4GP6

Polynucleotide kinase

> Summary

Summary for 4GP6

Related4GP7 3TY5 3TY8 3TY9 4DRF 4E6N
DescriptorMetallophosphoesterase (E.C.2.7.1.78)
Functional Keywordspolynucleotide kinase phosphatase, rna repair, transferase
Biological sourceClostridium thermocellum
Total number of polymer chains2
Total molecular weight39843.91
Authors
Wang, L.K.,Das, U.,Smith, P.,Shuman, S. (deposition date: 2012-08-20, release date: 2012-11-14, modification date: 2012-12-05)
Primary citation
Wang, L.K.,Das, U.,Smith, P.,Shuman, S.
Structure and mechanism of the polynucleotide kinase component of the bacterial Pnkp-Hen1 RNA repair system.
Rna, 18:2277-2286, 2012
PubMed: 23118415
DOI: 10.1261/rna.036061.112
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (2.1 Å)
?

Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.2171000.6%0.9%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 4gp6
no rotation
Molmil generated image of 4gp6
rotated about x axis by 90°
Molmil generated image of 4gp6
rotated about y axis by 90°

More Biological unit images

Molmil generated image of 4gp6
no rotation
Molmil generated image of 4gp6
rotated about x axis by 90°
Molmil generated image of 4gp6
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 (4gp6.pdb1.gz [124.27 KB])

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A, BMetallophosphoesterasepolymer17119470.42
UniProt (A3DJ38)
Pfam (PF13671)
Clostridium thermocellum
ADENOSINE-5'-DIPHOSPHATEnon-polymer427.22
MAGNESIUM IONnon-polymer24.32
waterwater18.0237

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains2
Total molecular weight38940.9
Non-Polymers*Number of molecules4
Total molecular weight903.0
All*Total molecular weight39843.9
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2.1 Å)

Cell axes43.69071.560118.610
Cell angles90.0090.0090.00
SpacegroupP 21 21 21
Resolution limits35.78 - 2.10
the highest resolution shell value2.162 - 2.100
R-factor0.181
R-work0.17690
the highest resolution shell value0.209
R-free0.22820
the highest resolution shell value0.275
RMSD bond length0.007
RMSD bond angle1.095

Data Collection Statistics

Resolution limits45.60 - 2.10
the highest resolution shell value -
Number of reflections22214
Completeness98.9
I/sigma(I)-3

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP7.5298

Crystallization Reagents

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

> Functional details

?

Functional Information from GO Data

ChainGOidnamespacecontents
A0005524molecular_functionATP binding
A0005525molecular_functionGTP binding
A0016787molecular_functionhydrolase activity
A0046872molecular_functionmetal ion binding
B0005524molecular_functionATP binding
B0005525molecular_functionGTP binding
B0016787molecular_functionhydrolase activity
B0046872molecular_functionmetal ion binding
?

Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC114BINDING SITE FOR RESIDUE ADP A 1001
ChainResidue
ASER16
AGLY18
ASER19
AGLY20
ALYS21
ASER22
ATHR23
AARG116
AARG120
AMG1002
AHOH1101
AHOH1151
AHOH1200
AHOH1204

AC26BINDING SITE FOR RESIDUE MG A 1002
ChainResidue
ASER22
AADP1001
AHOH1101
AHOH1102
AHOH1103
AHOH1204

AC319BINDING SITE FOR RESIDUE ADP B 1001
ChainResidue
BSER16
BGLY18
BSER19
BGLY20
BLYS21
BSER22
BTHR23
BGLN51
BTHR52
BARG116
BARG120
BMG1002
BHOH1103
BHOH1104
BHOH1120
BHOH1135
BHOH1163
BHOH1176
BHOH1197

AC46BINDING SITE FOR RESIDUE MG B 1002
ChainResidue
BSER22
BADP1001
BHOH1101
BHOH1102
BHOH1103
BHOH1104

?

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

site_idNumber of ResiduesDetails
ADP_4gp6_A_100114ADENOSINE-5'-DIPHOSPHATE binding site
ChainResidueligand
ASER16-PHE24ADP: ADENOSINE-5'-DIPHOSPHATE
AASP78ADP: ADENOSINE-5'-DIPHOSPHATE
AARG116ADP: ADENOSINE-5'-DIPHOSPHATE
AASN119-ARG120ADP: ADENOSINE-5'-DIPHOSPHATE
AASP122ADP: ADENOSINE-5'-DIPHOSPHATE

ADP_4gp6_B_100114ADENOSINE-5'-DIPHOSPHATE binding site
ChainResidueligand
BSER16-PHE24ADP: ADENOSINE-5'-DIPHOSPHATE
BASP78ADP: ADENOSINE-5'-DIPHOSPHATE
BARG116ADP: ADENOSINE-5'-DIPHOSPHATE
BASN119-ARG120ADP: ADENOSINE-5'-DIPHOSPHATE
BASP122ADP: ADENOSINE-5'-DIPHOSPHATE

?

Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
?

Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
?

Catalytic Information from CSA

site_idNumber of ResiduesDetails
?

Catalytic Information from CATRES

site_idNumber of ResiduesDetails

> Sequence Neighbor

> Downloads

PDBj@FacebookPDBj@TwitterwwPDBwwPDB FoundationEM DataBank

Copyright © 2013-2016 Protein Data Bank Japan