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- PDB-4bdp: CRYSTAL STRUCTURE OF BACILLUS DNA POLYMERASE I FRAGMENT COMPLEXED... -

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Basic information

Entry
Database: PDB / ID: 4bdp
TitleCRYSTAL STRUCTURE OF BACILLUS DNA POLYMERASE I FRAGMENT COMPLEXED TO 11 BASE PAIRS OF DUPLEX DNA AFTER ADDITION OF TWO DATP RESIDUES
Components
  • DNA (5'-D(*GP*CP*AP*TP*CP*AP*TP*GP*CP*AP*A)-3')
  • DNA (5'-D(*TP*AP*TP*TP*GP*CP*AP*TP*GP*AP*TP*GP*C)-3')
  • PROTEIN (DNA POLYMERASE I)
KeywordsTRANSFERASE/DNA / BACILLUS STEAROTHERMOPHILUS DNA POLYMERASE / BF THERMOPHILUS POLYMERASE / COMPLEX (NUCLEOTIDYLTRANSFERASE-DNA) / TRANSFERASE-DNA complex
Function / homology
Function and homology information


double-strand break repair via alternative nonhomologous end joining / 3'-5' exonuclease activity / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding
Similarity search - Function
DNA polymerase I-like, H3TH domain / 5'-3' exonuclease, C-terminal SAM fold / 5'-3' exonuclease, alpha-helical arch, N-terminal / 5'-3' exonuclease, N-terminal resolvase-like domain / 5'-3' exonuclease / 5'-3' exonuclease / Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / DNA polymerase 1 / Alpha-Beta Plaits - #370 ...DNA polymerase I-like, H3TH domain / 5'-3' exonuclease, C-terminal SAM fold / 5'-3' exonuclease, alpha-helical arch, N-terminal / 5'-3' exonuclease, N-terminal resolvase-like domain / 5'-3' exonuclease / 5'-3' exonuclease / Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / DNA polymerase 1 / Alpha-Beta Plaits - #370 / 3'-5' exonuclease / 3'-5' exonuclease domain / Helix-hairpin-helix motif, class 2 / Helix-hairpin-helix class 2 (Pol1 family) motifs / 5'-3' exonuclease, C-terminal domain superfamily / DNA polymerase A / DNA polymerase family A / DNA-directed DNA polymerase, family A, conserved site / DNA polymerase family A signature. / DNA-directed DNA polymerase, family A, palm domain / DNA polymerase A domain / PIN-like domain superfamily / 5' to 3' exonuclease, C-terminal subdomain / Ribonuclease H-like superfamily/Ribonuclease H / DNA polymerase; domain 1 / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA polymerase I
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKiefer, J.R. / Mao, C. / Beese, L.S.
Citation
Journal: Nature / Year: 1998
Title: Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal.
Authors: Kiefer, J.R. / Mao, C. / Braman, J.C. / Beese, L.S.
#1: Journal: Structure / Year: 1997
Title: Crystal Structure of a Thermostable Bacillus DNA Polymerase I Large Fragment at 2.1 A Resolution
Authors: Kiefer, J.R. / Mao, C. / Hansen, C.J. / Basehore, S.L. / Hogrefe, H.H. / Braman, J.C. / Beese, L.S.
History
DepositionNov 17, 1997Processing site: NDB
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_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_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_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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _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
P: DNA (5'-D(*GP*CP*AP*TP*CP*AP*TP*GP*CP*AP*A)-3')
T: DNA (5'-D(*TP*AP*TP*TP*GP*CP*AP*TP*GP*AP*TP*GP*C)-3')
A: PROTEIN (DNA POLYMERASE I)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8618
Polymers73,5253
Non-polymers3375
Water9,980554
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.241, 93.275, 106.374
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

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DNA chain , 2 types, 2 molecules PT

#1: DNA chain DNA (5'-D(*GP*CP*AP*TP*CP*AP*TP*GP*CP*AP*A)-3')


Mass: 3342.212 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*TP*AP*TP*TP*GP*CP*AP*TP*GP*AP*TP*GP*C)-3')


Mass: 3981.608 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Protein , 1 types, 1 molecules A

#3: Protein PROTEIN (DNA POLYMERASE I) / BF


Mass: 66200.859 Da / Num. of mol.: 1 / Fragment: RESIDUES 297-876
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: P52026

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Non-polymers , 3 types, 559 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 554 / 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: 2.9 Å3/Da / Density % sol: 57.55 %
Description: LTI/SIGMA(I)> FOR THE DATA SET : 18.9 LTI/SIGMA(I)> FOR SHELL : 5.6
Crystal growpH: 5.8 / Details: pH 5.8
Crystal
*PLUS
Density % sol: 63.4 %
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Details: drop solution was mixed with an equal volume of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
255 %(v/v)satammonium sulfate1reservoir
3100 mMMES1reservoir
42.5-7.0 %(v/v)MPD1reservoir
50.02 %(w/v)sodium azide1reservoir

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Data collection

DiffractionMean temperature: 90 K
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 72444 / Num. obs: 72444 / % possible obs: 90.6 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 24.5 Å2 / Rsym value: 0.047
Reflection shellResolution: 1.8→1.83 Å / Rsym value: 0.133 / % possible all: 76.6
Reflection
*PLUS
Num. measured all: 314981 / Rmerge(I) obs: 0.047
Reflection shell
*PLUS
% possible obs: 76.6 % / Rmerge(I) obs: 0.133 / Mean I/σ(I) obs: 5.6

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BDP

2bdp


Resolution: 1.8→20 Å / Rfactor Rfree error: 0.005 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.296 3680 5.1 %RANDOM
Rwork0.248 ---
obs0.248 72346 85.9 %-
all-72346 --
Displacement parametersBiso mean: 21.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20 Å2
2---0.38 Å20 Å2
3---0.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.25 Å
Luzzati d res low-20 Å
Luzzati sigma a-0.13 Å
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4650 486 17 554 5707
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.94
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it0.751.5
X-RAY DIFFRACTIONx_mcangle_it1.282
X-RAY DIFFRACTIONx_scbond_it1.392
X-RAY DIFFRACTIONx_scangle_it2.272.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.018
RfactorNum. reflection% reflection
Rfree0.422 520 5.2 %
Rwork0.421 9491 -
obs--72.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3DNA-RNA-MULTI-ENDO.PARAMDNA-RNA-MULTI-ENDO.TOP
X-RAY DIFFRACTION4PARAM_SULFATE.TXTTOP_SULFATE.TXT
X-RAY DIFFRACTION5PARAMETER.ELEMENTS
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.94
LS refinement shell
*PLUS
Rfactor obs: 0.421

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