Oxidoreductases; Acting on the CH-NH2 group of donors; With NAD+ or NADP+ as acceptor / nucleotide binding / metal ion binding Similarity search - Function
Mass: 27876.744 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanosarcina barkeri (archaea) / Strain: Fusaro / Gene: Mbar_A0835 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q46E80, Oxidoreductases; Acting on the CH-NH2 group of donors; With NAD+ or NADP+ as acceptor
Resolution: 1.8→1.9 Å / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 2.5 / % possible all: 96.6
-
Processing
Software
Name
Version
Classification
XDS
datascaling
PHASER
phasing
REFMAC
5.7.0029
refinement
XDS
datareduction
XSCALE
datascaling
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: SeMet-model; coordinates have not been deposited Resolution: 1.8→10 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / SU B: 6.68 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.267 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.21766
4797
5 %
RANDOM
Rwork
0.17867
-
-
-
all
0.186
91179
-
-
obs
0.18061
91179
92.2 %
-
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: 34.313 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.83 Å2
0 Å2
0 Å2
2-
-
0.9 Å2
0 Å2
3-
-
-
-0.08 Å2
Refinement step
Cycle: LAST / Resolution: 1.8→10 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
7808
0
252
558
8618
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.005
0.019
8212
X-RAY DIFFRACTION
r_angle_refined_deg
1.147
2.014
11184
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
4.952
5
1032
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
36.734
25.75
320
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.657
15
1316
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
9.673
15
20
X-RAY DIFFRACTION
r_chiral_restr
0.068
0.2
1304
X-RAY DIFFRACTION
r_gen_planes_refined
0.004
0.021
6092
X-RAY DIFFRACTION
r_rigid_bond_restr
0.817
3
8211
X-RAY DIFFRACTION
r_sphericity_free
26.168
5
186
X-RAY DIFFRACTION
r_sphericity_bonded
12.516
5
8432
LS refinement shell
Resolution: 1.8→1.845 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.324
353
-
Rwork
0.278
6708
-
obs
-
-
96.26 %
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
0.1777
0.0266
-0.0338
0.0812
0.0141
0.0132
0.0078
-0.0179
0.004
0.0091
-0.0027
0.0112
-0.0096
0.0083
-0.0051
0.1053
-0.0004
0.0007
0.0623
-0.0038
0.0665
-1.8649
78.6377
-1.1679
2
0.1524
0.0339
0.0674
0.0514
0.0152
0.0948
0.0056
-0.0013
-0.0132
-0.0013
0.0093
-0.0146
0.0084
0.0051
-0.015
0.1069
0.0051
-0.0014
0.0586
-0.0095
0.0736
-11.6463
48.8496
-16.8965
3
0.1409
0.0634
-0.1347
0.1982
-0.0488
0.1773
-0.0034
0.0136
0.046
0.008
0.0198
0.0522
0.0099
-0.0048
-0.0164
0.1076
0.0015
-0.0045
0.0042
0.0033
0.114
-9.7268
111.0657
-9.5276
4
0.4059
-0.08
-0.1336
0.1864
0.0384
0.1113
0.006
-0.0161
0.0731
-0.0183
0.0227
-0.0612
-0.0033
0.0111
-0.0286
0.1079
-0.0085
-0.0025
0.0057
-0.022
0.1192
34.2391
114.5952
-22.1955
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
1 - 259
2
X-RAY DIFFRACTION
1
A
901 - 904
3
X-RAY DIFFRACTION
2
B
1 - 259
4
X-RAY DIFFRACTION
2
B
901 - 904
5
X-RAY DIFFRACTION
3
C
1 - 259
6
X-RAY DIFFRACTION
3
C
901 - 904
7
X-RAY DIFFRACTION
4
D
1 - 259
8
X-RAY DIFFRACTION
4
D
901 - 904
+
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