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

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Basic information

Entry
Database: PDB / ID: 4fly
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: 2.3 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
T: Template strand
P: Primer strand
A: DNA polymerase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,4746
Polymers98,2303
Non-polymers2443
Water10,142563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-36 kcal/mol
Surface area35600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.100, 114.340, 128.580
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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DNA chain , 2 types, 2 molecules TP

#1: DNA chain Template strand


Mass: 4008.594 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemical synthesis / Source: (synth.) synthetic construct (others)
#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)

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Protein , 1 types, 1 molecules A

#3: 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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Non-polymers , 3 types, 566 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 563 / 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: 2.59 Å3/Da / Density % sol: 52.43 %
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: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.99187 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 9, 2010
RadiationMonochromator: channel cut cryogenically cooled monochromator crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99187 Å / Relative weight: 1
ReflectionResolution: 2.3→44 Å / Num. obs: 44918 / % possible obs: 97.8 % / Redundancy: 4.1 % / Biso Wilson estimate: 34.8 Å2 / Rmerge(I) obs: 0.141 / Net I/σ(I): 10.7
Reflection shellResolution: 2.32→2.42 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.6 / Num. unique all: 6401 / Rsym value: 0.37 / % possible all: 97.3

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Processing

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

4flw


Resolution: 2.3→44 Å / Cor.coef. Fo:Fc: 0.9346 / Cor.coef. Fo:Fc free: 0.9081 / SU R Cruickshank DPI: 0.262 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.219 2265 5.05 %RANDOM
Rwork0.1756 ---
obs0.1778 44868 97.58 %-
Displacement parametersBiso mean: 32.82 Å2
Baniso -1Baniso -2Baniso -3
1-2.1742 Å20 Å20 Å2
2--4.2588 Å20 Å2
3----6.433 Å2
Refine analyzeLuzzati coordinate error obs: 0.249 Å
Refinement stepCycle: LAST / Resolution: 2.3→44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5984 426 14 563 6987
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016633HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.089074HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3100SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes132HARMONIC2
X-RAY DIFFRACTIONt_gen_planes914HARMONIC5
X-RAY DIFFRACTIONt_it6633HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.31
X-RAY DIFFRACTIONt_other_torsion3.05
X-RAY DIFFRACTIONt_chiral_improper_torsion863SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact7692SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2619 169 5.26 %
Rwork0.1991 3044 -
all0.2025 3213 -
obs--97.58 %
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)
11.9298-0.8197-0.88871.36320.27230.9096-0.066-0.29490.2330.19190.1223-0.1319-0.0570.091-0.0562-0.09380.0113-0.0388-0.0794-0.0398-0.003122.956751.7109-8.8857
21.4044-1.00530.21261.54-0.05830.62570.0496-0.0234-0.1088-0.0544-0.0125-0.05660.09920.0085-0.0371-0.081-0.01520.0092-0.09670.00160.021434.928722.5102-24.073
32.35530.72911.01040.89221.04773.43430.0892-0.25080.10510.08580.0452-0.21860.4236-0.2423-0.1344-0.01490.0051-0.0514-0.06020.052-0.08258.42142.856-12.5044
40.6898-0.2422-0.14821.51760.19160.56080.09780.0774-0.0963-0.1448-0.13940.14660.0083-0.01430.0416-0.05360.0347-0.0233-0.08540.0066-0.0381-0.180433.9102-31.9561
51.21920.03671.34270.24860.32712.00530.0671-0.1509-0.00640.0378-0.0644-0.05450.1154-0.0252-0.0028-0.0781-0.0374-0.0152-0.08640.00410.012213.1424.2958-16.6088
60.9344-0.1636-1.00040.7108-0.25680.3458-0.00530.03420.0704-0.0044-0.0160.04730.00240.03850.0213-0.1186-0.05780.06560.0089-0.00530.15796.182716.72191.4171
701.1735-1.22310.21880.77380.215-0.021-0.0204-0.0053-0.090.0354-0.0459-0.0487-0.0209-0.0144-0.0095-0.0387-0.02-0.07550.04080.039917.92516.2975-9.9678
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|1 - 133}A1 - 133
2X-RAY DIFFRACTION2{A|134 - 356}A134 - 356
3X-RAY DIFFRACTION3{A|357 - 383}A357 - 383
4X-RAY DIFFRACTION4{A|392 - 570}A392 - 570
5X-RAY DIFFRACTION5{A|571 - 757}A571 - 757
6X-RAY DIFFRACTION6{P|1 - 4}P1 - 4
7X-RAY DIFFRACTION7{P|5 - 8}P5 - 8

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