coli
Components
SUCCINYLORNITHINE TRANSAMINASE
Keywords
TRANSFERASE / PLP ENZYMES / AMINOTRANSFERASE
Function / homology
Function and homology information
succinylornithine transaminase / succinylornithine transaminase activity / ornithine catabolic process / arginine catabolic process to succinate / N2-acetyl-L-ornithine:2-oxoglutarate 5-aminotransferase activity / arginine catabolic process to glutamate / arginine biosynthetic process via ornithine / arginine catabolic process / pyridoxal phosphate binding / identical protein binding Similarity search - Function
Mass: 18.015 Da / Num. of mol.: 320 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details
SUCCINYLORNITHINE (SUO): SUCCINYLORNITHINE SYNTHESISED IN HOUSE
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 4
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Sample preparation
Crystal
Density Matthews: 3.43 Å3/Da / Density % sol: 64.2 % / Description: NONE
Crystal grow
Temperature: 293 K / pH: 9 Details: 1.5 M AMMONIUM SULFATE, 10% (V/V) MMT (MALATE-MES-TRIS) BUFFER AT PH 9.0, 293K, 150 PLUS 150 NL DROPS. PROTEIN HAD PLP AND SUCCINYLORNITHINE PREVIOUSLY ADDED.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.95369 Å / Relative weight: 1
Reflection
Resolution: 2.45→19.8 Å / Num. obs: 85143 / % possible obs: 99.8 % / Observed criterion σ(I): 1 / Redundancy: 5.9 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 10.6
Reflection shell
Resolution: 2.45→2.58 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.9 / % possible all: 100
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Processing
Software
Name
Version
Classification
REFMAC
5.6.0117
refinement
XDS
datareduction
SCALA
datascaling
PHASER
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: PREVIOUSLY-DETERMINED NATIVE Resolution: 2.45→108.46 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.919 / SU B: 7.609 / SU ML: 0.166 / Cross valid method: THROUGHOUT / ESU R: 0.277 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN TH INPUT. U VALUES REFINED INDIVIDUALLY. THERE IS A SMALL AMOUNT OF POSITIVE ELECTRON DENSITY THAT COULD NOT BE MODELLED WELL.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.22534
4254
5 %
RANDOM
Rwork
0.17026
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obs
0.17303
80886
99.77 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK