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- PDB-4irc: Polymerase-DNA complex -

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Basic information

Entry
Database: PDB / ID: 4irc
TitlePolymerase-DNA complex
Components
  • DNA (5'-D(*CP*TP*AP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
  • DNA (5'-D(*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
  • DNA (5'-D(*TP*CP*TP*GP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
  • DNA polymerase IV
KeywordsTransferase/DNA / DNA Polymerase / Y-family / Transferase-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 damage response / magnesium ion binding ...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 damage response / magnesium ion binding / cytoplasm / cytosol
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
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsNair, D.T. / Sharma, A.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: A strategically located serine residue is critical for the mutator activity of DNA polymerase IV from Escherichia coli.
Authors: Sharma, A. / Kottur, J. / Narayanan, N. / Nair, D.T.
History
DepositionJan 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1May 29, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_asym_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_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
G: DNA (5'-D(*TP*CP*TP*GP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
H: DNA (5'-D(*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
B: DNA (5'-D(*TP*CP*TP*GP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
C: DNA (5'-D(*CP*TP*AP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
F: DNA polymerase IV
A: DNA polymerase IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,12512
Polymers97,0966
Non-polymers1,0306
Water1,67593
1
G: DNA (5'-D(*TP*CP*TP*GP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
H: DNA (5'-D(*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
F: DNA polymerase IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6096
Polymers48,0953
Non-polymers5153
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-50 kcal/mol
Surface area20640 Å2
MethodPISA
2
B: DNA (5'-D(*TP*CP*TP*GP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
C: DNA (5'-D(*CP*TP*AP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
A: DNA polymerase IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5166
Polymers49,0013
Non-polymers5153
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-53 kcal/mol
Surface area21430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.140, 56.950, 110.810
Angle α, β, γ (deg.)90.00, 93.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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DNA chain , 3 types, 4 molecules GBHC

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


Mass: 5508.553 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*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
#3: DNA chain DNA (5'-D(*CP*TP*AP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')


Mass: 5188.360 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Protein , 1 types, 2 molecules FA

#4: Protein DNA polymerase IV / Pol IV


Mass: 38304.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: k12 / Gene: b0231, dinB, dinP, JW0221 / Production host: Escherichia coli (E. coli) / Strain (production host): C41DE3 / References: UniProt: Q47155, DNA-directed DNA polymerase

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Non-polymers , 3 types, 99 molecules

#5: 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
#6: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.79 Å3/Da / Density % sol: 55.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 15% MPD , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.67→50 Å / Num. all: 29306 / Num. obs: 29306 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 10.7
Reflection shellResolution: 2.67→2.81 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.529 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.67→45.3 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.911 / SU B: 37.941 / SU ML: 0.345 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.209 / ESU R Free: 0.363 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27504 1529 5 %RANDOM
Rwork0.22456 ---
obs0.22696 29306 99.6 %-
all-29306 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.213 Å2
Baniso -1Baniso -2Baniso -3
1--3.36 Å2-0 Å2-0.59 Å2
2---3.83 Å20 Å2
3---7.17 Å2
Refinement stepCycle: LAST / Resolution: 2.67→45.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5376 1358 60 93 6887
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0177055
X-RAY DIFFRACTIONr_angle_refined_deg1.4311.7889829
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0275682
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.75622.439246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.25715982
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0971562
X-RAY DIFFRACTIONr_chiral_restr0.0880.21039
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214838
LS refinement shellResolution: 2.67→2.739 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 143 -
Rwork0.353 2123 -
obs--100 %
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)
12.44120.8033-0.46430.4811-0.38850.58510.0711-0.1005-0.01790.1308-0.00080.0180.08790.2452-0.07040.43140.1351-0.02420.3181-0.07040.0201-27.8092-8.15743.3557
21.06360.2932-0.71570.33090.3131.56750.2542-0.11250.06710.01090.0406-0.0881-0.21240.2948-0.29480.3841-0.00170.04520.3057-0.09470.0815-25.95478.176-15.2382
30.8017-0.06080.13811.0164-0.00632.840.00130.00380.14940.0327-0.03970.12920.082-0.20360.03840.35440.00990.05550.30680.05380.0658-52.2101-9.7597-4.3629
41.0989-0.17940.08191.1563-0.16711.3519-0.00940.13370.00690.02310.00080.00390.14650.13640.00860.33150.07110.03970.2941-0.02140.0413-28.3001-15.4513-32.7087
50.5686-0.59290.45640.6646-0.36951.0240.00080.09350.0624-0.0236-0.1277-0.12930.01970.11330.12690.2258-0.03150.04170.2418-0.00920.31624.2221-14.2474-70.3591
60.3833-0.27630.22990.47970.18581.5292-0.11860.01990.0816-0.1277-0.12040.0091-0.127-0.06610.2390.26680.012-0.03560.1884-0.04020.3278-13.73962.6426-69.855
72.2145-0.56560.22460.57310.49270.8496-0.0637-0.0196-0.0650.0261-0.0294-0.0592-0.0923-0.10010.09310.27330.0017-0.03570.2179-0.01690.32250.0052-15.3187-45.0206
81.5464-0.7453-0.17260.93710.4240.8612-0.0641-0.10440.1097-0.13560.0508-0.04950.1075-0.24580.01320.208-0.03780.03350.3258-0.06250.1665-31.6966-19.626-64.4744
90.07750.23870.14151.00810.59850.3555-0.0138-0.0173-0.04220.0933-0.01290.04540.0518-0.00110.02670.39030.00340.02360.27770.00790.1544-43.2619-20.4569-24.1504
101.12980.45140.10480.7756-0.16870.0918-0.0909-0.1597-0.0119-0.05740.0331-0.1535-0.0093-0.09980.05780.22380.0250.02930.3688-0.09170.2171-19.6036-23.9258-53.1304
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 10
2X-RAY DIFFRACTION1A77 - 166
3X-RAY DIFFRACTION2A11 - 76
4X-RAY DIFFRACTION3A167 - 231
5X-RAY DIFFRACTION4A241 - 341
6X-RAY DIFFRACTION5F1 - 10
7X-RAY DIFFRACTION5F77 - 166
8X-RAY DIFFRACTION6F11 - 76
9X-RAY DIFFRACTION7F167 - 231
10X-RAY DIFFRACTION8F241 - 341
11X-RAY DIFFRACTION9B837 - 854
12X-RAY DIFFRACTION9C857 - 873
13X-RAY DIFFRACTION9A401
14X-RAY DIFFRACTION9A402
15X-RAY DIFFRACTION9A403
16X-RAY DIFFRACTION10G837 - 854
17X-RAY DIFFRACTION10H860 - 873
18X-RAY DIFFRACTION10F401
19X-RAY DIFFRACTION10F402
20X-RAY DIFFRACTION10F403

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