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- PDB-4fm0: Pyrococcus abyssi B family DNA polymerase bound to a dsDNA, in ed... -

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Basic information

Entry
Database: PDB / ID: 4fm0
TitlePyrococcus abyssi B family DNA polymerase bound to a dsDNA, in edition mode
Components
  • DNA polymerase 1DNA polymerase I
  • Primer strand
  • Template strandTranscription (biology)
KeywordsTRANSFERASE/DNA / DNA polymerase / DNA binding / TRANSFERASE-DNA complex
Function / homology
Function and homology information


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
Similarity search - Component
Biological speciesPyrococcus abyssi (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.12 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

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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)99,0296
Polymers98,8893
Non-polymers1413
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-41 kcal/mol
Surface area34880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.610, 114.720, 128.090
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 / Transcription (biology)


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 / DNA polymerase I / 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, 90 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 / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.59 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, 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: 0.98011 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 5, 2010
RadiationMonochromator: channel cut cryogenically cooled monochromator crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 3.1→43 Å / Num. obs: 18760 / % possible obs: 99.5 % / Redundancy: 3.9 % / Biso Wilson estimate: 96.51 Å2 / Rmerge(I) obs: 0.131 / Net I/σ(I): 8.4
Reflection shellResolution: 3.12→3.29 Å / Redundancy: 4 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.4 / Num. unique all: 2699 / Rsym value: 0.36 / % possible all: 99.8

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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: 3.12→31.32 Å / Cor.coef. Fo:Fc: 0.9307 / Cor.coef. Fo:Fc free: 0.8963 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2082 965 5.16 %RANDOM
Rwork0.1772 ---
obs0.1788 18715 99.25 %-
Displacement parametersBiso mean: 69.09 Å2
Baniso -1Baniso -2Baniso -3
1-8.5701 Å20 Å20 Å2
2--3.3274 Å20 Å2
3----11.8975 Å2
Refine analyzeLuzzati coordinate error obs: 0.522 Å
Refinement stepCycle: LAST / Resolution: 3.12→31.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5894 462 8 87 6451
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016555HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.118986HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3034SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes114HARMONIC2
X-RAY DIFFRACTIONt_gen_planes910HARMONIC5
X-RAY DIFFRACTIONt_it6555HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3
X-RAY DIFFRACTIONt_other_torsion2.91
X-RAY DIFFRACTIONt_chiral_improper_torsion866SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact7100SEMIHARMONIC4
LS refinement shellResolution: 3.12→3.31 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2981 158 5.26 %
Rwork0.2235 2843 -
all0.2273 3001 -
obs--99.25 %
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)
14.1155-1.34992.29252.6126-1.26963.77810.0383-0.2548-0.53930.2850.05560.30870.3684-0.1217-0.0939-0.1167-0.04290.1112-0.167-0.0367-0.092311.9743-52.0754-8.9362
22.904-1.6407-0.33093.37060.29641.72220.13630.11080.3239-0.1535-0.0548-0.0805-0.2258-0.1394-0.0815-0.1102-0.0108-0.0529-0.0904-0.0277-0.0941-0.5084-22.7804-24.06
32.58270.5625-0.91052.518-2.91041.64560.1268-0.1850.15640.1366-0.12020.0901-0.35320.1981-0.00660.0123-0.03110.0703-0.0958-0.152-0.191830.4774-33.7256-19.0628
42.57210.0133-0.75533.16920.35552.55070.14730.0639-0.1064-0.1598-0.0572-0.15180.21420.2195-0.0901-0.08340.02520.0133-0.1092-0.0355-0.116432.1707-41.7249-28.101
52.5708-1.2805-0.85536.68032.02814.35650.05490.1103-0.0556-0.4114-0.2969-0.06020.34090.21410.242-0.093-0.03870.0727-0.12540.0473-0.071837.687-21.6092-38.1774
63.5759-0.188-2.60950.1991-0.57033.8070.1659-0.45970.33370.3026-0.0704-0.0909-0.38730.1305-0.0955-0.0088-0.06150.1208-0.1165-0.066-0.051920.0573-1.8341-12.6507
70.68950.02350.10050.9932-2.91041.8615-0.0212-0.0226-0.09310.04130.0140.010.13090.1680.0072-0.2170.0188-0.1520.1568-0.10160.115328.5278-17.74331.2314
80.69080.11770.64710.5085-1.01620.0836-0.0001-0.00410.07810.04510.07870.0114-0.0160.0155-0.0786-0.0851-0.1520.02660.0464-0.0531-0.003516.8414-16.7372-9.9027
90.0821-1.57490.9660-0.657800.00330.0820.0954-0.03240.00080.1922-0.0608-0.1863-0.0042-0.23080.1520.1520.14020.1194-0.12273.7327-42.0632-8.1263
1002.91040.19960.0274-2.91040-0.0180.03580.0482-0.0302-0.0121-0.03350.01590.07150.03010.0489-0.152-0.10840.1162-0.05670.136916.9606-31.6822-11.2471
113.54040.4985-2.792701.58930.12130.0306-0.00450.0145-0.0958-0.0807-0.10240.03350.12940.0501-0.1837-0.1090.08120.1259-0.0961-0.020825.5731-15.5986-9.7027
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 - 355}A134 - 355
3X-RAY DIFFRACTION3{A|356 - 404}A356 - 404
4X-RAY DIFFRACTION4{A|405 - 520}A405 - 520
5X-RAY DIFFRACTION5{A|521 - 599}A521 - 599
6X-RAY DIFFRACTION6{A|600 - 757}A600 - 757
7X-RAY DIFFRACTION7{P|1 - 4}P1 - 4
8X-RAY DIFFRACTION8{P|5 - 8}P5 - 8
9X-RAY DIFFRACTION9{T|1 - 4}T1 - 4
10X-RAY DIFFRACTION10{T|5 - 8}T5 - 8
11X-RAY DIFFRACTION11{T|9 - 13}T9 - 13

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