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- PDB-4fm1: Pyrococcus abyssi B family DNA polymerase bound to a dsDNA, in ed... -

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Basic information

Entry
Database: PDB / ID: 4fm1
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


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: 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_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_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)98,6277
Polymers98,2303
Non-polymers3974
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-29 kcal/mol
Surface area35840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.070, 114.220, 128.190
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 / 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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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 / Transcription (biology)


Mass: 4008.594 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, 260 molecules

#4: 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
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.57 Å3/Da / Density % sol: 52.21 %
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: 1.89231 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 7, 2010
RadiationMonochromator: channel cut cryogenically cooled monochromator crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.89231 Å / Relative weight: 1
ReflectionResolution: 3→44.01 Å / Num. all: 505777 / % possible obs: 92.7 % / Redundancy: 2.6 % / Biso Wilson estimate: 59.7 Å2 / Rmerge(I) obs: 0.147 / Net I/σ(I): 6.9
Reflection shellResolution: 3→3.16 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2844 / Rsym value: 0.38 / % possible all: 95.1

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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→44.01 Å / Cor.coef. Fo:Fc: 0.9175 / Cor.coef. Fo:Fc free: 0.861 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.226 988 5.15 %RANDOM
Rwork0.1648 ---
obs0.1677 19178 91.52 %-
Displacement parametersBiso mean: 36.55 Å2
Baniso -1Baniso -2Baniso -3
1-8.4371 Å20 Å20 Å2
2--4.162 Å20 Å2
3----12.5991 Å2
Refine analyzeLuzzati coordinate error obs: 0.313 Å
Refinement stepCycle: LAST / Resolution: 3→44.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6043 426 20 256 6745
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016676HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.129120HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3135SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes143HARMONIC2
X-RAY DIFFRACTIONt_gen_planes912HARMONIC5
X-RAY DIFFRACTIONt_it6676HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.2
X-RAY DIFFRACTIONt_other_torsion3.22
X-RAY DIFFRACTIONt_chiral_improper_torsion861SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact7413SEMIHARMONIC4
LS refinement shellResolution: 3→3.16 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2913 162 5.7 %
Rwork0.1975 2680 -
all0.2028 2842 -
obs--91.52 %
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)
11.2761-0.93780.25351.6591-0.25370.2786-0.0101-0.0512-0.07570.070.01890.1843-0.0155-0.0661-0.0089-0.03740.00910.0508-0.1091-0.0006-0.09574.3291-40.791-14.0539
23.1694-0.85120.00172.38850.23010.63190.1171-0.06630.2043-0.0049-0.1342-0.1398-0.1240.0980.0171-0.0155-0.00520.0012-0.0934-0.0052-0.12951.4148-21.0744-24.2724
31.0468-0.0944-0.15311.7136-0.2830.71330.12290.03170.0982-0.0255-0.1201-0.12640.02190.0864-0.0028-0.01720.01590.0078-0.0787-0.0298-0.138331.2116-35.8294-27.4063
41.146-0.2567-0.89680.3057-0.30191.90260.0607-0.0917-0.03650.0778-0.13150.0407-0.0606-0.02970.0708-0.0368-0.03560.0057-0.092-0.0041-0.073422.7941-5.8183-18.5367
50.2442-1.10712.36600.33810.9790.02370.0179-0.0493-0.0539-0.0223-0.0860.12870.0074-0.00140.0012-0.1287-0.00540.0028-0.00560.012222.4035-16.6143-4.2861
60-2.07130.98240.38331.10930.193-0.0085-0.00370.09460.0493-0.06440.0672-0.0098-0.03890.0729-0.1299-0.00830.1008-0.13160.07420.10369.9379-38.5806-6.7659
70.9074-2.90051.56180.3238-0.71728.28670.01890.0797-0.0691-0.199-0.0521-0.02260.22830.02780.0332-0.114-0.14670.03010.1083-0.02070.033923.4788-16.5675-7.4147
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|0 - 202}A0 - 202
2X-RAY DIFFRACTION2{A|203 - 330}A203 - 330
3X-RAY DIFFRACTION3{A|331 - 557}A331 - 557
4X-RAY DIFFRACTION4{A|558 - 757}A558 - 757
5X-RAY DIFFRACTION5{P|1 - 8}P1 - 8
6X-RAY DIFFRACTION6{T|1 - 4}T1 - 4
7X-RAY DIFFRACTION7{T|5 - 13}T5 - 13

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