- PDB-3mw8: Crystal structure of an UROPORPHYRINOGEN-III SYNTHASE (Sama_3255)... -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 3mw8
Title
Crystal structure of an UROPORPHYRINOGEN-III SYNTHASE (Sama_3255) from SHEWANELLA AMAZONENSIS SB2B at 1.65 A resolution
Components
Uroporphyrinogen-III synthase
Keywords
LYASE / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / HemD-like / heme
Function / homology
Function and homology information
uroporphyrinogen-III synthase / uroporphyrinogen-III synthase activity / uroporphyrinogen III biosynthetic process / protoporphyrinogen IX biosynthetic process Similarity search - Function
Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. CLEAVAGE OF ...THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. CLEAVAGE OF THE TAG WITH TEV PROTEASE LEAVES ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. HOWEVER, THE CLEAVAGE OF THE TAG WAS INCOMPLETE LEAVING A MIXTURE OF PROTEIN WITH THE INTACT TAG AND CLEAVED TAG.
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.91 Å3/Da / Density % sol: 57.74 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1500M di-ammonium hydrogen phosphate, 33.0000% polyethylene glycol 3350, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Monochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97927 Å / Relative weight: 1
Reflection
Resolution: 1.65→38.525 Å / Num. obs: 35551 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 25.002 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 13.48
Reflection shell
Resolution (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
% possible all
1.65-1.71
0.442
2.4
13207
3628
99.8
1.71-1.78
0.299
3.5
13266
3595
100
1.78-1.86
0.213
4.9
12945
3486
99.8
1.86-1.96
0.147
7.1
13286
3600
99.9
1.96-2.08
0.092
10.6
12881
3485
99.9
2.08-2.24
0.068
14.4
13169
3557
99.8
2.24-2.46
0.056
17.8
12856
3476
99.5
2.46-2.82
0.05
20.9
13189
3618
99.5
2.82-3.55
0.039
25.5
12925
3547
98.5
3.55-38.525
0.036
27.8
12299
3550
95.8
-
Phasing
Phasing
Method: SAD
-
Processing
Software
Name
Version
Classification
NB
REFMAC
5.5.0109
refinement
PHENIX
refinement
SHELX
phasing
MolProbity
3beta29
modelbuilding
XSCALE
datascaling
PDB_EXTRACT
3.006
dataextraction
XDS
datareduction
SHELXD
phasing
autoSHARP
phasing
Refinement
Method to determine structure: SAD / Resolution: 1.65→38.525 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.959 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 3.519 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.086 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. ETHYLENE GLYCOL (EDO) MODELED ARE PRESENT CRYO SOLUTION.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.203
1814
5.1 %
RANDOM
Rwork
0.175
-
-
-
obs
0.177
35537
99.26 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
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