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

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Basic information

Entry
Database: PDB / ID: 4flz
TitlePyrococcus abyssi B family DNA polymerase bound to a dsDNA, in edition mode
Components
  • DNA polymerase 1
  • Primer strand
  • Template strand
KeywordsTRANSFERASE/DNA / DNA polymerase / DNA binding / TRANSFERASE-DNA complex
Function / homology
Function and homology information


DNA-templated 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-directed DNA polymerase, family B, multifunctional domain / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B signature. ...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-directed DNA polymerase, family B, multifunctional domain / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B signature. / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Helix Hairpins / 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
Similarity search - Component
Biological speciesPyrococcus abyssi (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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 1.3Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_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: DNA polymerase 1
P: Primer strand
T: Template strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,0216
Polymers98,8813
Non-polymers1413
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-34 kcal/mol
Surface area35300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.050, 115.150, 128.520
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 DNA polymerase 1 / Pab 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) / Strain: GE5 / Orsay / Gene: polI, pol, PYRAB17200, PAB1128 / Production host: Escherichia coli (E. coli) / References: UniProt: P0CL77, DNA-directed DNA polymerase

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DNA chain , 2 types, 2 molecules PT

#2: DNA chain Primer strand


Mass: 2411.606 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemical synthesis / Source: (synth.) synthetic construct (others)
#3: DNA chain Template strand


Mass: 4659.032 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemical synthesis / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 69 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.58 Å3/Da / Density % sol: 52.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 7-12% PEG 20000, 100 mM MES pH 6.5, seeding , 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: 3.2→47.04 Å / Num. obs: 17526 / % possible obs: 99.9 % / Redundancy: 4 % / Biso Wilson estimate: 86.39 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 12.3
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.36 / % possible all: 100

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
BUSTER2.11.2refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→47.04 Å / Cor.coef. Fo:Fc: 0.9262 / Cor.coef. Fo:Fc free: 0.8956 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2039 883 5.05 %RANDOM
Rwork0.1747 ---
obs0.1762 17479 99.93 %-
Displacement parametersBiso mean: 65.68 Å2
Baniso -1Baniso -2Baniso -3
1-3.4563 Å20 Å20 Å2
2--10.2193 Å20 Å2
3----13.6756 Å2
Refine analyzeLuzzati coordinate error obs: 0.559 Å
Refinement stepCycle: LAST / Resolution: 3.2→47.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5989 470 8 66 6533
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016674HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.139141HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3112SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes143HARMONIC2
X-RAY DIFFRACTIONt_gen_planes911HARMONIC5
X-RAY DIFFRACTIONt_it6674HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.11
X-RAY DIFFRACTIONt_other_torsion3.23
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion866SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7291SEMIHARMONIC4
LS refinement shellResolution: 3.2→3.39 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.3 130 4.71 %
Rwork0.2222 2630 -
all0.226 2760 -
obs--99.93 %
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)
12.85711.13730.6422.33581.53922.6552-0.12830.3265-0.5261-0.28920.0952-0.44860.30140.28580.0331-0.05030.10190.119-0.1720.0315-0.00523.0144-52.1868.9461
23.21141.9594-0.84655.0628-1.4813.58470.1724-0.19390.25030.2345-0.3716-0.1016-0.54360.54420.1992-0.2315-0.0489-0.1518-0.02230.1226-0.173437.1677-20.289623.8828
31.61950.2951-0.50861.87110.28271.6760.0735-0.078-0.10770.1091-0.12310.03920.0603-0.25250.0496-0.0840.0407-0.0136-0.05780.0584-0.1365.3567-39.392325.6539
43.7074-0.1156-1.33598.3145-0.06496.7870.0267-0.1626-0.02730.372-0.37840.05340.3008-0.08520.3517-0.14830.05250.0129-0.1303-0.0052-0.1411-1.564-20.689338.5497
52.786-0.724-2.91041.3741.61554.48990.12720.34320.201-0.08410.02510.0111-0.2557-0.1178-0.1523-0.04640.09120.0787-0.0860.0533-0.036514.8073-1.277412.1508
60.75950.4386-1.14861.02752.39060.9728-0.02370.0065-0.07990.0071-0.00540.01050.0616-0.13510.0291-0.215-0.152-0.1520.1966-0.00610.11476.3462-17.6823-1.2547
700.07290.69242.0553-0.057300.0181-0.014-0.0110.08450.02230.0420.0395-0.0069-0.0404-0.05120.1520.0542-0.04610.030.029117.8874-16.84979.8715
80.01010.464-0.82230-0.687100.007-0.03150.0769-0.0399-0.0778-0.1279-0.08270.1160.0708-0.0421-0.1520.1520.1007-0.066-0.120831.0304-41.88788.2148
90-0.6917-1.02773.075-0.2230-0.0102-0.0760.0091-0.00360.0059-0.02910.0137-0.08280.00430.02040.13030.1416-0.03040.12570.20217.5223-30.069310.5844
100-0.1156-0.6080-0.71350.01760.02910.00330.0080.038-0.03530.05640.0113-0.10030.0062-0.16910.1519-0.01450.1170.0925-0.03998.931-13.848.6329
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|-1 - 133}A-1 - 133
2X-RAY DIFFRACTION2{A|134 - 323}A134 - 323
3X-RAY DIFFRACTION3{A|324 - 525}A324 - 525
4X-RAY DIFFRACTION4{A|526 - 605}A526 - 605
5X-RAY DIFFRACTION5{A|606 - 757}A606 - 757
6X-RAY DIFFRACTION6{P|1 - 4}P1 - 4
7X-RAY DIFFRACTION7{P|5 - 8}P5 - 8
8X-RAY DIFFRACTION8{T|1 - 4}T1 - 4
9X-RAY DIFFRACTION9{T|5 - 9}T5 - 9
10X-RAY DIFFRACTION10{T|10 - 13}T10 - 13

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