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- PDB-6juq: mutant PolIV-DNA incoming nucleotide complex 2 -

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Basic information

Entry
Database: PDB / ID: 6juq
Titlemutant PolIV-DNA incoming nucleotide complex 2
Components
  • (DNA polymerase ...) x 2
  • DNA (5'-D(P*CP*TP*GP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
  • DNA (5'-D(P*GP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
  • DNA (5'-D(P*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
KeywordsREPLICATION/DNA / DNA polymerase / REPLICATION / REPLICATION-DNA complex
Function / homology
Function and homology information


SOS response / error-free translesion synthesis / DNA synthesis involved in DNA repair / error-prone translesion synthesis / DNA-templated DNA replication / DNA-directed DNA polymerase / damaged DNA binding / DNA-directed DNA polymerase activity / DNA damage response / magnesium ion binding ...SOS response / error-free translesion synthesis / DNA synthesis involved in DNA repair / error-prone translesion synthesis / DNA-templated DNA replication / DNA-directed DNA polymerase / damaged DNA binding / DNA-directed DNA polymerase activity / DNA damage response / magnesium ion binding / cytosol / cytoplasm
Similarity search - Function
: / DNA polymerase-iota, thumb domain / 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 / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain ...: / DNA polymerase-iota, thumb domain / 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 / 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. / 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
Chem-2TM / : / DNA / DNA (> 10) / DNA polymerase IV / DNA polymerase IV
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 Å
AuthorsNair, D.T. / Johnson, M.K.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (India)Intramural India
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: A polar filter in DNA polymerases prevents ribonucleotide incorporation.
Authors: Johnson, M.K. / Kottur, J. / Nair, D.T.
History
DepositionApr 15, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Derived calculations
Category: pdbx_struct_assembly_gen / pdbx_struct_assembly_prop ...pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / struct_conn
Item: _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value
Revision 1.2Nov 22, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: DNA polymerase IV
G: DNA (5'-D(P*CP*TP*GP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
H: DNA (5'-D(P*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
A: DNA polymerase IV
B: DNA (5'-D(P*CP*TP*GP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
C: DNA (5'-D(P*GP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,11912
Polymers95,9376
Non-polymers1,1826
Water25214
1
F: DNA polymerase IV
G: DNA (5'-D(P*CP*TP*GP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
H: DNA (5'-D(P*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4246
Polymers47,8333
Non-polymers5913
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-46 kcal/mol
Surface area20670 Å2
MethodPISA
2
A: DNA polymerase IV
B: DNA (5'-D(P*CP*TP*GP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
C: DNA (5'-D(P*GP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6966
Polymers48,1053
Non-polymers5913
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-50 kcal/mol
Surface area21380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.151, 57.244, 110.793
Angle α, β, γ (deg.)90.00, 92.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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DNA polymerase ... , 2 types, 2 molecules FA

#1: Protein DNA polymerase IV / Pol IV


Mass: 38346.426 Da / Num. of mol.: 1 / Mutation: F13A, T43C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: dinB, dbh, dinB_1, dinB_2, A8C65_11955, A9R57_12995, ACU57_05495, AML35_26730, AUQ13_19210, BANRA_02184, BANRA_03427, BET08_31995, BHS87_01175, BJJ90_21040, BMT91_15875, BUE81_28425, C5N07_ ...Gene: dinB, dbh, dinB_1, dinB_2, A8C65_11955, A9R57_12995, ACU57_05495, AML35_26730, AUQ13_19210, BANRA_02184, BANRA_03427, BET08_31995, BHS87_01175, BJJ90_21040, BMT91_15875, BUE81_28425, C5N07_13800, C9E25_22940, CA593_02435, CRM83_14635, CV83915_01335, CWS33_23695, D0X26_15110, D2185_22400, D3O91_23685, D3Y67_06560, D9D20_20085, D9D69_23735, D9E22_12045, D9F57_19765, D9H66_20200, D9H68_19465, D9I18_13635, D9J11_18290, D9J11_27145, D9J44_21795, DNQ41_05075, DTL43_23485, EAI44_14085, EAI52_15440, EC1094V2_3597, EC3234A_186c00130, EC3426_01008, EC382_20155, EC382_27145, ECTO6_03825, EEP23_17825, EFV02_01800, EFV04_12320, EFV12_23405, EFV17_17010, ERS085365_04420, ERS139211_04423, ERS150873_03537, HW43_04975, NCTC10865_04963, NCTC11022_04998, NCTC11126_03759, NCTC13148_06847, NCTC13462_02133, NCTC8985_02971, NCTC9037_04075, NCTC9045_04586, NCTC9058_02901, NCTC9062_04328, NCTC9073_03243, NCTC9117_04957, NCTC9706_01202, RK56_027425, SAMEA3472043_03017, SAMEA3472047_03125, SAMEA3472070_01946, SAMEA3484427_04943, SAMEA3484429_04916, SAMEA3752557_00095, SAMEA3752559_04620, SAMEA3753300_00345, SK85_00262, WQ89_22460, WR15_21380
Production host: Escherichia coli (E. coli)
References: UniProt: W8STT9, UniProt: Q47155*PLUS, DNA-directed DNA polymerase
#4: Protein DNA polymerase IV / Pol IV


