- PDB-2jh3: The crystal structure of DR2241 from Deinococcus radiodurans at 1... -
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Basic information
Entry
Database: PDB / ID: 2jh3
Title
The crystal structure of DR2241 from Deinococcus radiodurans at 1.9 A resolution reveals a multi-domain protein with structural similarity to chelatases but also with two additional novel domains
Components
RIBOSOMAL PROTEIN S2-RELATED PROTEIN
Keywords
RIBOSOMAL PROTEIN / CBIX / SAD PHASING / STRUCTURAL GENOMICS / CHELATASE SUPER-FAMILY FOLD / 4FE-4S IRON-SULPHUR CLUSTER
Function / homology
Function and homology information
sirohydrochlorin cobaltochelatase activity / cobalamin biosynthetic process / 4 iron, 4 sulfur cluster binding / ribosome / metal ion binding Similarity search - Function
Journal: J.Struct.Biol. / Year: 2007 Title: The Crystal Structure of Dr2241 from Deinococcus Radiodurans at 1.9 A Resolution Reveals a Multi-Domain Protein with Structural Similarity to Chelatases But Also with Two Additional Novel Domains Authors: Leiros, H.-K.S. / Mcsweeney, S.M.
A: RIBOSOMAL PROTEIN S2-RELATED PROTEIN B: RIBOSOMAL PROTEIN S2-RELATED PROTEIN C: RIBOSOMAL PROTEIN S2-RELATED PROTEIN D: RIBOSOMAL PROTEIN S2-RELATED PROTEIN hetero molecules
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.933 Å / Relative weight: 1
Reflection
Resolution: 1.9→20 Å / Num. obs: 168727 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 22.06 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.3
Reflection shell
Resolution: 1.9→2 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 1.9 / % possible all: 98.6
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Processing
Software
Name
Version
Classification
XDS
datareduction
XDS
datascaling
SHARP
phasing
SOLVE
phasing
REFMAC
5.2.0005
refinement
Refinement
Method to determine structure: SIRAS / Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.019 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SOME RESIDUES ARE LEFT OUT IN THE DEPOSITED MODEL. THERE ARE 2 EXTRA RESIDUES FROM THE HIS-TAG IN THE N- TERMINUS.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.238
3400
2 %
RANDOM
Rwork
0.189
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obs
0.19
165141
98.7 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK