1E3P

TUNGSTATE DERIVATIVE OF STREPTOMYCES ANTIBIOTICUS PNPASE/ GPSI ENZYME

> Summary

Summary for 1E3P

Related1E3H
DescriptorGUANOSINE PENTAPHOSPHATE SYNTHETASE (E.C.2.7.7.8, 2.7.6.5)
Functional Keywordspolyribonucleotide transferase, atp-gtp diphosphotransferase rna processing, rna degradation
Biological sourceSTREPTOMYCES ANTIBIOTICUS
Total number of polymer chains1
Total molecular weight82434.44
Authors
Symmons, M.F.,Jones, G.H.,Luisi, B.F. (deposition date: 2000-06-20, release date: 2000-11-03, modification date: 2009-02-24)
Primary citation
Symmons, M.F.,Jones, G.H.,Luisi, B.F.
A Duplicated Fold is the Structural Basis for Polynucleotide Phosphorylase Catalytic Activity, Processivity, and Regulation
Structure, 8:1215-, 2000
PubMed: 11080643
DOI: 10.1016/S0969-2126(00)00521-9
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (2.5 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.238111.6%2.2%11.0%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 1e3p
no rotation
Molmil generated image of 1e3p
rotated about x axis by 90°
Molmil generated image of 1e3p
rotated about y axis by 90°

More Biological unit images

Molmil generated image of 1e3p
no rotation
Molmil generated image of 1e3p
rotated about x axis by 90°
Molmil generated image of 1e3p
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 (1e3p.pdb1.gz [303.63 KB])

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
AGUANOSINE PENTAPHOSPHATE SYNTHETASEpolymer75781226.01
UniProt (Q53597)
Pfam (PF00013)
Pfam (PF00575)
Pfam (PF01138)
Pfam (PF03726)
STREPTOMYCES ANTIBIOTICUSPOLYNUCLEOTIDE PHOSPHORYLASE, GUANOSINE PENTAPHOSPHATE SYNTHETASE
SULFATE IONnon-polymer96.110
TUNGSTATE(VI)IONnon-polymer247.81
waterwater18.0305

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains1
Total molecular weight81226.0
Non-Polymers*Number of molecules11
Total molecular weight1208.4
All*Total molecular weight82434.4
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2.5 Å)

Cell axes130.830130.830328.732
Cell angles90.0090.00120.00
SpacegroupH 3 2
Resolution limits19.84 - 2.50
the highest resolution shell value2.660 - 2.500
R-factor0.213
R-work0.21300
the highest resolution shell value0.341
R-free0.24700
the highest resolution shell value0.367
RMSD bond length0.006
RMSD bond angle1.300 (23.900*)

Data Collection Statistics

Resolution limits20.00 - 2.50
the highest resolution shell value -
Number of reflections37642
Number of measurements462572*
Rmerge_l_obs0.080*
Completeness99.3
Redundancy6.5
the highest resolution shell value2.8

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1Vapor diffusion*7 (8.5*)20**

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
11dropprotein7 (mg/ml)
21drop15 (mM)
31reservoirammonium sulfate2 (M)
41reservoirTris-HCl100 (mM)
51reservoirdithiothreitol5 (mM)
61reservoir0.75 (mM)
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
A0005737cellular_componentcytoplasm
A0000175molecular_function3'-5'-exoribonuclease activity
A0000287molecular_functionmagnesium ion binding
A0004654molecular_functionpolyribonucleotide nucleotidyltransferase activity
A0003723molecular_functionRNA binding
A0006402biological_processmRNA catabolic process
A0006396biological_processRNA processing
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC14BINDING SITE FOR RESIDUE SO4 A 901
ChainResidue
APHE84
AARG86
AGLN388
AHOH2081

AC23BINDING SITE FOR RESIDUE SO4 A 902
ChainResidue
AILE569
AASP570
ATHR571

AC33BINDING SITE FOR RESIDUE SO4 A 903
ChainResidue
ALYS421
AARG422
AHOH2297

AC42BINDING SITE FOR RESIDUE SO4 A 904
ChainResidue
AGLY415
AARG416

AC55BINDING SITE FOR RESIDUE SO4 A 905
ChainResidue
ASER54
ALYS55
AASN56
ALYS58
AHOH2052

AC65BINDING SITE FOR RESIDUE SO4 A 906
ChainResidue
APHE64
ALYS112
AGLY113
AARG115
AHOH2299

AC76BINDING SITE FOR RESIDUE SO4 A 907
ChainResidue
AARG160
AASP183
AVAL185
AGLU202
AGLU204
AHOH2301

AC86BINDING SITE FOR RESIDUE SO4 A 908
ChainResidue
AGLU207
AARG397
AARG399
AARG442
AHOH2236
AHOH2302

AC97BINDING SITE FOR RESIDUE SO4 A 909
ChainResidue
AHIS131
ALEU132
ATYR133
ALEU392
ASER393
AHOH2112
AHOH2303

BC11BINDING SITE FOR RESIDUE SO4 A 910
ChainResidue
AARG360

BC26BINDING SITE FOR RESIDUE WO4 A 911
ChainResidue
AHIS427
ASER461
ATHR462
ASER463
ALYS522
AHOH2305

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

site_idNumber of ResiduesDetails
WO4_1e3p_A_9118TUNGSTATE(VI)ION binding site
ChainResidueligand
ATYR404WO4: TUNGSTATE(VI)ION
AHIS427WO4: TUNGSTATE(VI)ION
ASER458WO4: TUNGSTATE(VI)ION
AGLY460-SER463WO4: TUNGSTATE(VI)ION
ALYS522WO4: TUNGSTATE(VI)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
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Catalytic Information from CATRES

site_idNumber of ResiduesDetails

> Sequence Neighbor

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