4J2A

RB69 DNA Polymerase L415A Ternary Complex

> Summary

Summary for 4J2A

Related4J2B 4J2D 4J2E
DescriptorDNA polymerase (E.C.2.7.7.7)/dna
Functional Keywordsrb69, dna polymerase, l415a, polymerase, transferase-dna complex, transferase/dna
Biological sourceEnterobacteria phage RB69
Total number of polymer chains3
Total molecular weight114623.58
Authors
Xia, S.,Wang, J.,Konigsberg, W.H. (deposition date: 2013-02-04, release date: 2014-02-19)
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 (1.8 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.211302.0%2.6%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 4j2a
no rotation
Molmil generated image of 4j2a
rotated about x axis by 90°
Molmil generated image of 4j2a
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
ADNA polymerasepolymer901104351.61
UniProt (Q38087)
Enterobacteria phage RB69Gp43
TDNA (5'-D(*TP*CP*GP*AP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')polymer185541.61
PDNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*C)-3')polymer133967.61
THYMIDINE-5'-TRIPHOSPHATEnon-polymer482.21
CALCIUM IONnon-polymer40.17
waterwater18.0854

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains3
Total molecular weight113860.8
Non-Polymers*Number of molecules8
Total molecular weight762.7
All*Total molecular weight114623.6
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (1.8 Å)

Cell axes75.013120.310130.628
Cell angles90.0090.0090.00
SpacegroupP 21 21 21
Resolution limits45.63 - 1.80
the highest resolution shell value1.847 - 1.800
R-factor0.18021
R-work0.17855
the highest resolution shell value0.282
R-free0.21124
the highest resolution shell value0.313
RMSD bond length0.007
RMSD bond angle1.104

Data Collection Statistics

Resolution limits50.00 - 1.80
the highest resolution shell value -
Number of reflections103190
Completeness94.7
I/sigma(I)1.2

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
AC122BINDING SITE FOR RESIDUE TTP A 1001
ChainResidue
AASP411
ALEU412
ATHR413
ASER414
AALA415
ATYR416
AARG482
ALYS560
AASN564
AASP623
ACA
ACA
AHOH
AHOH
AHOH
AHOH
AHOH
AHOH
AHOH
PDC13
TDA4
TDG5

AC25BINDING SITE FOR RESIDUE CA A 1002
ChainResidue
AASP411
ALEU412
AASP623
ATTP
ACA

AC35BINDING SITE FOR RESIDUE CA A 1003
ChainResidue
AASP411
AASP623
ATTP
ACA
PHOH

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

AC57BINDING SITE FOR RESIDUE CA A 1005
ChainResidue
AGLU716
AHOH
AHOH
AHOH
AHOH
AHOH
AHOH

AC63BINDING SITE FOR RESIDUE CA A 1006
ChainResidue
AGLU116
AHOH
AHOH

AC73BINDING SITE FOR RESIDUE CA A 1007
ChainResidue
ALEU857
AASP860
AASP861

AC84BINDING SITE FOR RESIDUE CA P 201
ChainResidue
THOH
THOH
THOH
THOH

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

site_idNumber of ResiduesDetails
TTP_4j2a_A_100118THYMIDINE-5'-TRIPHOSPHATE binding site
ChainResidueligand
AASP411-PRO417TTP: THYMIDINE-5'-TRIPHOSPHATE
AARG482TTP: THYMIDINE-5'-TRIPHOSPHATE
ALYS486TTP: THYMIDINE-5'-TRIPHOSPHATE
ALYS560-LEU561TTP: THYMIDINE-5'-TRIPHOSPHATE
AASN564TTP: THYMIDINE-5'-TRIPHOSPHATE
ATYR567TTP: THYMIDINE-5'-TRIPHOSPHATE
ATHR622-ASP623TTP: THYMIDINE-5'-TRIPHOSPHATE
TDA4-DG5TTP: THYMIDINE-5'-TRIPHOSPHATE
PDC115TTP: THYMIDINE-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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