4M3W

RB69 DNA polymerase ternary complex with dT/dG at position n-4 of primer/template duplex

> Summary

Summary for 4M3W

Related4M3R 4M3T 4M3U
DescriptorDNA polymerase (E.C.2.7.7.7)
Functional Keywordsrb69 pol, quadruple, dt/dg, n-4, rb69, hydrolase-dna complex, hydrolase/dna
Biological sourceEnterobacteria phage RB69
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Total number of polymer chains3
Total molecular weight114392.38
Authors
Xia, S.,Konigsberg, W.H. (deposition date: 2013-08-06, release date: 2014-02-12, modification date: 2014-04-09)
Primary citation
Xia, S.,Konigsberg, W.H.
Mispairs with Watson-Crick base-pair geometry observed in ternary complexes of an RB69 DNA polymerase variant.
Protein Sci., 23:508-513, 2014
PubMed: 24458997
DOI: 10.1002/pro.2434
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (2.1 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.22810.1%2.6%1.7%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 4m3w
no rotation
Molmil generated image of 4m3w
rotated about x axis by 90°
Molmil generated image of 4m3w
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
ADNA polymerasepolymer903104449.71
UniProt (Q38087)
Pfam (PF00136)
Pfam (PF03104)
Enterobacteria phage RB69Gp43
TDNA templatepolymer175243.41
PDNA primerpolymer133951.61
ADENOSINE-5'-TRIPHOSPHATEnon-polymer507.21
CALCIUM IONnon-polymer40.16
waterwater18.0442

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains3
Total molecular weight113644.7
Non-Polymers*Number of molecules7
Total molecular weight747.7
All*Total molecular weight114392.4
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2.1 Å)

Cell axes78.518118.774129.773
Cell angles90.0090.0090.00
SpacegroupP 21 21 21
Resolution limits47.41 - 2.10
the highest resolution shell value2.155 - 2.101
R-factor0.17978
R-work0.17762
the highest resolution shell value0.204
R-free0.22037
the highest resolution shell value0.230
RMSD bond length0.006
RMSD bond angle1.053

Data Collection Statistics

Resolution limits50.00 - 2.10
the highest resolution shell value -
Number of reflections58582
Completeness82.6
I/sigma(I)1.4

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
A0046872molecular_functionmetal ion binding
A0000166molecular_functionnucleotide binding
A0039693biological_processviral DNA genome replication
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC121BINDING SITE FOR RESIDUE ATP A 1001
ChainResidue
AASP411
ALEU412
ATHR413
ASER414
AALA415
ATYR416
AARG482
ALYS560
AASN564
AASP623
ACA1002
ACA1003
AHOH1107
AHOH1139
AHOH1241
AHOH1266
AHOH1267
AHOH1292
PDC115
TDT4
TDG5

AC25BINDING SITE FOR RESIDUE CA A 1002
ChainResidue
AASP411
ALEU412
AASP623
AATP1001
ACA1003

AC35BINDING SITE FOR RESIDUE CA A 1003
ChainResidue
AASP411
AASP623
AATP1001
ACA1002
AHOH1193

AC46BINDING SITE FOR RESIDUE CA A 1004
ChainResidue
AASN505
AASN507
ALYS531
AHOH1195
AHOH1317
AHOH1319

AC56BINDING SITE FOR RESIDUE CA A 1005
ChainResidue
AGLU716
AHOH1107
AHOH1216
AHOH1239
AHOH1240
AHOH1401

AC64BINDING SITE FOR RESIDUE CA A 1006
ChainResidue
AGLU116
AHOH1289
AHOH1290
AHOH1454

AC74BINDING SITE FOR RESIDUE CA A 1007
ChainResidue
AASP192
ALEU857
AASP860
AASP861

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

site_idNumber of ResiduesDetails
ATP_4m3w_A_100117ADENOSINE-5'-TRIPHOSPHATE binding site
ChainResidueligand
AASP411-PRO417ATP: ADENOSINE-5'-TRIPHOSPHATE
AARG482ATP: ADENOSINE-5'-TRIPHOSPHATE
ALYS486ATP: ADENOSINE-5'-TRIPHOSPHATE
ALYS560ATP: ADENOSINE-5'-TRIPHOSPHATE
AASN564-GLY565ATP: ADENOSINE-5'-TRIPHOSPHATE
ATHR622-ASP623ATP: ADENOSINE-5'-TRIPHOSPHATE
TDT4-DG5ATP: ADENOSINE-5'-TRIPHOSPHATE
PDC115ATP: 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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