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- PDB-6jup: Mutant PolIV-DNA incoming nucleotide complex -

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Basic information

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


DNA synthesis involved in DNA repair / error-free translesion synthesis / SOS response / error-prone translesion synthesis / DNA-templated DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA repair / DNA damage response ...DNA synthesis involved in DNA repair / error-free translesion synthesis / SOS response / error-prone translesion synthesis / DNA-templated DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA repair / DNA damage response / 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 / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily ...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 / 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-0KX / DNA / DNA (> 10) / DNA polymerase IV / DNA polymerase IV
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 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
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 / pdbx_struct_conn_angle / struct_conn
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_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_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_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*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*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
C: 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)99,74212
Polymers98,7126
Non-polymers1,0306
Water72140
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*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)49,8636
Polymers49,3493
Non-polymers5153
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-51 kcal/mol
Surface area20890 Å2
MethodPISA
2
A: DNA polymerase IV
B: DNA (5'-D(P*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
C: 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)49,8786
Polymers49,3643
Non-polymers5153
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-56 kcal/mol
Surface area21390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.184, 56.974, 111.136
Angle α, β, γ (deg.)90.00, 92.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules FA

#1: Protein DNA polymerase IV / / Pol IV


Mass: 38346.426 Da / Num. of mol.: 2 / Mutation: F13A, T43C
Source method: isolated from a genetically manipulated source
Details: DNA Polymerase / 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 , 2 types, 4 molecules GHBC

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


Mass: 5493.541 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA template / 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: 5508.553 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: DNA primer / Source: (synth.) Escherichia coli (E. coli)

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Non-polymers , 3 types, 46 molecules

#4: Chemical ChemComp-0KX / 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine


Mass: 466.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H17N4O12P3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.77 Å3/Da / Density % sol: 55.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: MPD 2%, Sodium Phosphate buffer pH 4.5 / PH range: 4.5-5.1

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100 K / 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: 2.44→69.71 Å / Num. obs: 40567 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Net I/σ(I): 14.4
Reflection shellResolution: 2.44→2.57 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.755 / Num. unique obs: 5837 / CC1/2: 0.666 / Rpim(I) all: 0.313 / % possible all: 99.1

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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: 2.44→69.71 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.949 / SU B: 35.653 / SU ML: 0.311 / Cross valid method: THROUGHOUT / ESU R Free: 0.286
RfactorNum. reflection% reflectionSelection details
Rfree0.24505 1788 5 %RANDOM
Rwork0.22105 ---
obs0.22227 33768 99.96 %-
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--1.87 Å2-0 Å2-0.05 Å2
2---2.81 Å2-0 Å2
3---4.66 Å2
Refinement stepCycle: 1 / Resolution: 2.44→69.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5378 1351 60 40 6829
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0177053
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1831.7919787
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4055682
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.65822.459244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.53515980
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.321562
X-RAY DIFFRACTIONr_chiral_restr0.0420.21034
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214815
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_it0.9848.7512734
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.66913.1213414
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.3939.1474319
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined3.70411180
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr6.35937053
X-RAY DIFFRACTIONr_sphericity_free0520
X-RAY DIFFRACTIONr_sphericity_bonded43.06756794
LS refinement shellResolution: 2.44→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 148 -
Rwork0.361 2436 -
obs--99.61 %
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)
12.3579-0.93851.24571.829-0.61233.52850.16080.1055-0.08940.0268-0.05340.1668-0.3927-0.1365-0.10740.16070.04350.06650.07440.04080.0876115.555538.4445-40.0799
23.3276-0.2394-0.54790.90490.09120.2589-0.03850.1059-0.09770.01620.0134-0.01510.1413-0.16670.02510.1893-0.09080.02730.1526-0.00270.0107116.552321.7592-58.1522
32.0588-0.3471-0.41230.3196-0.24381.46750.07920.0433-0.0639-0.0213-0.0822-0.10760.09870.20160.0030.18050.01020.03730.0526-0.01460.1231137.598418.1783-50.2371
41.52550.58940.47661.18490.45632.3118-0.07120.0615-0.0655-0.0975-0.02970.11290.1344-0.09110.1010.0818-0.02630.04480.1171-0.0050.0662117.726914.3648-22.1742
50.756-0.66180.64821.0047-0.56940.59430.01640.0374-0.1005-0.11360.0325-0.08620.06690.06-0.04890.1444-0.01540.07480.1204-0.00840.1241132.190610.0104-31.6077
60.29290.4755-0.05621.426-0.06180.01510.11660.0632-0.01340.2339-0.1371-0.1482-0.0314-0.02330.02050.1301-0.0144-0.02910.11740.0060.2531103.321932.024915.0394
70.2778-0.28610.54410.6692-0.35761.2988-0.00590.03460.03590.1788-0.08350.05180.0491-0.06770.08940.0958-0.0030.03230.1094-0.00630.226684.863115.407914.7687
81.80151.43880.29861.9862-0.01460.136-0.0307-0.0123-0.0575-0.1906-0.0162-0.03980.020.01020.04690.08120.0123-0.02650.1203-0.01860.206389.671214.6879-10.5057
91.7880.2969-0.62591.14740.02220.4282-0.02420.03580.22390.03690.04710.03720.07620.0605-0.02290.03370.0092-0.01070.13560.01470.1791120.64339.91499.3477
101.157-0.3938-0.64411.80411.09780.8219-0.08140.0855-0.0230.00070.04820.0390.03260.00450.03320.05140.00670.0010.12360.03140.1531109.20034.0533-2.5281
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 74
2X-RAY DIFFRACTION2A0 - 10
3X-RAY DIFFRACTION2A75 - 166
4X-RAY DIFFRACTION3A167 - 244
5X-RAY DIFFRACTION4A245 - 341
6X-RAY DIFFRACTION5B837 - 854
7X-RAY DIFFRACTION5C858 - 873
8X-RAY DIFFRACTION6F12 - 79
9X-RAY DIFFRACTION7F0 - 11
10X-RAY DIFFRACTION7F80 - 166
11X-RAY DIFFRACTION8F167 - 230
12X-RAY DIFFRACTION9F231 - 341
13X-RAY DIFFRACTION10G838 - 855
14X-RAY DIFFRACTION10H860 - 873

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