4FBU

Dpo4 polymerase pre-insertion binary complex with the N-(deoxyguanosin-8-yl)-1-aminopyrene lesion

> Summary

Summary for 4FBU

Related4FBT
DescriptorDNA polymerase IV (E.C.2.7.7.7)/DNA complex
Functional Keywordsdna polymerase, transferase-dna complex, transferase/dna
Biological sourceSulfolobus solfataricus
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Cellular locationCytoplasm (Probable) Q97W02
Total number of polymer chains6
Total molecular weight95175.56
Authors
Kirouac, K.,Basu, A.,Ling, H. (deposition date: 2012-05-23, release date: 2013-06-12, modification date: 2013-11-13)
Primary citation
Kirouac, K.N.,Basu, A.K.,Ling, H.
Structural mechanism of replication stalling on a bulky amino-polycyclic aromatic hydrocarbon DNA adduct by a y family DNA polymerase.
J.Mol.Biol., 425:4167-4176, 2013
PubMed: 23876706
DOI: 10.1016/j.jmb.2013.07.020
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (2.6 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.261270.3%5.9%6.9%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

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

More Biological unit images

Molmil generated image of 4fbu
no rotation
Molmil generated image of 4fbu
rotated about x axis by 90°
Molmil generated image of 4fbu
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 (4fbu.pdb1.gz [144.03 KB])
Coordinate files for Biological unit (4fbu.pdb2.gz [143.42 KB])

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A, BDNA polymerase IVpolymer34139019.92
UniProt (Q97W02)
Pfam (PF00817)
Pfam (PF11798)
Pfam (PF11799)
Sulfolobus solfataricusPol IV
P, DDNA primerpolymer133880.62
T, CDNA templatepolymer144607.12
CALCIUM IONnon-polymer40.14
waterwater18.0248

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains6
Total molecular weight95015.2
Non-Polymers*Number of molecules4
Total molecular weight160.3
All*Total molecular weight95175.6
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2.6 Å)

Cell axes52.774181.45852.744
Cell angles90.00109.4990.00
SpacegroupP 1 21 1
Resolution limits31.24 - 2.60
the highest resolution shell value2.704 - 2.600
R-factor0.2198
R-work0.21750
the highest resolution shell value0.328
R-free0.26140
the highest resolution shell value0.320
RMSD bond length0.007
RMSD bond angle1.222

Data Collection Statistics

Resolution limits31.24 - 2.60
the highest resolution shell value -
Number of reflections25790
Completeness95.8
I/sigma(I)1

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP7298

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
A0005737cellular_componentcytoplasm
A0003684molecular_functiondamaged DNA binding
A0003887molecular_functionDNA-directed DNA polymerase activity
A0000287molecular_functionmagnesium ion binding
A0006281biological_processDNA repair
A0006261biological_processDNA-dependent DNA replication
B0005737cellular_componentcytoplasm
B0003684molecular_functiondamaged DNA binding
B0003887molecular_functionDNA-directed DNA polymerase activity
B0000287molecular_functionmagnesium ion binding
B0006281biological_processDNA repair
B0006261biological_processDNA-dependent DNA replication
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC14BINDING SITE FOR RESIDUE CA A 401
ChainResidue
AASP7
AASP105
AGLU106
PDC13

AC23BINDING SITE FOR RESIDUE CA A 402
ChainResidue
AASP7
APHE8
AASP105

AC36BINDING SITE FOR RESIDUE CA B 401
ChainResidue
BASP7
BASP105
BGLU106
BCA
BHOH
DDC13

AC46BINDING SITE FOR RESIDUE CA B 402
ChainResidue
BASP7
BPHE8
BASP105
BCA
BHOH
BHOH

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

site_idNumber of ResiduesDetails
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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
SWS_FT_FI11
ChainResidueDetails
AGLU106

SWS_FT_FI41
ChainResidueDetails
BGLU106

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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

> Downloads

Resources

File formatFile name (file size)
PDBallpdb4fbu.ent.gz (292.87 KB)
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all (no-compress)pdb4fbu.ent (1.1 MB)
header onlypdb4fbu.ent.gz (10.67 KB)
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PDBx/mmCIF4fbu.cif.gz (354.37 KB)
PDBMLall4fbu.xml.gz (534.58 KB)
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no-atom4fbu-noatom.xml.gz (42.17 KB)
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ext-atom4fbu-extatom.xml.gz (162.43 KB)
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PDBMLplusall4fbu-plus.xml.gz (536.08 KB)
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no-atom4fbu-plus-noatom.xml.gz (43.67 KB)
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add only4fbu-add.xml.gz (1.5 KB)
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RDF4fbu.rdf.gz (75.99 KB)
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Structure factorsr4fbusf.ent.gz (294.13 KB)
Biological unit (PDB format)4fbu.pdb1.gz (144.03 KB) (A,P,T)
*author and software defined assembly, 3 molecule(s) (trimeric)
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4fbu.pdb2.gz (143.42 KB) (B,D,C)
*author and software defined assembly, 3 molecule(s) (trimeric)
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Validation reportsPDF4fbu​_validation.pdf.gz (302.15 KB)
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PDF-full4fbu​_full​_validation.pdf.gz (339.53 KB)
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XML4fbu​_validation.xml.gz (37.79 KB)
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PNG4fbu​_multipercentile​_validation.png.gz (157.5 KB)
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SVG4fbu​_multipercentile​_validation.svg.gz (949 B)
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Sequence (fasta)4fbu​_seq.txt
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