4J2E

RB69 DNA Polymerase L415M Ternary Complex

> Summary

Summary for 4J2E

Related4J2A 4J2B 4J2D
DescriptorDNA polymerase (E.C.2.7.7.7)
Functional Keywordsrb69, dna polymerase, l415m, polymerase, transferase-dna complex, transferase/dna
Biological sourceEnterobacteria phage RB69
Total number of polymer chains3
Total molecular weight114659.62
Authors
Xia, S.,Wang, J.,Konigsberg, W.H. (deposition date: 2013-02-04, release date: 2014-02-19, modification date: 2014-12-10)
Primary citation
Xia, S.,Wood, M.,Bradley, M.J.,De La Cruz, E.M.,Konigsberg, W.H.
Alteration in the cavity size adjacent to the active site of RB69 DNA polymerase changes its conformational dynamics.
Nucleic Acids Res., 41:9077-9089, 2013
PubMed: 23921641
DOI: 10.1093/nar/gkt674
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (2.02 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.214201.4%3.0%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 4j2e
no rotation
Molmil generated image of 4j2e
rotated about x axis by 90°
Molmil generated image of 4j2e
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
ADNA polymerasepolymer901104411.71
UniProt (Q38087)
Enterobacteria phage RB69Gp43
TDNA (5'-D(*TP*CP*GP*TP*CP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')polymer185492.61
PDNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*G)-3')polymer134007.61
ADENOSINE-5'-TRIPHOSPHATEnon-polymer507.21
CALCIUM IONnon-polymer40.16
waterwater18.0502

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains3
Total molecular weight113912.0
Non-Polymers*Number of molecules7
Total molecular weight747.7
All*Total molecular weight114659.6
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2.02 Å)

Cell axes74.989120.502130.763
Cell angles90.0090.0090.00
SpacegroupP 21 21 21
Resolution limits45.66 - 2.02
the highest resolution shell value2.071 - 2.019
R-factor0.1803
R-work0.17859
the highest resolution shell value0.211
R-free0.21317
the highest resolution shell value0.244
RMSD bond length0.006
RMSD bond angle1.059

Data Collection Statistics

Resolution limits50.00 - 2.02
the highest resolution shell value -
Number of reflections72335
Completeness94.9
I/sigma(I)2.8

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION6.5298

Crystallization Reagents

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

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
A0008408molecular_function3'-5' exonuclease activity
A0003677molecular_functionDNA binding
A0003887molecular_functionDNA-directed DNA polymerase activity
A0000166molecular_functionnucleotide binding
A0039693biological_processviral DNA genome replication
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC119BINDING SITE FOR RESIDUE ATP A 1001
ChainResidue
AASP411
ALEU412
ATHR413
ASER414
AMET415
ATYR416
AARG482
ALYS560
AASN564
AASP623
ACA
ACA
AHOH
AHOH
AHOH
AHOH
PDG13
TDT4
TDC5

AC24BINDING SITE FOR RESIDUE CA A 1002
ChainResidue
AASP411
ALEU412
AASP623
AATP

AC33BINDING SITE FOR RESIDUE CA A 1003
ChainResidue
AASP411
AASP623
AATP

AC46BINDING SITE FOR RESIDUE CA A 1004
ChainResidue
AASN505
AASN507
ALYS531
AHOH
AHOH
AHOH

AC54BINDING SITE FOR RESIDUE CA A 1005
ChainResidue
AGLU716
AHOH
AHOH
AHOH

AC64BINDING SITE FOR RESIDUE CA A 1006
ChainResidue
AGLU116
AHOH
AHOH
AHOH

AC73BINDING SITE FOR RESIDUE CA P 201
ChainResidue
THOH
THOH
THOH

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

site_idNumber of ResiduesDetails
ATP_4j2e_A_100119ADENOSINE-5'-TRIPHOSPHATE binding site
ChainResidueligand
AASP411-PRO417ATP: ADENOSINE-5'-TRIPHOSPHATE
AARG482ATP: ADENOSINE-5'-TRIPHOSPHATE
ALYS486ATP: ADENOSINE-5'-TRIPHOSPHATE
ALYS560-LEU561ATP: ADENOSINE-5'-TRIPHOSPHATE
AASN564-SER565ATP: ADENOSINE-5'-TRIPHOSPHATE
ATYR567ATP: ADENOSINE-5'-TRIPHOSPHATE
ATHR622-ASP623ATP: ADENOSINE-5'-TRIPHOSPHATE
TDT4-DC5ATP: ADENOSINE-5'-TRIPHOSPHATE
PDG115ATP: ADENOSINE-5'-TRIPHOSPHATE

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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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