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- PDB-1unn: Complex of beta-clamp processivity factor and little finger domai... -

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Basic information

Entry
Database: PDB / ID: 1unn
TitleComplex of beta-clamp processivity factor and little finger domain of PolIV
Components
  • DNA POLYMERASE III BETA SUBUNIT
  • DNA POLYMERASE IV
KeywordsBETA-CLAMP / POL IV / TRANSLESION / TRANSFERASE / DNA-DIRECTED DNA POLYMERASE / DNA REPLICATION
Function / homology
Function and homology information


Hda-beta clamp complex / bacterial-type DNA replication / replication inhibiting complex / DNA polymerase III complex / SOS response / replisome / regulation of DNA-templated DNA replication initiation / error-free translesion synthesis / DNA synthesis involved in DNA repair / DNA strand elongation involved in DNA replication ...Hda-beta clamp complex / bacterial-type DNA replication / replication inhibiting complex / DNA polymerase III complex / SOS response / replisome / regulation of DNA-templated DNA replication initiation / error-free translesion synthesis / DNA synthesis involved in DNA repair / DNA strand elongation involved in DNA replication / error-prone translesion synthesis / negative regulation of DNA-templated DNA replication initiation / 3'-5' exonuclease activity / DNA-templated DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA replication / DNA damage response / magnesium ion binding / protein homodimerization activity / DNA binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
DNA Polymerase III; Chain A, domain 2 / DNA Polymerase III, subunit A, domain 2 / : / DNA polymerase-iota, thumb domain / DNA polymerase III, beta sliding clamp / DNA polymerase III, beta sliding clamp, N-terminal / DNA polymerase III, beta sliding clamp, C-terminal / DNA polymerase III, beta sliding clamp, central / DNA polymerase III beta subunit, N-terminal domain / DNA polymerase III beta subunit, central domain ...DNA Polymerase III; Chain A, domain 2 / DNA Polymerase III, subunit A, domain 2 / : / DNA polymerase-iota, thumb domain / DNA polymerase III, beta sliding clamp / DNA polymerase III, beta sliding clamp, N-terminal / DNA polymerase III, beta sliding clamp, C-terminal / DNA polymerase III, beta sliding clamp, central / DNA polymerase III beta subunit, N-terminal domain / DNA polymerase III beta subunit, central domain / DNA polymerase III beta subunit, C-terminal domain / DNA polymerase III beta subunit / DNA polymerase IV / : / DNA polymerase, Y-family, little finger domain / : / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family / UmuC domain profile. / Dna Ligase; domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Roll / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Beta sliding clamp / Beta sliding clamp / DNA polymerase IV
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBunting, K.A. / Roe, S.M. / Pearl, L.H.
CitationJournal: Embo J. / Year: 2003
Title: Structural Basis for Recruitment of Translesion DNA Polymerase Pol Iv/Dinb to the Beta-Clamp
Authors: Bunting, K.A. / Roe, S.M. / Pearl, L.H.
History
DepositionSep 11, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2003Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA POLYMERASE III BETA SUBUNIT
B: DNA POLYMERASE III BETA SUBUNIT
C: DNA POLYMERASE IV
D: DNA POLYMERASE IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,5666
Polymers108,3744
Non-polymers1922
Water17,060947
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)146.451, 70.117, 110.916
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2034-

HOH

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Components

#1: Protein DNA POLYMERASE III BETA SUBUNIT


Mass: 40630.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PET17B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834DE3
References: UniProt: P00583, UniProt: P0A988*PLUS, DNA-directed DNA polymerase
#2: Protein DNA POLYMERASE IV / POL IV


Mass: 13556.599 Da / Num. of mol.: 2 / Fragment: LITTLE FINGER, RESIDUES 243-351
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PET11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834DE3 / References: UniProt: Q47155, DNA-directed DNA polymerase
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 947 / 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: 2.4 Å3/Da / Density % sol: 48.28 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: CRYSTALS WERE OBTAINED USING HANGING DROP METHOD AT 14C. WELL CONSISTED OF 1.2M AMMONIUM SULPHATE, 50MM SODIUM ACETATE PH 4.6. 2UL DROP CONSISTED OF 1UL WELL SOLUTION PLUS 1UL PROTEIN ...Details: CRYSTALS WERE OBTAINED USING HANGING DROP METHOD AT 14C. WELL CONSISTED OF 1.2M AMMONIUM SULPHATE, 50MM SODIUM ACETATE PH 4.6. 2UL DROP CONSISTED OF 1UL WELL SOLUTION PLUS 1UL PROTEIN SOLUTION (50MM HEPES PH7.0, 2MM MAGNESIUM CHLORIDE, 200MM SODIUM CHLORIDE AND PROTEIN AT 6MG/ML).
Crystal grow
*PLUS
Temperature: 14 ℃ / pH: 4.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
16 mg/mlprotein1drop
21.2 Mammonium sulfate1reservoir
350 mMsodium acetate1reservoirpH4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.9→100 Å / Num. obs: 90134 / % possible obs: 96.5 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.3
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.201 / Mean I/σ(I) obs: 3.5 / % possible all: 87.4
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 62.1 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 87.4 % / Redundancy: 2.7 % / Num. unique obs: 12565 / Rmerge(I) obs: 0.201 / Mean I/σ(I) obs: 3.5

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2POL

2pol


Resolution: 1.9→62.1 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.914 / SU B: 2.981 / SU ML: 0.09 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24 4388 5 %RANDOM
Rwork0.179 ---
obs-83223 96.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 21.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20 Å20 Å2
2--0.4 Å20 Å2
3----1.07 Å2
Refinement stepCycle: LAST / Resolution: 1.9→62.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7528 0 10 947 8485
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.0217671
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.7121.96910377
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0125951
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.3010.21175
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.025792
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2540.24569
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2060.2992
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3780.2124
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2360.236
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6311.54759
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.79227682
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.66432912
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.4874.52695
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: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.254 289
Rwork0.199 5475
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)
10.35190.1518-0.17110.07130.07990.55040.02860.03460.0365-0.07080.00570.0247-0.0248-0.1563-0.03420.12580.09140.00320.07240.03290.156550.56110.27218.014
20.34190.008-0.01910.14610.14920.28780.013-0.0844-0.0011-0.11870.0090.017-0.08130.0627-0.0220.13210.02680.00750.05590.00380.145684.49523.27532.543
30.24580.3086-0.41250.2303-0.07561.5476-0.03460.2280.0197-0.00320.0492-0.01220.15290.1081-0.01450.090.03760.05490.1622-0.01290.095290.66718.813-19.167
40.647-0.0994-0.37350.07650.00441.0305-0.0714-0.2008-0.00780.0116-0.00410.03270.09340.15910.07550.07090.03550.01650.13730.04240.145849.3532.63969.663
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 366
2X-RAY DIFFRACTION2B1 - 366
3X-RAY DIFFRACTION3C241 - 351
4X-RAY DIFFRACTION4D240 - 351
Refinement
*PLUS
Lowest resolution: 62.1 Å / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS

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