- PDB-4v1x: The structure of the hexameric atrazine chlorohydrolase, AtzA -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4v1x
Title
The structure of the hexameric atrazine chlorohydrolase, AtzA
Components
ATRAZINE CHLOROHYDROLASE
Keywords
HYDROLASE / BIOREMEDIATION / PROTEIN EVOLUTION
Function / homology
Function and homology information
atrazine chlorohydrolase / atrazine chlorohydrolase activity / atrazine catabolic process / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / metal ion binding / cytoplasm Similarity search - Function
Mass: 18.015 Da / Num. of mol.: 887 / Source method: isolated from a natural source / Formula: H2O
Sequence details
HIS-TAG AT N-TERMINUS FOR PURIFICATION.
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.68 Å3/Da / Density % sol: 54.2 % Description: 3HPA WAS USED TO SOLVE A LOW RESOLUTION STRUCTURE OF ATZA IN A DIFFERENT SPACEGROUP. THIS STRUCTURE WAS THEN USED TO SOLVE THE STRUCTURE DEPOSITED NOW.
Crystal grow
pH: 7.3 Details: THE PROTEIN (AFTER HIS-TAG REMOVAL) WAS CONCENTRATED TO 11 MG/ML AND SET IN A 1:1 RATIO, 200 NL PLUS 200 NL, WITH 50 MM HEPES PH 7.3, 4.6 % PEG 10,000.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9537 Å / Relative weight: 1
Reflection
Resolution: 2.2→48.7 Å / Num. obs: 170140 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 15.1 % / Rmerge(I) obs: 0.24 / Net I/σ(I): 11.6
Reflection shell
Resolution: 2.2→2.24 Å / Redundancy: 15.3 % / Rmerge(I) obs: 1.15 / Mean I/σ(I) obs: 3.2 / % possible all: 99.2
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Processing
Software
Name
Version
Classification
REFMAC
5.8.0073
refinement
XDS
datareduction
Aimless
datascaling
PHASER
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→117.19 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.937 / SU B: 9.419 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED THE PROTEIN WAS SET UP IN A CO-CRYSTALLIZATION EXPERIMENT WITH ATRAZINE, AND ALTHOUGH THERE IS SOME DENSITY IN SOME ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED THE PROTEIN WAS SET UP IN A CO-CRYSTALLIZATION EXPERIMENT WITH ATRAZINE, AND ALTHOUGH THERE IS SOME DENSITY IN SOME OF THE ACTIVE SITES, IT WAS NOT DEFINITIVE ENOUGH TO PLACE THE SUBSTRATE.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.19631
8345
4.9 %
RANDOM
Rwork
0.16553
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obs
0.16703
161715
99.46 %
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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