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- PDB-4flu: Pyrococcus abyssi B family DNA polymerase bound to a dsDNA, in ed... -

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Basic information

Entry
Database: PDB / ID: 4flu
TitlePyrococcus abyssi B family DNA polymerase bound to a dsDNA, in edition mode
Components
  • Primer strand
  • Pyrococcus abyssi B family DNA polymerase
  • Template strand
KeywordsTRANSFERASE/DNA / DNA polymerase / DNA binding / TRANSFERASE-DNA complex
Function / homology
Function and homology information


nucleotide-excision repair, DNA gap filling / DNA replication proofreading / 3'-5'-DNA exonuclease activity / SOS response / base-excision repair, gap-filling / 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
DNA / DNA (> 10) / DNA polymerase 1 / DNA polymerase 1
Similarity search - Component
Biological speciesPyrococcus abyssi (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsGouge, J. / Delarue, M.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Molecular Recognition of Canonical and Deaminated Bases by P. abyssi Family B DNA Polymerase.
Authors: Gouge, J. / Ralec, C. / Henneke, G. / Delarue, M.
History
DepositionJun 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2012Group: Database references
Revision 1.2Jan 29, 2020Group: Data collection / Database references / Source and taxonomy
Category: pdbx_entity_src_syn / reflns / struct_ref_seq_dif
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific ..._pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _reflns.pdbx_Rmerge_I_obs / _struct_ref_seq_dif.details
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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: Pyrococcus abyssi B family DNA polymerase
P: Primer strand
T: Template strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,5537
Polymers99,2173
Non-polymers3364
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6440 Å2
ΔGint-35 kcal/mol
Surface area35500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.970, 114.420, 128.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Pyrococcus abyssi B family DNA polymerase


Mass: 91809.938 Da / Num. of mol.: 1 / Mutation: D215A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi (archaea) / Production host: Escherichia coli (E. coli)
References: UniProt: P0CL77, UniProt: P0CL76*PLUS, DNA-directed DNA polymerase

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DNA chain , 2 types, 2 molecules PT

#2: DNA chain Primer strand


Mass: 3399.223 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemical synthesis / Source: (synth.) synthetic construct (others)
#3: DNA chain Template strand


Mass: 4007.609 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemical synthesis / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 216 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.56 Å3/Da / Density % sol: 51.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 7-12% PEG 20000, 100 mM MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 29, 2011
RadiationMonochromator: ID14-1 Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 3.1→44 Å / Num. obs: 18522 / % possible obs: 97.7 % / Redundancy: 4 % / Biso Wilson estimate: 60.05 Å2 / Rmerge(I) obs: 0.158 / Net I/σ(I): 10
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 4 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3 / Num. unique all: 2703 / Rsym value: 0.25 / % possible all: 98.8

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
BUSTER2.11.2refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4FLW

4flw


Resolution: 3.1→44 Å / Cor.coef. Fo:Fc: 0.9223 / Cor.coef. Fo:Fc free: 0.8628 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2174 950 5.14 %RANDOM
Rwork0.1631 ---
obs0.1657 18500 96.88 %-
Displacement parametersBiso mean: 32.07 Å2
Baniso -1Baniso -2Baniso -3
1-4.5652 Å20 Å20 Å2
2--3.01 Å20 Å2
3----7.5752 Å2
Refine analyzeLuzzati coordinate error obs: 0.467 Å
Refinement stepCycle: LAST / Resolution: 3.1→44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6125 492 20 212 6849
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016839HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.099339HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3240SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes145HARMONIC2
X-RAY DIFFRACTIONt_gen_planes921HARMONIC5
X-RAY DIFFRACTIONt_it6839HARMONIC20
X-RAY DIFFRACTIONt_nbd5SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.21
X-RAY DIFFRACTIONt_other_torsion3.12
X-RAY DIFFRACTIONt_chiral_improper_torsion873SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact7536SEMIHARMONIC4
LS refinement shellResolution: 3.1→3.29 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.257 173 5.79 %
Rwork0.185 2817 -
all0.1893 2990 -
obs--96.88 %
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)
13.35911.23050.78771.84661.31532.006-0.06910.5387-0.5442-0.1490.1115-0.24460.24330.2296-0.0424-0.102-0.00180.073-0.1527-0.02730.015423.2143-51.86549.4257
21.55550.56190.1110.7940.02330.48090.0627-0.01240.06530.1126-0.0578-0.09-0.16660.0533-0.0049-0.03390.0030.0111-0.07510.0149-0.042731.1437-25.135622.6976
30.63810.1338-0.07251.73230.07090.69520.0317-0.14020.03340.2156-0.06570.11490.0064-0.07650.034-0.0791-0.0408-0.0014-0.08910.0043-0.04-0.0278-34.255232.0975
41.3250.0001-0.48050.47770.41461.37290.14090.10880.0611-0.0759-0.0262-0.0091-0.14740.215-0.1146-0.10890.03410.0395-0.0980.0066-0.001714.0972-4.805716.1611
50.4013-0.25221.21560.0930.221.86680.00170.21180.0209-0.0608-0.01950.0661-0.0098-0.14120.0178-0.0126-0.1176-0.0277-0.0533-0.03980.112-0.78-0.350620.0897
61.04380.24320.15140.66920.01870-0.0170.0484-0.07930.07430.07350.04920.0623-0.0272-0.0565-0.16310.0479-0.11210.0117-0.06150.1067.9552-16.7229-0.6313
70-1.95231.592800.937900.00960.09320.0622-0.13190.0806-0.15220.0097-0.0855-0.09020.0295-0.01470.0595-0.0960.04010.109624.0568-15.314815.7756
802.77060.99530.698-0.09390.55250.00390.02240.1954-0.03450.0035-0.0516-0.05320.0094-0.00740.04120.04920.0844-0.004-0.08950.047124.4915-38.79637.0161
91.72282.15980.15221.9445-1.04080.37950.00170.0498-0.02820.071-0.0060.06660.10640.00970.0043-0.02820.0007-0.0973-0.03540.1520.19513.1313-23.758413.2545
100.37622.135-1.22750.0157-0.37190.0495-0.0264-0.03890.04710.10220.03890.0972-0.0182-0.0536-0.0125-0.24040.0814-0.02620.0531-0.00180.13219.5388-10.80132.9068
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|-2 - 134}A-2 - 134
2X-RAY DIFFRACTION2{A|135 - 391}A135 - 391
3X-RAY DIFFRACTION3{A|392 - 569}A392 - 569
4X-RAY DIFFRACTION4{A|570 - 741}A570 - 741
5X-RAY DIFFRACTION5{A|742 - 757}A742 - 757
6X-RAY DIFFRACTION6{P|1 - 5}P1 - 5
7X-RAY DIFFRACTION7{P|6 - 11}P6 - 11
8X-RAY DIFFRACTION8{T|1 - 4}T1 - 4
9X-RAY DIFFRACTION9{T|5 - 8}T5 - 8
10X-RAY DIFFRACTION10{T|9 - 13}T9 - 13

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