5BJR

Crystal structure of the N-terminal RRM domain from MEC-8

> Summary

Summary for 5BJR

DescriptorMec-8 protein, AMMONIUM ION (3 entities in total)
Functional Keywordsalternative splicing, mrna, rna-binding protein, splicing
Biological sourceCaenorhabditis elegans
Total number of polymer chains2
Total molecular weight20686.06
Authors
Soufari, H.,Mackereth, C.D. (deposition date: 2016-10-22, release date: 2017-01-11, Last modification date: 2017-03-01)
Primary citation
Soufari, H.,Mackereth, C.D.
Conserved binding of GCAC motifs by MEC-8, couch potato, and the RBPMS protein family.
RNA, 23:308-316, 2017
PubMed: 28003515 (PDB entries with the same primary citation)
DOI: 10.1261/rna.059733.116
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (2.6 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.28612002.9%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 5bjr
no rotation
Molmil generated image of 5bjr
rotated about x axis by 90°
Molmil generated image of 5bjr
rotated about y axis by 90°

More Biological unit images

Molmil generated image of 5bjr
no rotation
Molmil generated image of 5bjr
rotated about x axis by 90°
Molmil generated image of 5bjr
rotated about y axis by 90°
(*)In the case of coarse surface representation, the asymmetric unit is shown as red ribbon representation.
Coordinate files for Biological unit (5bjr.pdb1.gz [29.65 KB])
Coordinate files for Biological unit (5bjr.pdb2.gz [28.1 KB])

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A, BMec-8 proteinpolymer9410316.02
UniProt (G5ECJ4)
Pfam (PF00076)
Caenorhabditis elegans
AMMONIUM IONnon-polymer18.03
waterwater18.037

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains2
Total molecular weight20632.0
Non-Polymers*Number of molecules3
Total molecular weight54.1
All*Total molecular weight20686.1
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2.6 Å)

Cell axes52.59096.420109.990
Cell angles90.0090.0090.00
SpacegroupI 2 2 2
Resolution limits35.36 - 2.60
the highest resolution shell value2.763 - 2.600
R-factor0.2421
R-work0.23720
R-free0.28530
RMSD bond length0.002
RMSD bond angle0.571

Data Collection Statistics

Resolution limits35.36 - 2.60
the highest resolution shell value -
Number of reflections8842
Rmerge_l_obs0.085
the highest resolution shell value0.344
Completeness98.9
Redundancy1.9

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, SITTING DROP7.5293

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
A0005634cellular_componentnucleus
A0003676molecular_functionnucleic acid binding
A0009792biological_processembryo development ending in birth or egg hatching
A0031581biological_processhemidesmosome assembly
A0007638biological_processmechanosensory behavior
A0048644biological_processmuscle organ morphogenesis
A0002119biological_processnematode larval development
A0048666biological_processneuron development
B0005634cellular_componentnucleus
B0003676molecular_functionnucleic acid binding
B0009792biological_processembryo development ending in birth or egg hatching
B0031581biological_processhemidesmosome assembly
B0007638biological_processmechanosensory behavior
B0048644biological_processmuscle organ morphogenesis
B0002119biological_processnematode larval development
B0048666biological_processneuron development
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC11binding site for residue NH4 A 201
ChainResidue
AARG107

AC21binding site for residue NH4 A 202
ChainResidue
AARG97

AC32binding site for residue NH4 B 201
ChainResidue
BARG90
BHOH303

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
NH4_5bjr_A_2015AMMONIUM ION binding site
ChainResidueligand
ASER36-GLY37NH4: AMMONIUM ION
ASER73NH4: AMMONIUM ION
AVAL75NH4: AMMONIUM ION
AARG107NH4: AMMONIUM ION

NH4_5bjr_A_2024AMMONIUM ION binding site
ChainResidueligand
AGLY95-ARG97NH4: AMMONIUM ION
BTYR48NH4: AMMONIUM ION

NH4_5bjr_B_2011AMMONIUM ION binding site
ChainResidueligand
BARG90NH4: AMMONIUM ION

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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
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Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

> Downloads

Resources

File formatFile name (file size)
PDBallpdb5bjr.ent.gz (32.5 KB)
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all (no-compress)pdb5bjr.ent (141.12 KB)
header onlypdb5bjr.ent.gz (5 KB)
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PDBx/mmCIF5bjr.cif.gz (44.11 KB)
PDBMLall5bjr.xml.gz (54.91 KB)
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no-atom5bjr-noatom.xml.gz (12.24 KB)
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ext-atom5bjr-extatom.xml.gz (31.47 KB)
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PDBMLplusall5bjr-plus.xml.gz (56.53 KB)
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no-atom5bjr-plus-noatom.xml.gz (13.86 KB)
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add only5bjr-add.xml.gz (1.62 KB)
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RDF5bjr.rdf.gz (24.69 KB)
Display
Structure factorsr5bjrsf.ent.gz (182.92 KB)
Biological unit (PDB format)5bjr.pdb1.gz (29.65 KB) (A)
*author and software defined assembly, 2 molecule(s) (dimeric)
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5bjr.pdb2.gz (28.1 KB) (B)
*author and software defined assembly, 2 molecule(s) (dimeric)
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Validation reportsPDF5bjr​_validation.pdf.gz (420.02 KB)
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PDF-full5bjr​_full​_validation.pdf.gz (421.08 KB)
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XML5bjr​_validation.xml.gz (8.68 KB)
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PNG5bjr​_multipercentile​_validation.png.gz (139.02 KB)
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SVG5bjr​_multipercentile​_validation.svg.gz (897 B)
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Sequence (fasta)5bjr​_seq.txt
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