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)
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
APHE101
AARG103
AGLN405
AHOH

AC23BINDING SITE FOR RESIDUE SO4 A 902
ChainResidue
AILE586
AASP587
ATHR588

AC33BINDING SITE FOR RESIDUE SO4 A 903
ChainResidue
ALYS438
AARG439
AHOH

AC42BINDING SITE FOR RESIDUE SO4 A 904
ChainResidue
AGLY432
AARG433

AC55BINDING SITE FOR RESIDUE SO4 A 905
ChainResidue
ASER71
ALYS72
AASN73
ALYS75
AHOH

AC65BINDING SITE FOR RESIDUE SO4 A 906
ChainResidue
APHE81
ALYS129
AGLY130
AARG132
AHOH

AC76BINDING SITE FOR RESIDUE SO4 A 907
ChainResidue
AARG177
AASP200
AVAL202
AGLU219
AGLU221
AHOH

AC86BINDING SITE FOR RESIDUE SO4 A 908
ChainResidue
AGLU224
AARG414
AARG416
AARG459
AHOH
AHOH

AC97BINDING SITE FOR RESIDUE SO4 A 909
ChainResidue
AHIS148
ALEU149
ATYR150
ALEU409
ASER410
AHOH
AHOH

BC11BINDING SITE FOR RESIDUE SO4 A 910
ChainResidue
AARG377

BC26BINDING SITE FOR RESIDUE WO4 A 911
ChainResidue
AHIS444
ASER478
ATHR479
ASER480
ALYS539
AHOH

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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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