- PDB-3cin: CRYSTAL STRUCTURE OF A MYO-INOSITOL-1-PHOSPHATE SYNTHASE-RELATED ... -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 3cin
Title
CRYSTAL STRUCTURE OF A MYO-INOSITOL-1-PHOSPHATE SYNTHASE-RELATED PROTEIN (TM_1419) FROM THERMOTOGA MARITIMA MSB8 AT 1.70 A RESOLUTION
Components
Myo-inositol-1-phosphate synthase-related protein
Keywords
ISOMERASE / MYO-INOSITOL-1-PHOSPHATE SYNTHASE-RELATED PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information
inositol-3-phosphate synthase activity / inositol biosynthetic process / phospholipid biosynthetic process / nucleotide binding / metal ion binding Similarity search - Function
Resolution: 1.7→41.135 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / SU B: 4.19 / SU ML: 0.067 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. RESIDUE ASP 208 IS A RAMACHANDRAN OUTLIER, HOWEVER, THE ELECTRON DENSITY IS UNAMBIGUOUS FOR THIS RESIDUE. 3. CHLORINE ATOMS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. RESIDUE ASP 208 IS A RAMACHANDRAN OUTLIER, HOWEVER, THE ELECTRON DENSITY IS UNAMBIGUOUS FOR THIS RESIDUE. 3. CHLORINE ATOMS WERE MODELED SINCE THEY REFINED TO A BETTER B-FACTOR AGREEMENT WITH SURROUNDING RESIDUES. 4. THE NICOTINAMIDE RING WAS MODELED IN THE SAME ORIENTATION AS OBSERVED IN HOMOLOGS, DESPITE RESIDUAL FO-FC DENSITY INDICATION AT LEAST PARTIAL OCCUPANCY OF THE ORIENTATION ROTATED BY 180 DEGREES. 5. MAGNESIUM WAS MODELED BASED ON COORDINATION GEOMETRY AND ELECTRON DENSITY PEAK HEIGHT. 6. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.194
2181
5 %
RANDOM
Rwork
0.16
-
-
-
obs
0.161
43592
92.68 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 27.035 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-1.06 Å2
0 Å2
0 Å2
2-
-
2.65 Å2
0 Å2
3-
-
-
-1.59 Å2
Refinement step
Cycle: LAST / Resolution: 1.7→41.135 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2956
0
48
233
3237
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.018
0.022
3144
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
2103
X-RAY DIFFRACTION
r_angle_refined_deg
1.711
1.987
4283
X-RAY DIFFRACTION
r_angle_other_deg
0.998
3
5168
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.78
5
389
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
36.215
24.783
138
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.116
15
533
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
17.122
15
15
X-RAY DIFFRACTION
r_chiral_restr
0.112
0.2
486
X-RAY DIFFRACTION
r_gen_planes_refined
0.008
0.02
3470
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
606
X-RAY DIFFRACTION
r_nbd_refined
0.22
0.2
624
X-RAY DIFFRACTION
r_nbd_other
0.195
0.2
2144
X-RAY DIFFRACTION
r_nbtor_refined
0.184
0.2
1561
X-RAY DIFFRACTION
r_nbtor_other
0.089
0.2
1623
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.186
0.2
194
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.333
0.2
48
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.284
0.2
78
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.159
0.2
24
X-RAY DIFFRACTION
r_mcbond_it
2.552
3
2079
X-RAY DIFFRACTION
r_mcbond_other
0.669
3
782
X-RAY DIFFRACTION
r_mcangle_it
3.261
5
3122
X-RAY DIFFRACTION
r_scbond_it
5.256
8
1339
X-RAY DIFFRACTION
r_scangle_it
7.257
11
1160
LS refinement shell
Resolution: 1.7→1.747 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.282
127
-
Rwork
0.219
2167
-
all
-
2294
-
obs
-
-
66.03 %
Refinement TLS params.
Method: refined / Origin x: 21.2655 Å / Origin y: 18.7264 Å / Origin z: 40.872 Å
11
12
13
21
22
23
31
32
33
T
-0.13 Å2
-0.0183 Å2
0.0048 Å2
-
-0.1562 Å2
0.0235 Å2
-
-
-0.0989 Å2
L
1.6217 °2
-0.4263 °2
0.7978 °2
-
0.5168 °2
-0.4268 °2
-
-
1.0463 °2
S
-0.0071 Å °
0.0218 Å °
0.0177 Å °
-0.0027 Å °
0.0433 Å °
0.0166 Å °
0.0312 Å °
-0.073 Å °
-0.0362 Å °
+
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