Mass: 38289.375 Da / Num. of mol.: 1 / Mutation: F13A, T43C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: dinB, dbh, dinB_1, dinB_2, A8C65_11955, A9R57_12995, ACU57_05495, AML35_26730, AUQ13_19210, BANRA_02184, BANRA_03427, BET08_31995, BHS87_01175, BJJ90_21040, BMT91_15875, BUE81_28425, C5N07_ ...Gene: dinB, dbh, dinB_1, dinB_2, A8C65_11955, A9R57_12995, ACU57_05495, AML35_26730, AUQ13_19210, BANRA_02184, BANRA_03427, BET08_31995, BHS87_01175, BJJ90_21040, BMT91_15875, BUE81_28425, C5N07_13800, C9E25_22940, CA593_02435, CRM83_14635, CV83915_01335, CWS33_23695, D0X26_15110, D2185_22400, D3O91_23685, D3Y67_06560, D9D20_20085, D9D69_23735, D9E22_12045, D9F57_19765, D9H66_20200, D9H68_19465, D9I18_13635, D9J11_18290, D9J11_27145, D9J44_21795, DNQ41_05075, DTL43_23485, EAI44_14085, EAI52_15440, EC1094V2_3597, EC3234A_186c00130, EC3426_01008, EC382_20155, EC382_27145, ECTO6_03825, EEP23_17825, EFV02_01800, EFV04_12320, EFV12_23405, EFV17_17010, ERS085365_04420, ERS139211_04423, ERS150873_03537, HW43_04975, NCTC10865_04963, NCTC11022_04998, NCTC11126_03759, NCTC13148_06847, NCTC13462_02133, NCTC8985_02971, NCTC9037_04075, NCTC9045_04586, NCTC9058_02901, NCTC9062_04328, NCTC9073_03243, NCTC9117_04957, NCTC9706_01202, RK56_027425, SAMEA3472043_03017, SAMEA3472047_03125, SAMEA3472070_01946, SAMEA3484427_04943, SAMEA3484429_04916, SAMEA3752557_00095, SAMEA3752559_04620, SAMEA3753300_00345, SK85_00262, WQ89_22460, WR15_21380
Production host: Escherichia coli (E. coli)
References: UniProt: W8STT9, UniProt: Q47155*PLUS, DNA-directed DNA polymerase

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DNA chain , 3 types, 4 molecules GBHC

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


Mass: 5204.359 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#3: DNA chain DNA (5'-D(P*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')


Mass: 4281.779 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#5: DNA chain DNA (5'-D(P*GP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')


Mass: 4610.984 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)

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Non-polymers , 3 types, 20 molecules

#6: Chemical ChemComp-2TM / 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine / CMPcPP


Mass: 481.184 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H18N3O13P3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.85 Å3/Da / Density % sol: 56.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.7 / Details: MDP 1%, Phosphate buffer ph 4.7 / PH range: 4.4-5.1

