- PDB-7zs8: Mixed-valence, active form, of cytochrome c peroxidase from oblig... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 7zs8
Title
Mixed-valence, active form, of cytochrome c peroxidase from obligate human pathogenic bacterium Neisseria gonorrhoeae at 1.4 Angstrom resolution
Components
Cytochrome-c peroxidase
Keywords
ELECTRON TRANSPORT / Neisseria gonorrhoeae / bacterial peroxidase / ROS detoxification
Function / homology
Function and homology information
cytochrome-c peroxidase / cytochrome-c peroxidase activity / periplasmic space / electron transfer activity / heme binding / metal ion binding Similarity search - Function
Di-c-type haem protein, MauG/cytochrome c peroxidase / Di-haem cytochrome c peroxidase / Di-haem cytochrome c peroxidase / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. Similarity search - Domain/homology
Resolution: 1.4→39.95 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.368 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.22096
6220
5 %
RANDOM
Rwork
0.19638
-
-
-
obs
0.19763
118011
99.6 %
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Solvent computation
Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parameters
Biso mean: 18.815 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.22 Å2
0 Å2
-0 Å2
2-
-
-1.55 Å2
-0 Å2
3-
-
-
1.77 Å2
Refinement step
Cycle: LAST / Resolution: 1.4→39.95 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
5050
0
176
577
5803
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.012
0.018
5438
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.019
5040
X-RAY DIFFRACTION
r_angle_refined_deg
1.972
1.92
7423
X-RAY DIFFRACTION
r_angle_other_deg
1.193
2.74
11646
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.726
5
666
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
36.305
23.841
276
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
11.688
15
897
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
19.409
15
26
X-RAY DIFFRACTION
r_chiral_restr
0.126
0.2
759
X-RAY DIFFRACTION
r_gen_planes_refined
0.011
0.02
6287
X-RAY DIFFRACTION
r_gen_planes_other
0.012
0.02
1241
X-RAY DIFFRACTION
r_mcbond_it
1.784
1.667
2624
X-RAY DIFFRACTION
r_mcbond_other
1.781
1.666
2623
X-RAY DIFFRACTION
r_mcangle_it
2.322
2.501
3276
X-RAY DIFFRACTION
r_mcangle_other
2.322
2.502
3277
X-RAY DIFFRACTION
r_scbond_it
3.027
1.905
2814
X-RAY DIFFRACTION
r_scbond_other
3.028
1.905
2812
X-RAY DIFFRACTION
r_scangle_other
4.261
2.738
4138
X-RAY DIFFRACTION
r_long_range_B_refined
4.92
20.533
6529
X-RAY DIFFRACTION
r_long_range_B_other
4.864
20.071
6383
LS refinement shell
Resolution: 1.4→1.436 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.293
477
-
Rwork
0.276
8622
-
obs
-
-
99.42 %
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