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- PDB-4fm2: Pyrococcus abyssi B family DNA polymerase (triple mutant) bound t... -

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Basic information

Entry
Database: PDB / ID: 4fm2
TitlePyrococcus abyssi B family DNA polymerase (triple mutant) 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 polymerase family B signature. / DNA-directed DNA polymerase, family B, multifunctional domain / DNA-directed DNA polymerase, family B, conserved site ...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, multifunctional domain / 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 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: 2.9 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_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 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)98,8595
Polymers98,7423
Non-polymers1162
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint-32 kcal/mol
Surface area34910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.730, 115.020, 127.260
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: 4667.005 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: 91663.883 Da / Num. of mol.: 1 / Mutation: D4A, D215A, E251A, D343A
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, 141 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / 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.: 139 / 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: 2.55 Å3/Da / Density % sol: 51.71 %
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: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.91936 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 21, 2010
RadiationMonochromator: channel cut cryogenically cooled monochromator crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91936 Å / Relative weight: 1
ReflectionResolution: 2.9→44.11 Å / Num. obs: 21903 / % possible obs: 97.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 86.47 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 11
Reflection shellResolution: 2.92→3.08 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 2 / Num. unique all: 3183 / Rsym value: 0.49 / % 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: 2.9→44.11 Å / Cor.coef. Fo:Fc: 0.9301 / Cor.coef. Fo:Fc free: 0.9097 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2215 1116 5.21 %RANDOM
Rwork0.1826 ---
obs0.1845 21411 92.97 %-
Displacement parametersBiso mean: 72.17 Å2
Baniso -1Baniso -2Baniso -3
1-11.9797 Å20 Å20 Å2
2--3.7585 Å20 Å2
3----15.7382 Å2
Refine analyzeLuzzati coordinate error obs: 0.378 Å
Refinement stepCycle: LAST / Resolution: 2.9→44.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5928 470 7 139 6544
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016606HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.129049HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3076SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes124HARMONIC2
X-RAY DIFFRACTIONt_gen_planes909HARMONIC5
X-RAY DIFFRACTIONt_it6606HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.09
X-RAY DIFFRACTIONt_other_torsion3.02
X-RAY DIFFRACTIONt_chiral_improper_torsion867SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact7364SEMIHARMONIC4
LS refinement shellResolution: 2.9→3.04 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2764 134 4.69 %
Rwork0.2382 2722 -
all0.24 2856 -
obs--92.97 %
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)
16.0852-1.9712.63553.4484-1.42062.7508-0.0514-0.3799-0.45680.54060.04660.5370.1031-0.19180.0048-0.1833-0.09430.1115-0.1914-0.0013-0.043412.265-52.5713-7.7171
23.8147-1.3532-0.48234.58160.89192.35090.14960.14840.1783-0.2602-0.21960.0318-0.4132-0.31440.07-0.2610.0393-0.1055-0.0636-0.046-0.0783-2.2835-21.1333-24.3029
31.65220.2582-0.54512.5041-0.16141.05870.0860.10570.0386-0.1809-0.0928-0.04610.05510.07530.0068-0.11310.0003-0.0411-0.0651-0.0511-0.159731.5952-35.901-28.7723
42.9609-0.2492-1.27420.1588-0.26932.1790.0144-0.21910.0730.1827-0.06260.09-0.1544-0.16220.0482-0.0908-0.01350.0614-0.13860.029-0.013721.5113-3.4419-15.4318
50.34960.30390.0690.6572-0.64360.4408-0.015-0.016-0.0761-0.0170.0133-0.0130.05910.12320.0017-0.04850.1243-0.14860.0577-0.07410.098228.0221-17.82591.2538
60.10540.04420.66580-0.86250-0.00080.02390.0123-0.06830.02850.0460.00090.0112-0.0277-0.1283-0.0980.0721-0.0797-0.07590.116516.5545-16.613-9.9021
70.0909-0.3979-1.000400.99200.00420.01810.08280.0572-0.0270.0091-0.0848-0.08060.0228-0.24060.14720.14880.00320.14910.11683.595-42.155-7.6757
800.78691.9251.118-2.46190-0.01910.0060.02450.01850.0153-0.0066-0.07220.0620.00390.06540.0962-0.09280.0157-0.03160.097415.5946-31.9942-10.8144
95.1007-0.921-1.48891.6535-0.58780.3490.0115-0.047-0.0006-0.0299-0.036-0.12650.03270.05680.0245-0.2043-0.1345-0.15120.1014-0.0870.014724.9586-14.1877-5.9177
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|1 - 128}A1 - 128
2X-RAY DIFFRACTION2{A|129 - 330}A129 - 330
3X-RAY DIFFRACTION3{A|331 - 577}A331 - 577
4X-RAY DIFFRACTION4{A|578 - 757}A578 - 757
5X-RAY DIFFRACTION5{P|1 - 4}P1 - 4
6X-RAY DIFFRACTION6{P|5 - 8}P5 - 8
7X-RAY DIFFRACTION7{T|1 - 2}T-1 - 2
8X-RAY DIFFRACTION8{T|3 - 6}T3 - 6
9X-RAY DIFFRACTION9{T|7 - 13}T7 - 13

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