4I9Q

Crystal structure of the ternary complex of the D714A mutant of RB69 DNA polymerase

> Summary

Summary for 4I9Q

Related4I9L 4KHN
DescriptorDNA polymerase (E.C.2.7.7.7)/DNA complex
Functional Keywordspalm subdomain, hydrolase, transferase, transferase-dna complex, transferase/dna
Biological sourceEnterobacteria phage RB69
More
Total number of polymer chains6
Total molecular weight230129.07
Authors
Guja, K.E.,Jacewicz, A.,Trzemecka, A.,Plochocka, D.,Yakubovskaya, E.,Bebenek, A.,Garcia-Diaz, M. (deposition date: 2012-12-05, release date: 2013-10-09, modification date: 2013-10-23)
Primary citation
Jacewicz, A.,Trzemecka, A.,Guja, K.E.,Plochocka, D.,Yakubovskaya, E.,Bebenek, A.,Garcia-Diaz, M.
A Remote Palm Domain Residue of RB69 DNA Polymerase Is Critical for Enzyme Activity and Influences the Conformation of the Active Site.
Plos One, 8:e76700-e76700, 2013
PubMed: 24116139
DOI: 10.1371/journal.pone.0076700
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (2.3 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.29340.4%1.9%3.1%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 4i9q
no rotation
Molmil generated image of 4i9q
rotated about x axis by 90°
Molmil generated image of 4i9q
rotated about y axis by 90°

More Biological unit images

Molmil generated image of 4i9q
no rotation
Molmil generated image of 4i9q
rotated about x axis by 90°
Molmil generated image of 4i9q
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 (4i9q.pdb1.gz [324.32 KB])
Coordinate files for Biological unit (4i9q.pdb2.gz [328.37 KB])

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A, BDNA polymerasepolymer903104519.82
UniProt (Q38087)
Pfam (PF00136)
Pfam (PF03104)
Enterobacteria phage RB69Gp43
T, DDNA (5'-D(*TP*CP*AP*CP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')polymer185501.62
Synthetic construct
P, CDNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*C)-3')polymer133967.62
Synthetic construct
2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINEnon-polymer506.24
CALCIUM IONnon-polymer40.12
SODIUM IONnon-polymer23.02
waterwater18.0398

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains6
Total molecular weight227978.1
Non-Polymers*Number of molecules8
Total molecular weight2150.9
All*Total molecular weight230129.1
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2.3 Å)

Cell axes73.781119.412146.016
Cell angles90.0090.2690.00
SpacegroupP 1 21 1
Resolution limits38.40 - 2.30
the highest resolution shell value2.326 - 2.300
R-factor0.2537
R-work0.25190
the highest resolution shell value0.266
R-free0.28710
the highest resolution shell value0.294
RMSD bond length0.012
RMSD bond angle0.781

Data Collection Statistics

Resolution limits39.12 - 2.30
the highest resolution shell value -
Number of reflections110655

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP5.6298

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
B0008408molecular_function3'-5' exonuclease activity
B0003677molecular_functionDNA binding
B0003887molecular_functionDNA-directed DNA polymerase activity
B0000166molecular_functionnucleotide binding
B0039693biological_processviral DNA genome replication
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC117BINDING SITE FOR RESIDUE XG4 A 1001
ChainResidue
ALEU412
ASER414
ALEU415
ATYR416
AARG482
ALYS560
AASN564
ATHR622
AASP623
ACA1003
ANA1004
AHOH1105
AHOH1314
AHOH1316
PDC115
TDC4
TDG5

AC213BINDING SITE FOR RESIDUE XG4 A 1002
ChainResidue
ASER36
APHE38
ALYS48
ATYR49
AARG59
AMET85
APHE370
ALYS374
AASN377
ALYS378
AVAL379
AILE380
AHOH1218

AC34BINDING SITE FOR RESIDUE CA A 1003
ChainResidue
AASP411
ALEU412
AXG41001
AHOH1315

AC46BINDING SITE FOR RESIDUE NA A 1004
ChainResidue
ALEU412
ATHR413
ASER414
ALEU415
AASP623
AXG41001

AC516BINDING SITE FOR RESIDUE XG4 B 1001
ChainResidue
BLEU412
BSER414
BLEU415
BTYR416
BARG482
BLYS560
BASN564
BASP623
BCA1003
BNA1004
BHOH1120
BHOH1233
BHOH1234
CDC115
DDC4
DDG5

