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

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Basic information

Entry
Database: PDB / ID: 4flv
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


nucleotide-excision repair, DNA gap filling / DNA replication proofreading / 3'-5'-DNA exonuclease activity / SOS response / base-excision repair, gap-filling / 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
Similarity search - Component
Biological speciesPyrococcus abyssi (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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: DNA polymerase 1
P: Primer strand
T: Template strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,5937
Polymers99,2573
Non-polymers3364
Water6,539363
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6610 Å2
ΔGint-32 kcal/mol
Surface area35520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.030, 115.000, 129.210
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: 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: 4047.633 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, 367 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.: 363 / 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: 2.58 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, 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: 2.7→47 Å / Num. obs: 28989 / % possible obs: 100 % / Redundancy: 4.9 % / Biso Wilson estimate: 58.09 Å2 / Rmerge(I) obs: 0.132 / Net I/σ(I): 13
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.4 / Num. unique all: 4136 / Rsym value: 0.33 / % 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
Starting model: PDB ENTRY 4FLW

4flw


Resolution: 2.7→47 Å / Cor.coef. Fo:Fc: 0.9307 / Cor.coef. Fo:Fc free: 0.9074 / SU R Cruickshank DPI: 1.21 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2149 1473 5.09 %RANDOM
Rwork0.1716 ---
obs0.1739 28934 99.94 %-
Displacement parametersBiso mean: 42.77 Å2
Baniso -1Baniso -2Baniso -3
1-4.285 Å20 Å20 Å2
2--5.508 Å20 Å2
3----9.793 Å2
Refine analyzeLuzzati coordinate error obs: 0.299 Å
Refinement stepCycle: LAST / Resolution: 2.7→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6091 481 20 363 6955
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016815HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.089313HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3218SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes143HARMONIC2
X-RAY DIFFRACTIONt_gen_planes921HARMONIC5
X-RAY DIFFRACTIONt_it6815HARMONIC20
X-RAY DIFFRACTIONt_nbd5SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.26
X-RAY DIFFRACTIONt_other_torsion3.12
X-RAY DIFFRACTIONt_chiral_improper_torsion872SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact7554SEMIHARMONIC4
LS refinement shellResolution: 2.7→2.79 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2586 151 5.44 %
Rwork0.2077 2625 -
all0.2106 2776 -
obs--99.94 %
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)
12.90630.76151.26911.66080.63581.936-0.06220.4889-0.54-0.20260.0994-0.30580.08980.1727-0.0372-0.1261-0.01020.0658-0.1063-0.0630.0396-11.3764-52.06859.531
21.96880.6024-0.10341.8653-0.48741.19470.05580.0169-0.00270.1511-0.0081-0.1168-0.2129-0.0361-0.0477-0.0618-0.0018-0.0265-0.09150.0085-0.04981.2987-22.267124.4099
32.7902-1.4174-0.97561.32872.90621.33520.01450.3380.0104-0.10190.0151-0.105-0.38980.0232-0.0296-0.0205-0.00070.0487-0.10450.0888-0.0174-27.6359-38.678315.8337
40.99320.2727-0.08832.01110.08710.58090.0355-0.0806-0.04130.2106-0.08910.1886-0.0124-0.04250.0537-0.0526-0.03690.0177-0.07350.0097-0.0403-34.594-34.898832.6016
51.7463-0.1563-1.25170.2490.43382.09690.10820.23530.0544-0.1157-0.0742-0.0227-0.17850.0299-0.034-0.05510.03970.0225-0.10620.0042-0.0247-21.361-3.533315.8611
60.44050.41020.26411.0819-1.58671.8129-0.00250.0905-0.13890.02130.00620.10430.0538-0.11-0.0037-0.110.0764-0.01-0.0191-0.01510.0788-23.6416-16.53432.4167
70.0507-0.02190.96120-1.77330.051-0.01010.03530.0672-0.11360.0578-0.0454-0.0171-0.1087-0.0478-0.01990.00470.0443-0.03820.00540.109-7.7441-15.3518.7171
80.0799-0.25211.57172.17580.98420.2585-0.00680.01670.0548-0.02760.0121-0.0476-0.0455-0.0445-0.00530.23780.00370.03730.28660.04270.2908-12.1745-37.05229.1861
93.7332.8873-0.48062.29880.89661.0095-0.0091-0.0337-0.07870.0973-0.01990.15580.0535-0.07750.0289-0.13810.152-0.082-0.06020.02770.0961-24.3852-15.26576.9996
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 - 347}A135 - 347
3X-RAY DIFFRACTION3{A|348 - 394}A348 - 394
4X-RAY DIFFRACTION4{A|395 - 575}A395 - 575
5X-RAY DIFFRACTION5{A|576 - 757}A576 - 757
6X-RAY DIFFRACTION6{P|1 - 7}P1 - 7
7X-RAY DIFFRACTION7{P|8 - 11}P8 - 11
8X-RAY DIFFRACTION8{T|1 - 5}T1 - 5
9X-RAY DIFFRACTION9{T|6 - 13}T6 - 13

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