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0723 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 2.74→86.01 Å / Num. obs: 28806 / % possible obs: 99.5 % / Redundancy: 6.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.104 / Net I/σ(I): 8.9
Reflection shellResolution: 2.74→2.89 Å / Redundancy: 6.7 % / Num. unique obs: 4105 / CC1/2: 0.475 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
MOSFLMdata reduction
SCALAdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IRC

4irc


Resolution: 2.74→86.01 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.928 / SU ML: 0.482 / Cross valid method: THROUGHOUT / ESU R Free: 0.384
RfactorNum. reflection% reflectionSelection details
Rfree0.27084 1380 5 %RANDOM
Rwork0.22566 ---
obs0.2279 26497 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.41 Å20 Å2-0.14 Å2
2---2.57 Å20 Å2
3---6.97 Å2
Refinement stepCycle: 1 / Resolution: 2.74→86.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5374 1292 62 14 6742
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0186980
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6651.7979686
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7375681
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.03822.459244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.5815980
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4931562
X-RAY DIFFRACTIONr_chiral_restr0.0950.21027
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214782
X-RAY DIFFRACTIONr_gen_planes_other
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_it4.5575.5182730
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it7.2288.2763409
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.4125.8534250
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined14.13829145
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: 2.768→2.84 Å
RfactorNum. reflection% reflection
Rfree0.396 67 -
Rwork-1921 -
obs--97.07 %
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)
16.6035-3.36161.66861.7915-0.8420.5170.60560.9831-0.3473-0.3233-0.37530.07010.04980.0712-0.23031.0365-0.00750.06420.77030.0970.377128.735735.8776-39.7117
23.8941-0.5114-1.0073.0931.7453.65980.22640.1194-0.2829-0.23450.11780.11440.2734-0.7164-0.34420.8236-0.1772-0.12450.43680.12960.110929.626219.253-57.932
30.9797-0.6143-0.23360.45240.15290.64370.04750.12270.2591-0.1790.031-0.27610.4413-0.0052-0.07851.0464-0.14260.05650.2907-0.1640.394350.913415.7092-50.2506
41.71520.39740.26121.27520.34464.6256-0.0817-0.17250.0099-0.18060.0394-0.03810.3877-0.19750.04230.6603-0.1578-0.04740.3580.05740.444631.348111.6118-22.1211
50.7259-0.8935-0.6663.0949-0.71951.8498-0.19270.02280.0038-0.0381-0.0769-0.21040.3549-0.04760.26960.8652-0.07540.01110.1395-0.02450.630245.29037.2282-32.1017
60.28380.59710.10861.30030.28580.276-0.0046-0.12580.07720.1743-0.3120.08260.2965-0.14020.31660.657-0.01570.00630.3272-0.03311.209317.149929.32814.975
71.52050.0067-0.07341.929-0.45541.5976-0.1119-0.03880.040.3128-0.08270.50650.03080.02670.19460.44650.02410.11490.23740.01390.9314-1.384712.676914.7524
84.33820.8598-1.13812.39170.08390.9776-0.13650.03430.0839-0.3614-0.0030.05870.04250.19160.13950.4937-0.0386-0.05640.34080.08350.72323.541111.9645-10.4842
93.15141.1103-0.14971.6885-0.87170.9427-0.12790.32290.28050.24740.16820.16190.20750.2593-0.04030.54460.10360.0260.54660.09020.667134.45877.03659.3117
102.7931-0.916-0.05471.46250.53140.24440.00160.3635-0.16840.0778-0.0130.0998-0.04910.010.01140.5283-0.00870.01210.38730.05220.698122.94891.9825-2.0806
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 74
2X-RAY DIFFRACTION2A1 - 10
3X-RAY DIFFRACTION2A75 - 166
4X-RAY DIFFRACTION3A167 - 244
5X-RAY DIFFRACTION4A245 - 341
6X-RAY DIFFRACTION5B838 - 854
7X-RAY DIFFRACTION5C859 - 873
8X-RAY DIFFRACTION6F12 - 79
9X-RAY DIFFRACTION7F0 - 11
10X-RAY DIFFRACTION7F80 - 166
11X-RAY DIFFRACTION8F167 - 230
12X-RAY DIFFRACTION9F231 - 341
13X-RAY DIFFRACTION10G838 - 854
14X-RAY DIFFRACTION10H860 - 873

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