AC615BINDING SITE FOR RESIDUE XG4 B 1002
ChainResidue
BTYR33
BSER36
BPHE38
BLYS48
BTYR49
BARG59
BGLY84
BMET85
BASP95
BPHE370
BLYS374
BASN377
BLYS378
BILE380
BHOH1195

AC73BINDING SITE FOR RESIDUE CA B 1003
ChainResidue
BASP411
BLEU412
BXG41001

AC86BINDING SITE FOR RESIDUE NA B 1004
ChainResidue
BLEU412
BTHR413
BSER414
BLEU415
BASP623
BXG41001

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

site_idNumber of ResiduesDetails
XG4_4i9q_A_1002182'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE binding site
ChainResidueligand
ATYR33XG4: 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE
ASER36-PHE38XG4: 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE
ALYS48-TYR49XG4: 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE
AARG59XG4: 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE
AGLY84-MET85XG4: 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE
AALA91XG4: 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE
AASP95XG4: 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE
APHE370XG4: 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE
ALEU373-LYS374XG4: 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE
AASN377-ILE380XG4: 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE

XG4_4i9q_A_1001202'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE binding site
ChainResidueligand
AASP411-PRO417XG4: 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE
AARG482XG4: 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE
ALYS486XG4: 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE
AGLN556XG4: 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE
ALYS560-LEU561XG4: 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE
AASN564-SER565XG4: 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE
AGLY568XG4: 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE
ATHR622-ASP623XG4: 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE
TDC4-DG5XG4: 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE
PDC115XG4: 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE

XG4_4i9q_B_1002172'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE binding site
ChainResidueligand
BTYR33XG4: 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE
BSER36XG4: 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE
BPHE38XG4: 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE
BLYS48-TYR49XG4: 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE
BARG59XG4: 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE
BGLY84-MET85XG4: 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE
BALA91XG4: 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE
BASP95XG4: 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE
BPHE370XG4: 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE
BLEU373-LYS374XG4: 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE
BASN377-ILE380XG4: 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE

XG4_4i9q_B_1001192'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE binding site
ChainResidueligand
BASP411-PRO417XG4: 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE
BARG482XG4: 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE
BLYS486XG4: 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE
BLYS560-LEU561XG4: 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE
BASN564-SER565XG4: 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE
BGLY568XG4: 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE
BTHR622-ASP623XG4: 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE
DDC4-DG5XG4: 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE
CDC115XG4: 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE

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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

> Downloads

Resources

File formatFile name (file size)
PDBallpdb4i9q.ent.gz (656.7 KB)
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all (no-compress)pdb4i9q.ent (2.52 MB)
header onlypdb4i9q.ent.gz (13.99 KB)
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PDBx/mmCIF4i9q.cif.gz (804.11 KB)
PDBMLall4i9q.xml.gz (1.18 MB)
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no-atom4i9q-noatom.xml.gz (76.48 KB)
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ext-atom4i9q-extatom.xml.gz (373 KB)
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PDBMLplusall4i9q-plus.xml.gz (1.18 MB)
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no-atom4i9q-plus-noatom.xml.gz (78.81 KB)
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add only4i9q-add.xml.gz (2.33 KB)
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RDF4i9q.rdf.gz (150.29 KB)
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Structure factorsr4i9qsf.ent.gz (955.52 KB)
Biological unit (PDB format)4i9q.pdb1.gz (324.32 KB) (A,T,P)
*author and software defined assembly, 3 molecule(s) (trimeric)
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4i9q.pdb2.gz (328.37 KB) (B,D,C)
*author and software defined assembly, 3 molecule(s) (trimeric)
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Validation reportsPDF4i9q​_validation.pdf.gz (317.27 KB)
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PDF-full4i9q​_full​_validation.pdf.gz (337.27 KB)
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XML4i9q​_validation.xml.gz (68.53 KB)
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PNG4i9q​_multipercentile​_validation.png.gz (154.13 KB)
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SVG4i9q​_multipercentile​_validation.svg.gz (952 B)
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Sequence (fasta)4i9q​_seq.txt
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