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

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Basic information

Entry
Database: PDB / ID: 4flx
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: 2.9 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_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
Revision 1.4Nov 6, 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)98,6828
Polymers98,2543
Non-polymers4285
Water7,927440
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5520 Å2
ΔGint-26 kcal/mol
Surface area35860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.070, 114.390, 128.130
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: 4032.619 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 , 4 types, 445 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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 440 / 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: 2.58 Å3/Da / Density % sol: 52.25 %
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: 2.9→44 Å / Num. obs: 22777 / % possible obs: 98.8 % / Redundancy: 3.5 % / Biso Wilson estimate: 55.08 Å2 / Rmerge(I) obs: 0.151 / Net I/σ(I): 8.8
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.4 / Num. unique all: 3297 / Rsym value: 0.31 / % possible all: 99.5

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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 Å / Cor.coef. Fo:Fc: 0.9224 / Cor.coef. Fo:Fc free: 0.8788 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2112 1171 5.15 %RANDOM
Rwork0.1603 ---
obs0.1631 22744 98.19 %-
Displacement parametersBiso mean: 33.4 Å2
Baniso -1Baniso -2Baniso -3
1-8.4928 Å20 Å20 Å2
2--2.682 Å20 Å2
3----11.1747 Å2
Refine analyzeLuzzati coordinate error obs: 0.287 Å
Refinement stepCycle: LAST / Resolution: 2.9→44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6124 428 26 440 7018
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016787HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.129258HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3214SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes151HARMONIC2
X-RAY DIFFRACTIONt_gen_planes919HARMONIC5
X-RAY DIFFRACTIONt_it6787HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.2
X-RAY DIFFRACTIONt_other_torsion3.14
X-RAY DIFFRACTIONt_chiral_improper_torsion865SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact7637SEMIHARMONIC4
LS refinement shellResolution: 2.9→3.04 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2866 168 5.58 %
Rwork0.1851 2841 -
all0.1909 3009 -
obs--98.19 %
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)
12.887-1.20841.38731.3731-0.73051.3543-0.1019-0.4176-0.31250.27490.19560.240.0176-0.2266-0.0937-0.0412-0.00360.0448-0.0885-0.0018-0.04711.7574-52.0616-7.8083
21.6767-0.7126-0.29152.25470.26330.68290.10920.04280.1198-0.1481-0.05330.0596-0.107-0.0505-0.056-0.08820.0175-0.0008-0.0747-0.0218-0.0741-0.9903-22.4765-24.3831
37.32351.9683-1.16220.2033-0.842.2260.0204-0.27840.07390.0740.09640.2331-0.3920.1517-0.11680.146-0.00990.0053-0.0447-0.0221-0.13326.9265-40.0035-14.7751
40.6907-0.2751-0.12281.6198-0.1280.68040.12850.13940.0607-0.1946-0.1359-0.2803-0.01480.03960.0073-0.03270.04260.0096-0.06820.0109-0.070334.8607-33.9867-32.1282
51.6008-0.1994-1.37890.2902-0.31471.8050.0641-0.150.01980.0806-0.0748-0.0214-0.21970.00430.0107-0.0718-0.03690.0196-0.07-0.0257-0.04921.32-3.3061-16.0861
62.63280.8441-0.31630.73962.34261.69250.00280.0208-0.2376-0.0047-0.1125-0.29960.0283-0.02970.1097-0.0178-0.1141-0.0192-0.1016-0.00870.089722.3229-16.5302-4.5326
70-2.02320.40710.89671.60120.002-0.00880.03560.16120.0172-0.0260.0107-0.1327-0.02610.0348-0.11820.00840.0937-0.1335-0.0790.1519.9555-38.72-7.0169
82.0959-2.9104-1.1320.9806-2.3328.31550.00110.1036-0.1538-0.1636-0.0398-0.09040.23110.06520.0386-0.2576-0.11950.03660.1469-0.02440.069923.4911-16.5039-7.6387
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|-1 - 126}A-1 - 126
2X-RAY DIFFRACTION2{A|127 - 348}A127 - 348
3X-RAY DIFFRACTION3{A|349 - 391}A349 - 391
4X-RAY DIFFRACTION4{A|392 - 575}A392 - 575
5X-RAY DIFFRACTION5{A|576 - 757}A576 - 757
6X-RAY DIFFRACTION6{P|1 - 8}P1 - 8
7X-RAY DIFFRACTION7{T|1 - 4}T1 - 4
8X-RAY DIFFRACTION8{T|5 - 13}T5 - 13

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