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- PDB-4k8x: Binary complex of 9N DNA polymerase in the replicative state -

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Basic information

Entry
Database: PDB / ID: 4k8x
TitleBinary complex of 9N DNA polymerase in the replicative state
Components
  • DNA (5'-D(*CP*GP*CP*GP*AP*AP*CP*TP*GP*CP*GP*(DOC))-3')
  • DNA (5'-D(P*AP*AP*AP*GP*GP*CP*GP*CP*AP*GP*TP*TP*CP*GP*CP*G)-3')
  • DNA polymerase
KeywordsTRANSFERASE/DNA / DNA polymerase / Binary complex / TRANSFERASE-DNA complex
Function / homology
Function and homology information


DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding
Similarity search - Function
DNA Polymerase; Chain A, domain 1 / DNA Polymerase, chain B, domain 1 / B family DNA polymerase, finger domain / Palm domain of DNA polymerase / B family DNA polymerase, palm domain / DNA polymerase family B, thumb domain / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B / DNA polymerase family B, exonuclease domain ...DNA Polymerase; Chain A, domain 1 / DNA Polymerase, chain B, domain 1 / B family DNA polymerase, finger domain / Palm domain of DNA polymerase / B family DNA polymerase, palm domain / DNA polymerase family B, thumb domain / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H-like superfamily/Ribonuclease H / Helix Hairpins / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-5CY / DNA / DNA (> 10) / DNA polymerase
Similarity search - Component
Biological speciesThermococcus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsBetz, K. / Diederichs, K. / Marx, A.
CitationJournal: Chembiochem / Year: 2013
Title: Structures of KOD and 9N DNA Polymerases Complexed with Primer Template Duplex
Authors: Bergen, K. / Betz, K. / Welte, W. / Diederichs, K. / Marx, A.
History
DepositionApr 19, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase
T: DNA (5'-D(P*AP*AP*AP*GP*GP*CP*GP*CP*AP*GP*TP*TP*CP*GP*CP*G)-3')
P: DNA (5'-D(*CP*GP*CP*GP*AP*AP*CP*TP*GP*CP*GP*(DOC))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,03317
Polymers98,4073
Non-polymers1,62614
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8470 Å2
ΔGint-158 kcal/mol
Surface area36840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.215, 142.616, 66.702
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase /


Mass: 89826.570 Da / Num. of mol.: 1 / Mutation: D141A, E143A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus (archaea) / Strain: 9oN-7 / Gene: pol, polA / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: Q56366, DNA-directed DNA polymerase

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DNA chain , 2 types, 2 molecules TP

#2: DNA chain DNA (5'-D(P*AP*AP*AP*GP*GP*CP*GP*CP*AP*GP*TP*TP*CP*GP*CP*G)-3')


Mass: 4948.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA template
#3: DNA chain DNA (5'-D(*CP*GP*CP*GP*AP*AP*CP*TP*GP*CP*GP*(DOC))-3')


Mass: 3632.382 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA primer

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Non-polymers , 5 types, 148 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-5CY / 1-(3-hydroxypropyl)-2-{(1E,3E,5E)-5-[1-(3-hydroxypropyl)-3,3-dimethyl-1,3-dihydro-2H-indol-2-ylidene]penta-1,3-dien-1-y l}-3,3-dimethyl-3H-indolium / N,N'-(dipropyl)-tetramethylindodicarbocyanine


Mass: 471.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H39N2O2
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2M Lithium chloride, 2.2M Ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97793 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 5, 2012
RadiationMonochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97793 Å / Relative weight: 1
ReflectionResolution: 2.28→48.712 Å / Num. all: 49646 / Num. obs: 49600 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 43.96 Å2 / Net I/σ(I): 9.07
Reflection shellResolution: 2.28→2.42 Å / Mean I/σ(I) obs: 0.82 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIXmodel building
PHENIX(phenix.refine: dev_1345)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QHT

1qht


Resolution: 2.28→48.712 Å / Occupancy max: 1 / Occupancy min: 0.33 / SU ML: 0.38 / Isotropic thermal model: isotropic and tls / σ(F): 1.99 / Phase error: 30.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2383 2524 5.09 %
Rwork0.1953 --
obs0.1976 49542 99.81 %
all-49586 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 180.4 Å2 / Biso mean: 61.701 Å2 / Biso min: 24.56 Å2
Refinement stepCycle: LAST / Resolution: 2.28→48.712 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6217 573 95 134 7019
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087194
X-RAY DIFFRACTIONf_angle_d1.1579849
X-RAY DIFFRACTIONf_dihedral_angle_d17.7182826
X-RAY DIFFRACTIONf_chiral_restr0.0721035
X-RAY DIFFRACTIONf_plane_restr0.0051196
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.28-2.32390.42171260.3662603100
2.3239-2.37130.38541330.34832563100
2.3713-2.42280.39831430.32882584100
2.4228-2.47920.35811360.30422584100
2.4792-2.54120.37611430.28672565100
2.5412-2.60990.27821330.26472582100
2.6099-2.68670.28841610.26522559100
2.6867-2.77340.32171350.25842581100
2.7734-2.87250.3341170.24982600100
2.8725-2.98750.32511510.25472586100
2.9875-3.12350.3241440.24632598100
3.1235-3.28810.29281350.21392607100
3.2881-3.49410.25311340.18612632100
3.4941-3.76370.23461380.1785260099
3.7637-4.14230.16321390.14682650100
4.1423-4.74130.15381400.12242644100
4.7413-5.97180.19711520.14632677100
5.9718-48.72350.18241640.1632803100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.6473-0.4046-0.20061.3190.71053.82820.02060.92070.2682-0.2214-0.03410.1697-0.0939-0.18260.02410.2563-0.0399-0.04490.59630.17240.5609-32.144939.1512-40.3743
25.43081.8564-2.50322.4759-1.46933.0655-0.16720.4184-0.32820.0020.10080.08160.099-0.68090.05090.24570.016-0.00020.5913-0.11570.4435-51.426929.519-12.1571
32.0972-0.24330.08220.96760.03110.6157-0.044-0.0959-0.15250.1334-0.0222-0.09820.08490.07280.06440.2627-0.019-0.0220.33010.02950.3865-19.428824.2237-14.4604
43.83530.4740.81281.7817-0.0561.56050.1827-0.4446-0.98850.33090.01810.26330.2539-0.291-0.16520.45830.01930.0860.50240.11760.871-24.08682.8494-1.5516
51.74680.320.74720.3294-0.21022.23710.16010.3177-0.9959-0.2326-0.37280.34750.3333-0.14840.22980.3951-0.04820.06190.5226-0.07431.0002-22.31394.9457-16.3651
60.2381-0.96480.29654.7352-2.36812.15010.57510.3973-1.6466-0.5994-0.2244-0.7420.8849-0.1494-0.37250.6738-0.03090.01530.5691-0.15581.593-22.7619-3.1801-17.2415
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:123)A1 - 123
2X-RAY DIFFRACTION2chain 'A' and (resseq 124:255 )A124 - 255
3X-RAY DIFFRACTION3chain 'A' and (resseq 256:553 )A256 - 553
4X-RAY DIFFRACTION4chain 'A' and (resseq 554:758 )A554 - 758
5X-RAY DIFFRACTION5chain 'T' and (resseq 1:16)T1 - 16
6X-RAY DIFFRACTION6chain 'P' and (resseq 1:11)P1 - 11

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