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- PDB-4o0i: Crystal structure of fragment DNA polymerase I from Bacillus stea... -

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Basic information

Entry
Database: PDB / ID: 4o0i
TitleCrystal structure of fragment DNA polymerase I from Bacillus stearothermophilus with 2'-MeSe-arabino-guanosine derivatized DNA
Components
  • 5'-D(*C*(1TW)P*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'
  • DNA polymerase I
KeywordsTRANSFERASE/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 / nucleotide binding / DNA binding / metal ion binding
Similarity search - Function
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 / DNA polymerase A / DNA polymerase family A / DNA-directed DNA polymerase, family A, conserved site / DNA polymerase family A signature. ...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 / 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 / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.203 Å
AuthorsJiang, S. / Gan, J. / Sun, H. / Huang, Z.
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of fragment DNA polymerase I from Bacillus stearothermophilus with 2'-MeSe-arabino-guanosine derivatized DNA
Authors: Jiang, S. / Gan, J. / Sun, H. / Huang, Z.
History
DepositionDec 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Sep 20, 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_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_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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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
A: DNA polymerase I
B: 5'-D(*C*(1TW)P*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'
C: 5'-D(*C*(1TW)P*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,41612
Polymers73,7023
Non-polymers7149
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6050 Å2
ΔGint-118 kcal/mol
Surface area27820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.770, 93.967, 106.041
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / DNA chain , 2 types, 3 molecules ABC

#1: Protein DNA polymerase I


Mass: 66188.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: DPO1 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D9N168, DNA-directed DNA polymerase
#2: DNA chain 5'-D(*C*(1TW)P*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'


Mass: 3756.379 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: 2'-MeSe-arabino-guanosine derivatized DNA

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Non-polymers , 4 types, 247 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.93 Å3/Da / Density % sol: 58.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG3350, 0.2 M ammonium sulfate, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 3, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.203→70.328 Å / Num. all: 44457 / Num. obs: 42234 / % possible obs: 95 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.081 / Χ2: 1.034 / Net I/σ(I): 10.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.203-2.284.10.3734430.724177.9
2.28-2.374.40.33937850.738187.1
2.37-2.484.70.28541280.752194
2.48-2.615.10.2542630.857197.4
2.61-2.775.30.20543250.969198.1
2.77-2.995.60.15743341.22198.4
2.99-3.2960.12243881.256199
3.29-3.766.40.09144241.093199.2
3.76-4.736.60.06544931.174199.5
4.73-306.70.03846511.12199.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4DWI

4dwi


Resolution: 2.203→30.039 Å / Occupancy max: 1 / Occupancy min: 0.43 / FOM work R set: 0.805 / SU ML: 0.28 / σ(F): 1.44 / Phase error: 25.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2276 2125 5.04 %RANDOM
Rwork0.1763 ---
obs0.1789 42200 94.81 %-
all-44510 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 148.67 Å2 / Biso mean: 48.839 Å2 / Biso min: 20.54 Å2
Refinement stepCycle: LAST / Resolution: 2.203→30.039 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4655 449 38 238 5380
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115277
X-RAY DIFFRACTIONf_angle_d1.2587228
X-RAY DIFFRACTIONf_chiral_restr0.048800
X-RAY DIFFRACTIONf_plane_restr0.006857
X-RAY DIFFRACTIONf_dihedral_angle_d20.1142070
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.203-2.25420.4039970.27492058215573
2.2542-2.31060.29651110.25082279239082
2.3106-2.3730.26871270.24712463259088
2.373-2.44280.31451260.22742583270993
2.4428-2.52160.2651400.22142702284297
2.5216-2.61170.29661510.21392706285797
2.6117-2.71620.28621430.20932720286398
2.7162-2.83980.27081630.20322736289998
2.8398-2.98930.29241400.20192777291799
2.9893-3.17640.27351560.19462759291599
3.1764-3.42140.24451420.16742800294299
3.4214-3.76510.19261490.15792823297299
3.7651-4.30860.17861720.143528172989100
4.3086-5.42310.17341500.13382861301199
5.4231-30.04210.19451580.160829913149100
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)
12.0942-0.2986-0.40771.7712-0.08431.7185-0.0316-0.1641-0.11050.21090.0310.0070.16170.05130.00140.3660.02530.04170.26370.00230.2513-9.982-21.196247.1959
21.0014-0.31110.03961.0180.8192.0031-0.0441-0.33130.3579-0.0868-0.0643-0.0094-0.0997-0.40350.14230.387-0.05490.05920.15350.06950.2424-23.8005-2.880127.8402
30.83790.4151.99331.7781.12283.99020.04130.0634-0.004-0.51470.06940.0208-0.0625-0.1289-0.0580.551-0.07910.05590.3525-0.01910.3576-35.7461-9.317512.762
41.28260.2386-0.65461.193-0.22941.59190.11370.01960.135-0.061-0.05160.225-0.0931-0.0902-0.00940.3599-0.01430.00530.224-0.03040.3044-12.60360.377522.2772
55.7340.47061.10593.3969-1.11543.98610.52670.3709-0.7164-0.5306-0.10970.44540.2820.0151-0.41840.56380.0786-0.15940.3688-0.07020.4183-8.3382-2.2487-0.2624
61.2404-0.7828-0.81722.44560.95341.60220.07060.0065-0.0246-0.1696-0.05780.0499-0.01420.0673-0.02750.3097-0.0022-0.01630.22670.01440.2206-4.5301-3.566322.5212
72.94541.1985-0.66483.8422-1.23372.46970.0789-0.5828-0.1476-0.6443-0.0842-0.54150.74460.03420.10680.78940.0208-0.02540.66270.03130.683-26.8979-15.787318.4765
85.7529-0.58371.25772.92250.83292.56760.4662-0.0541-0.6276-0.1744-0.21610.15871.0866-0.1835-0.18020.9895-0.1044-0.00270.57780.05030.6022-28.4422-17.443820.411
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 297 through 467 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 468 through 521 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 522 through 604 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 605 through 676 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 677 through 743 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 744 through 876 )A0
7X-RAY DIFFRACTION7chain 'B' and (resid 5 through 14 )B0
8X-RAY DIFFRACTION8chain 'C' and (resid 4 through 14 )C0

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