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- PDB-2y1j: CRYSTAL STRUCTURE OF A R-DIASTEREOMER ANALOGUE OF THE SPORE PHOTO... -

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Basic information

Entry
Database: PDB / ID: 2y1j
TitleCRYSTAL STRUCTURE OF A R-DIASTEREOMER ANALOGUE OF THE SPORE PHOTOPRODUCT IN COMPLEX WITH FRAGMENT DNA POLYMERASE I FROM BACILLUS STEAROTHERMOPHILUS
Components
  • 5'-D(*AP*GP*GP*GP*QBTP*THM*GP*GP*TP*CP)-3'
  • 5'-D(*GP*AP*CP*CP*AP*AP*CP*CP*CP*TP)-3'
  • DNA POLYMERASE I
KeywordsTRANSFERASE/DNA / TRANSFERASE-DNA COMPLEX / DNA REPAIR / SPORE PHOTOPRODUCT / PHOTOLESION / UV LESION / 5-THYMINYL-5 / 6-DIHYDROTHYMINE
Function / homology
Function and homology information


3'-5' exonuclease activity / DNA-templated DNA replication / double-strand break repair / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / metal ion binding
Similarity search - Function
: / DNA polymerase I, ribonuclease H-like domain / DNA polymerase 1 / Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / Alpha-Beta Plaits - #370 / 3'-5' exonuclease / 3'-5' exonuclease domain / DNA polymerase A / DNA polymerase family A ...: / DNA polymerase I, ribonuclease H-like domain / DNA polymerase 1 / Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / 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 polymerase I
Similarity search - Component
Biological speciesGEOBACILLUS STEAROTHERMOPHILUS (bacteria)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsHeil, K. / Schneider, S. / Mueller, M. / Kneuttinger, A.C. / Carell, T.
CitationJournal: Chemistry / Year: 2011
Title: Crystal Structures and Repair Studies Reveal the Identity and the Base-Pairing Properties of the Uv-Induced Spore Photoproduct DNA Lesion.
Authors: Heil, K. / Kneuttinger, A.C. / Schneider, S. / Lischke, U. / Carell, T.
History
DepositionDec 8, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2011Group: Database references
Revision 2.0May 15, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Polymer sequence
Category: chem_comp / entity_poly ...chem_comp / entity_poly / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / struct_biol / struct_site / struct_site_gen
Item: _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can ..._chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 3.0Jun 22, 2022Group: Data collection / Database references ...Data collection / Database references / Other / Polymer sequence
Category: chem_comp / database_2 ...chem_comp / database_2 / entity_poly / pdbx_database_status
Item: _chem_comp.mon_nstd_flag / _chem_comp.type ..._chem_comp.mon_nstd_flag / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.status_code_sf
Revision 3.1Dec 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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(*GP*AP*CP*CP*AP*AP*CP*CP*CP*TP)-3'
C: 5'-D(*AP*GP*GP*GP*QBTP*THM*GP*GP*TP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,4065
Polymers72,2143
Non-polymers1922
Water3,009167
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-35.8 kcal/mol
Surface area28100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.525, 93.382, 105.773
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA POLYMERASE I


Mass: 66201.984 Da / Num. of mol.: 1 / Fragment: RESIDUES 297-876
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GEOBACILLUS STEAROTHERMOPHILUS (bacteria)
Strain: DSM 22 / Description: GERMAN COLLECTION OF MICROORGANISMS (DSM) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: D7D223, UniProt: E1C9K5*PLUS, DNA-directed DNA polymerase
#2: DNA chain 5'-D(*GP*AP*CP*CP*AP*AP*CP*CP*CP*TP)-3'


Mass: 2973.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: DNA chain 5'-D(*AP*GP*GP*GP*QBTP*THM*GP*GP*TP*CP)-3'


Mass: 3038.075 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE ENTRY ABOVE IS NOT FROM STRAIN DSM22, BUT HAS MAXIMUM IDENTITY. ONLY T550 IS S IN OUR SEQUENCE.

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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: 3.31 Å3/Da / Density % sol: 62.91 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 47859 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.9
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3.7 / % possible all: 96

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1U45

1u45


Resolution: 2.15→46.84 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.908 / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.24103 2383 5 %RANDOM
Rwork0.19852 ---
obs0.20061 45357 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.394 Å2
Baniso -1Baniso -2Baniso -3
1-2.1 Å20 Å20 Å2
2---1.18 Å20 Å2
3----0.92 Å2
Refinement stepCycle: LAST / Resolution: 2.15→46.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4650 401 10 167 5228
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225189
X-RAY DIFFRACTIONr_bond_other_d00.023474
X-RAY DIFFRACTIONr_angle_refined_deg1.5292.0747096
X-RAY DIFFRACTIONr_angle_other_deg4.0122.9998479
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4295579
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.59724.105229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.86415878
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6891540
X-RAY DIFFRACTIONr_chiral_restr0.0930.2796
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215429
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02979
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8471.52898
X-RAY DIFFRACTIONr_mcbond_other01.51160
X-RAY DIFFRACTIONr_mcangle_it1.60124672
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.54432291
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.1764.52424
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.153→2.209 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 143 -
Rwork0.246 3063 -
obs--92.07 %

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