- PDB-3nso: Crystal Structure of S100A3 Protein Expressed in Insect Cell -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 3nso
Title
Crystal Structure of S100A3 Protein Expressed in Insect Cell
Components
Protein S100-A3
Keywords
METAL BINDING PROTEIN / EF-hand / Ca2+ / Zn2+ binding
Function / homology
Function and homology information
transition metal ion binding / calcium-dependent protein binding / calcium ion binding / Golgi apparatus / plasma membrane / cytosol Similarity search - Function
S-100 / S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / EF-hand / Recoverin; domain 1 / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha Similarity search - Domain/homology
Resolution: 1.45→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.973 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2226
1568
5.1 %
RANDOM
Rwork
0.19859
-
-
-
all
0.1998
30896
-
-
obs
0.1998
29306
98.85 %
-
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: 21.613 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.23 Å2
0.12 Å2
0 Å2
2-
-
0.23 Å2
0 Å2
3-
-
-
-0.35 Å2
Refinement step
Cycle: LAST / Resolution: 1.45→20 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1505
0
0
133
1638
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.019
0.022
1627
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.951
1.97
2219
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.652
5
209
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
30.207
24.321
81
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.957
15
295
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
12.454
15
10
X-RAY DIFFRACTION
r_chiral_restr
0.128
0.2
241
X-RAY DIFFRACTION
r_gen_planes_refined
0.012
0.021
1252
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
1.146
1.5
976
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
2.019
2
1589
X-RAY DIFFRACTION
r_scbond_it
3.467
3
651
X-RAY DIFFRACTION
r_scangle_it
5.415
4.5
619
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 1.45→1.488 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.36
102
-
Rwork
0.302
1982
-
obs
-
-
89.83 %
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
0.4225
0.6761
0.1188
3.1037
-0.1824
0.5809
0.1079
-0.06
0.0217
0.2676
-0.1438
0.0109
0.0282
-0.0749
0.0359
0.0342
-0.0254
-0.007
0.0454
0.0284
0.1781
20.529
30.397
4.963
2
0.3957
-0.6896
-0.1013
3.1787
-0.1289
0.5919
0.1091
0.0586
-0.0308
-0.2965
-0.1457
0.0293
-0.0293
-0.083
0.0366
0.0392
0.0254
0.0056
0.0481
0.0272
0.1795
20.247
37.465
-9.788
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
2 - 99
2
X-RAY DIFFRACTION
2
B
3 - 99
+
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