- PDB-4egr: 2.50 angstrom resolution structure of 3-phosphoshikimate 1-carbox... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4egr
Title
2.50 angstrom resolution structure of 3-phosphoshikimate 1-carboxyvinyltransferase (AroA) from Coxiella burnetii in complex with phosphoenolpyruvate
Components
3-phosphoshikimate 1-carboxyvinyltransferase
Keywords
TRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / 3-phosphoshikimate 1- carboxyvinyl transferase activity
Function / homology
Function and homology information
3-phosphoshikimate 1-carboxyvinyltransferase / 3-phosphoshikimate 1-carboxyvinyltransferase activity / shikimate kinase activity / shikimate 3-dehydrogenase (NADP+) activity / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / cytoplasm Similarity search - Function
Resolution: 2.5→29.75 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.948 / SU B: 8.532 / SU ML: 0.186 / Cross valid method: THROUGHOUT / ESU R: 0.352 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.22345
5942
5 %
RANDOM
Rwork
0.1766
-
-
-
obs
0.17897
112570
98.58 %
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all
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112570
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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
Displacement parameters
Biso mean: 48.873 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.2 Å2
0 Å2
0.49 Å2
2-
-
-0.53 Å2
0 Å2
3-
-
-
0.74 Å2
Refinement step
Cycle: LAST / Resolution: 2.5→29.75 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
19284
0
120
412
19816
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.013
0.019
19813
X-RAY DIFFRACTION
r_bond_other_d
0.002
0.02
13282
X-RAY DIFFRACTION
r_angle_refined_deg
1.72
1.992
26919
X-RAY DIFFRACTION
r_angle_other_deg
1.025
3.001
32681
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
3.304
5
2638
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
33.042
24.516
744
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.816
15
3407
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
13.936
15
132
X-RAY DIFFRACTION
r_chiral_restr
0.102
0.2
3208
X-RAY DIFFRACTION
r_gen_planes_refined
0.008
0.021
22073
X-RAY DIFFRACTION
r_gen_planes_other
0.002
0.02
3551
LS refinement shell
Resolution: 2.501→2.566 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.362
373
-
Rwork
0.284
7151
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obs
-
-
87.35 %
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