Mass: 26437.385 Da / Num. of mol.: 1 / Mutation: I91L,E93A Source method: isolated from a genetically manipulated source Details: Recombinant proastacin Glu93MAla, Ile91MLeu (UniProt Q9U918; numbering is based on the mature enzyme, see below) was expressed in Escherichia coli BL21(DE3) cells as inclusion bodies, ...Details: Recombinant proastacin Glu93MAla, Ile91MLeu (UniProt Q9U918; numbering is based on the mature enzyme, see below) was expressed in Escherichia coli BL21(DE3) cells as inclusion bodies, purified by Ni-NTA-affinity chromatography, and folded by dilution and removal of reducing agents and guanidinium chloride. Source: (gene. exp.) Astacus astacus (noble crayfish) / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P07584, astacin
Mass: 18.015 Da / Num. of mol.: 298 / Source method: isolated from a natural source / Formula: H2O
Compound details
THE FIRST 34 RESIDUES ARE FOR ACTIVATION PEPTIDE.
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.32 Å3/Da / Density % sol: 46.94 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: For crystallization, reservoir solutions were prepared by a Tecan robot and 200-nL crystallization drops were dispensed on 96x2-well MRC plates (Innovadyne) by a Cartesian (Genomic Solutions) ...Details: For crystallization, reservoir solutions were prepared by a Tecan robot and 200-nL crystallization drops were dispensed on 96x2-well MRC plates (Innovadyne) by a Cartesian (Genomic Solutions) nanodrop robot at the High-Throughput Crystallography Platform of the Barcelona Science Park. Best crystals appeared in a Bruker steady-temperature crystal farm at 4C with protein solution (10 mg/mL in 50mM AMPSO pH9.0) and 20% PEG 8000, 0.1M (NH4)2SO4, 0.01M MgCl2, 0.05M MES pH5.6 as reservoir solution. These conditions were efficiently scaled up to the microliter range with 24-well Cryschem crystallization dishes (Hampton Research). Crystals were cryo-protected with 16% PEG 8000, 20% glycerol, 0.1M (NH4)2SO4, 0.01M MgCl2, 0.05M MES pH5.6. , VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution: 1.45→41.92 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.29 / SU ML: 0.039 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.069 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.; THE NUMBERING USED IN THE PRIMARY CITATION IS: RESIDUES 1 TO 34 AND CHAIN P FOR THE PROPEPTIDE AND RESIDUES 1 TO 201 AND CHAIN M FOR THE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.; THE NUMBERING USED IN THE PRIMARY CITATION IS: RESIDUES 1 TO 34 AND CHAIN P FOR THE PROPEPTIDE AND RESIDUES 1 TO 201 AND CHAIN M FOR THE MATURE PROTEASE MOIETY.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.18046
768
1.7 %
RANDOM
Rwork
0.15169
-
-
-
all
0.15218
44284
-
-
obs
0.15218
43398
99.73 %
-
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: 7.029 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.69 Å2
0 Å2
0 Å2
2-
-
-0.87 Å2
0 Å2
3-
-
-
1.56 Å2
Refinement step
Cycle: LAST / Resolution: 1.45→41.92 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1859
0
24
298
2181
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.016
0.021
1998
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
1312
X-RAY DIFFRACTION
r_angle_refined_deg
1.532
1.943
2707
X-RAY DIFFRACTION
r_angle_other_deg
0.958
3
3176
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.213
5
242
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
31.382
23.96
101
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.504
15
308
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
19.977
15
12
X-RAY DIFFRACTION
r_chiral_restr
0.09
0.2
285
X-RAY DIFFRACTION
r_gen_planes_refined
0.008
0.02
2251
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
429
X-RAY DIFFRACTION
r_mcbond_it
1.219
1.5
1199
X-RAY DIFFRACTION
r_mcbond_other
0.508
1.5
496
X-RAY DIFFRACTION
r_mcangle_it
1.791
2
1934
X-RAY DIFFRACTION
r_scbond_it
2.694
3
799
X-RAY DIFFRACTION
r_scangle_it
3.675
4.5
773
X-RAY DIFFRACTION
r_rigid_bond_restr
1.356
3
3310
X-RAY DIFFRACTION
r_sphericity_free
5.332
3
300
X-RAY DIFFRACTION
r_sphericity_bonded
2.085
3
3260
LS refinement shell
Resolution: 1.45→1.488 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.273
48
-
Rwork
0.242
3107
-
obs
-
-
97.5 %
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
4.816
1.2244
-1.3121
1.6195
-0.6137
2.2532
0.1036
0.289
0.5818
0.0854
0.0436
0.0286
-0.2799
-0.0621
-0.1473
0.0927
0.0147
-0.0075
0.0902
0.0319
0.117
0.396
-0.588
-10.271
2
1.5124
-0.4658
0.4147
1.1497
-0.0657
0.5896
0.0403
0.1143
0.169
-0.0543
-0.0198
-0.1494
-0.0239
0.0108
-0.0204
0.0414
-0.0094
0.011
0.032
0.0205
0.0396
4.478
-9.052
-14.13
3
1.3651
-0.3315
0.3322
0.946
-0.0503
0.6697
0.0115
-0.0061
0.0797
0.0018
0.0134
-0.0976
-0.0129
-0.006
-0.0249
0.164
-0.0117
0.0087
0.1421
0.0081
0.113
4.923
-10.076
-10.479
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
1 - 34
2
X-RAY DIFFRACTION
2
A
35 - 201
3
X-RAY DIFFRACTION
2
A
999
4
X-RAY DIFFRACTION
3
A
501 - 504
5
X-RAY DIFFRACTION
3
A
505 - 802
+
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