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- PDB-4nlg: Y-family DNA polymerase chimera Dbh-Dpo4(243-245)-Dbh -

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Basic information

Entry
Database: PDB / ID: 4nlg
TitleY-family DNA polymerase chimera Dbh-Dpo4(243-245)-Dbh
Components
  • 5'-D(*GP*GP*CP*AP*CP*TP*GP*AP*TP*CP*GP*GP*G)-3'
  • 5'-D(*TP*TP*AP*CP*GP*CP*CP*CP*TP*GP*AP*TP*CP*AP*GP*TP*GP*CP*C)-3'
  • DNA polymerase IV
KeywordsTRANSFERASE/DNA / translesion synthesis / TRANSFERASE-DNA complex
Function / homology
Function and homology information


DNA-templated DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA repair / magnesium ion binding / cytoplasm
Similarity search - Function
DNA polymerase type-Y, HhH motif / IMS family HHH motif / DNA polymerase IV / : / DNA polymerase, Y-family, little finger domain / MutS, DNA mismatch repair protein, domain I - #60 / MutS, DNA mismatch repair protein, domain I / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family ...DNA polymerase type-Y, HhH motif / IMS family HHH motif / DNA polymerase IV / : / DNA polymerase, Y-family, little finger domain / MutS, DNA mismatch repair protein, domain I - #60 / MutS, DNA mismatch repair protein, domain I / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family / UmuC domain profile. / Reverse transcriptase/Diguanylate cyclase domain / Dna Ligase; domain 1 / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase IV
Similarity search - Component
Biological speciesSulfolobus acidocaldarius (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMukherjee, P. / Wilson, R.C. / Pata, J.D.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Three Residues of the Interdomain Linker Determine the Conformation and Single-base Deletion Fidelity of Y-family Translesion Polymerases.
Authors: Mukherjee, P. / Wilson, R.C. / Lahiri, I. / Pata, J.D.
History
DepositionNov 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Database references
Revision 1.2May 14, 2014Group: Database references
Revision 1.3Sep 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_asym_id / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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 IV
P: 5'-D(*GP*GP*CP*AP*CP*TP*GP*AP*TP*CP*GP*GP*G)-3'
T: 5'-D(*TP*TP*AP*CP*GP*CP*CP*CP*TP*GP*AP*TP*CP*AP*GP*TP*GP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3596
Polymers50,8123
Non-polymers5473
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-58 kcal/mol
Surface area20280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.193, 103.067, 53.049
Angle α, β, γ (deg.)90.00, 105.39, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase IV / Pol IV


Mass: 41022.805 Da / Num. of mol.: 1 / Mutation: K242R, I243K, P244S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic)
Gene: dbh, Saci_0554 / Production host: Escherichia coli (E. coli) / Strain (production host): BLR(DE3) pLysS / References: UniProt: Q4JB80, DNA-directed DNA polymerase

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DNA chain , 2 types, 2 molecules PT

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


Mass: 4032.622 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: primer DNA
#3: DNA chain 5'-D(*TP*TP*AP*CP*GP*CP*CP*CP*TP*GP*AP*TP*CP*AP*GP*TP*GP*CP*C)-3'


Mass: 5756.723 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: template DNA

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Non-polymers , 3 types, 44 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-DCP / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 3.12 Å3/Da / Density % sol: 60.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 14% PEG3350, 0.1 M calcium acetate, 5% glycerol, 0.25 M sucrose, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 24, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. all: 25089 / Num. obs: 23003 / % possible obs: 91.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 45.97 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 23.2
Reflection shellResolution: 2.4→2.43 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.191 / Mean I/σ(I) obs: 2.9 / Num. unique all: 1042 / % possible all: 80.7

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.3_1479)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4F4Y

4f4y


Resolution: 2.4→28.696 Å / SU ML: 0.32 / σ(F): 0.18 / Phase error: 27.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1161 5.15 %RANDOM
Rwork0.1739 ---
obs0.1769 22557 92.47 %-
all-24385 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→28.696 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2733 632 30 41 3436
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093508
X-RAY DIFFRACTIONf_angle_d1.184866
X-RAY DIFFRACTIONf_dihedral_angle_d20.9491407
X-RAY DIFFRACTIONf_chiral_restr0.047560
X-RAY DIFFRACTIONf_plane_restr0.005506
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.50920.32911300.25172315X-RAY DIFFRACTION81
2.5092-2.64140.31861270.24842507X-RAY DIFFRACTION86
2.6414-2.80680.32191370.23852557X-RAY DIFFRACTION89
2.8068-3.02330.28231480.22412650X-RAY DIFFRACTION92
3.0233-3.32710.24681510.1882778X-RAY DIFFRACTION96
3.3271-3.80760.22651500.17462809X-RAY DIFFRACTION97
3.8076-4.79360.20031530.14362868X-RAY DIFFRACTION99
4.7936-28.69770.19741650.1452912X-RAY DIFFRACTION99
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)
10.1791-0.78640.20243.8022.99982.83450.15640.19320.4795-0.0317-0.0337-0.4026-0.598-0.1843-0.14850.8335-0.10050.03510.4777-0.02810.508219.3314243.232122.4576
22.9486-0.54790.70442.32340.67854.7840.0076-0.0326-0.07670.14430.0748-0.32860.16630.8812-0.05590.3180.02320.00380.44880.01860.26431.4672222.097.063
32.22780.625-0.82973.349-0.05872.9973-0.13470.48861.2779-0.4740.3901-0.4495-1.37810.5549-0.2471.1782-0.2815-0.02980.83110.19830.998138.5914245.13813.5892
44.6118-0.11420.3772.83830.73275.99590.01510.29250.36150.0631-0.11630.0607-0.2775-0.07880.07830.3912-0.0130.05180.3432-0.0060.28196.1804233.795122.4076
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'P') or (chain 'T') or (chain 'A' and (resseq 403:403))
2X-RAY DIFFRACTION2chain 'A' and ((resseq 1:170))
3X-RAY DIFFRACTION3chain 'A' and ((resseq 171:245))
4X-RAY DIFFRACTION4chain 'A' and ((resseq 246:344))

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