- PDB-4wr2: Crystal structure of a putative pyrimidine-specific ribonucleosid... -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 4wr2
Title
Crystal structure of a putative pyrimidine-specific ribonucleoside hydrolase (RihA) Protein from Shewanella loihica PV-4 (SHEW_0697, Target PSI-029635) with divalent cation and PEG 400 bound at the active site
Components
Pyrimidine-specific ribonucleoside hydrolase RihA
Keywords
HYDROLASE / PYRIMIDINE-SPECIFIC / PROTEIN STRUCTURE INITIATIVE / PSI / DIVALENT CATION BINDING SITE / Structural Genomics / New York Structural Genomics Research Consortium / NYSGRC
Function / homology
Function and homology information
Hydrolases; Glycosylases / uridine nucleosidase activity / pyrimidine nucleobase metabolic process / nucleobase-containing small molecule interconversion / metal ion binding Similarity search - Function
Mass: 18.015 Da / Num. of mol.: 284 / Source method: isolated from a natural source / Formula: H2O
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 3.35 Å3/Da / Density % sol: 63.32 %
Crystal grow
Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: Protein (18.02 mg/ml, 20 mM HEPES pH 7.5, 150 mM Sodium Chloride, 5% v/v Glycerol, 5 mM DTT) was combined with an equal volume of Reservoir (100 mM Sodium Citrate pH 5.5, 40% PEG 600), ...Details: Protein (18.02 mg/ml, 20 mM HEPES pH 7.5, 150 mM Sodium Chloride, 5% v/v Glycerol, 5 mM DTT) was combined with an equal volume of Reservoir (100 mM Sodium Citrate pH 5.5, 40% PEG 600), Cryoprotection (100 mM Sodium Citrate pH 5.5, 40% PEG 600)
Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97931 Å / Relative weight: 1
Reflection
Resolution: 1.7→30 Å / Num. obs: 104560 / % possible obs: 99.5 % / Redundancy: 7.7 % / Biso Wilson estimate: 22.82 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Χ2: 1.005 / Net I/av σ(I): 26.701 / Net I/σ(I): 8.6 / Num. measured all: 803260
Reflection shell
Diffraction-ID: 1 / Rejects: _
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Num. unique all
Χ2
% possible all
1.7-1.76
7.6
0.97
10451
0.967
99.2
1.76-1.83
7.6
0.662
10416
0.98
99.3
1.83-1.91
7.6
0.44
10467
1.002
99.4
1.91-2.02
7.7
0.287
10448
1.008
99.6
2.02-2.14
7.7
0.181
10522
1.009
99.7
2.14-2.31
7.7
0.131
10417
0.991
99.8
2.31-2.54
7.7
0.111
10516
1.008
99.9
2.54-2.91
7.7
0.107
10509
1.036
100
2.91-3.66
7.8
0.06
10483
1.029
100
3.66-30
7.6
0.038
10331
1.015
98.1
-
Phasing
Phasing
Method: SAD
-
Processing
Software
Name
Version
Classification
SCALEPACK
HKLdataprocessingsystemVersion1.99.2
datascaling
PHENIX
1.9-1692
phasing
REFMAC
5.8.0073
refinement
PDB_EXTRACT
3.15
dataextraction
Refinement
Method to determine structure: SAD / Resolution: 1.7→29.767 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.968 / WRfactor Rfree: 0.1729 / WRfactor Rwork: 0.159 / FOM work R set: 0.8901 / SU B: 2.633 / SU ML: 0.042 / SU R Cruickshank DPI: 0.0805 / SU Rfree: 0.0665 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.081 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.1713
1997
3.7 %
RANDOM
Rwork
0.1566
52364
-
-
obs
0.1572
104560
99.19 %
-
Solvent computation
Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.3 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