- PDB-3o84: Structure of BasE N-terminal domain from Acinetobacter baumannii ... -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 3o84
Title
Structure of BasE N-terminal domain from Acinetobacter baumannii bound to 6-phenyl-1-(pyridin-4-ylmethyl)-1H-pyrazolo[3,4-b]pyridine-4-carboxylic acid.
Components
Peptide arylation enzyme
Keywords
LIGASE / Adenylation of 2 / 3-dihydroxybenzoate and transfer to pantetheine cofactor of BasF / Non-Ribosomal Peptide Synthetase (NRPS)
Function / homology
Function and homology information
2,3-dihydroxybenzoate--[aryl-carrier protein] ligase / siderophore biosynthetic process Similarity search - Function
Mass: 18.015 Da / Num. of mol.: 434 / Source method: isolated from a natural source / Formula: H2O
-
Details
Sequence details
THIS ENTRY USES A UNIPROT REFERENCE THAT IS FOR A DIFFERENT STRAIN OF A. BAUMANNI. THESE CHANGES ...THIS ENTRY USES A UNIPROT REFERENCE THAT IS FOR A DIFFERENT STRAIN OF A. BAUMANNI. THESE CHANGES ARE STRAIN RELATED DIFFERENCES AS FOUND IN GENBANK ENTRY ZP_04661818.
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.87 Å3/Da / Density % sol: 57.15 %
Crystal grow
Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 5-15% PEG 8000, 5% MPD, 250-600 mM CaCl2, 50 mM BTP , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 287K
Resolution: 2.1→29.8 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.567 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2107
4086
5 %
RANDOM
Rwork
0.18521
-
-
-
all
0.1865
78200
-
-
obs
0.1865
78200
99.7 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 34.368 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.41 Å2
-0 Å2
-0 Å2
2-
-
0.67 Å2
0 Å2
3-
-
-
-2.07 Å2
Refinement step
Cycle: LAST / Resolution: 2.1→29.8 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
6778
0
80
434
7292
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.01
0.022
7027
X-RAY DIFFRACTION
r_angle_refined_deg
1.182
1.97
9570
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.705
5
872
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
39.436
24.465
327
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.834
15
1114
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
17.139
15
39
X-RAY DIFFRACTION
r_chiral_restr
0.078
0.2
1065
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.021
5419
X-RAY DIFFRACTION
r_mcbond_it
0.624
1.5
4342
X-RAY DIFFRACTION
r_mcangle_it
1.196
2
7012
X-RAY DIFFRACTION
r_scbond_it
1.735
3
2685
X-RAY DIFFRACTION
r_scangle_it
3.002
4.5
2555
LS refinement shell
Resolution: 2.1→2.154 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.314
274
-
Rwork
0.265
5523
-
obs
-
-
96.97 %
+
About Yorodumi
-
News
-
Feb 9, 2022. New format data for meta-information of EMDB entries
New format data for meta-information of EMDB entries
Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi