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- PDB-4r8u: S-SAD structure of DINB-DNA Complex -

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Basic information

Entry
Database: PDB / ID: 4r8u
TitleS-SAD structure of DINB-DNA Complex
Components
  • (DNA polymerase ...) x 2
  • (DNA) x 3
KeywordsTRANSFERASE/DNA / nucleotidyl transferase / DNA Polymerase / TRANSFERASE-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 / 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-1FZ / DNA / DNA (> 10) / DNA polymerase IV
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsKottur, J. / Nair, D.T. / Weinert, T. / Oligeric, V. / Wang, M.
CitationJournal: Nat.Methods / Year: 2015
Title: Fast native-SAD phasing for routine macromolecular structure determination
Authors: Weinert, T. / Olieric, V. / Waltersperger, S. / Panepucci, E. / Chen, L. / Zhang, H. / Zhou, D. / Rose, J. / Ebihara, A. / Kuramitsu, S. / Li, D. / Howe, N. / Schnapp, G. / Pautsch, A. / ...Authors: Weinert, T. / Olieric, V. / Waltersperger, S. / Panepucci, E. / Chen, L. / Zhang, H. / Zhou, D. / Rose, J. / Ebihara, A. / Kuramitsu, S. / Li, D. / Howe, N. / Schnapp, G. / Pautsch, A. / Bargsten, K. / Prota, A.E. / Surana, P. / Kottur, J. / Nair, D.T. / Basilico, F. / Cecatiello, V. / Pasqualato, S. / Boland, A. / Weichenrieder, O. / Wang, B.C. / Steinmetz, M.O. / Caffrey, M. / Wang, M.
History
DepositionSep 3, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2015Group: Database references
Revision 1.2Sep 2, 2015Group: Source and taxonomy
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software
Revision 1.4Mar 20, 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
A: DNA polymerase IV
B: DNA polymerase IV
V: DNA
W: DNA
C: DNA
D: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,11210
Polymers97,1016
Non-polymers1,0114
Water1,13563
1
A: DNA polymerase IV
V: DNA
W: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4535
Polymers48,9473
Non-polymers5052
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA polymerase IV
C: DNA
D: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6595
Polymers48,1543
Non-polymers5052
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.950, 57.210, 110.600
Angle α, β, γ (deg.)90.00, 94.69, 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 AB

#1: Protein DNA polymerase IV / Pol IV


Mass: 38266.316 Da / Num. of mol.: 1 / Fragment: UNP residues 2-340
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: b0231, dinB, dinP, JW0221 / Production host: Escherichia coli (E. coli) / Strain (production host): C41DE3 / References: UniProt: Q47155, DNA-directed DNA polymerase
#2: Protein DNA polymerase IV / Pol IV


Mass: 38066.086 Da / Num. of mol.: 1 / Fragment: UNP residues 2-338
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / 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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DNA chain , 3 types, 4 molecules VCWD

#3: DNA chain DNA


Mass: 5188.360 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic oligonucleotide / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA


Mass: 5492.554 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic oligonucleotide / Source: (synth.) synthetic construct (others)
#5: DNA chain DNA


Mass: 4899.178 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic oligonucleotide / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 67 molecules

#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-1FZ / 5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine


Mass: 481.184 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H18N3O13P3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.83 Å3/Da / Density % sol: 56.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 18% MPD, 0.1M Citrate, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 298KK

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.7 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 18, 2014
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7 Å / Relative weight: 1
ReflectionResolution: 2.3→48.329 Å / Num. all: 93883 / Num. obs: 93883 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.3→2.3261 Å / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.9_1692)refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.3→48.23 Å / SU ML: 0.33 / σ(F): 1.92 / Phase error: 27.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2195 4705 5.01 %RANDOM
Rwork0.1808 ---
obs0.1828 93883 99.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→48.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5329 1389 60 63 6841
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097040
X-RAY DIFFRACTIONf_angle_d1.3619810
X-RAY DIFFRACTIONf_dihedral_angle_d20.9642774
X-RAY DIFFRACTIONf_chiral_restr0.0461099
X-RAY DIFFRACTIONf_plane_restr0.0071024
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3-2.32610.39881390.3278267590
2.3261-2.35350.35441530.308295597
2.3535-2.38220.29561520.28292098
2.3822-2.41240.33741540.2632295599
2.4124-2.44410.28631590.26132961100
2.4441-2.47760.30421630.253087100
2.4776-2.5130.3091520.24112878100
2.513-2.55050.26311570.23592985100
2.5505-2.59030.30911540.22833013100
2.5903-2.63280.29331590.24552988100
2.6328-2.67820.34631560.23992970100
2.6782-2.72690.29911590.24313059100
2.7269-2.77930.32351530.24682909100
2.7793-2.83610.2871580.24053028100
2.8361-2.89770.34521580.25253027100
2.8977-2.96510.28191560.23692969100
2.9651-3.03930.28131560.22492973100
3.0393-3.12140.26381600.21982988100
3.1214-3.21320.26571600.20862990100
3.2132-3.31690.22351600.20382975100
3.3169-3.43550.24441580.19832985100
3.4355-3.5730.27431590.19313043100
3.573-3.73550.26161550.18762929100
3.7355-3.93240.18061580.1692975100
3.9324-4.17860.19881600.15573015100
4.1786-4.5010.16711570.13852984100
4.501-4.95360.1621590.13913000100
4.9536-5.66940.19171620.14752978100
5.6694-7.13920.2021580.17092995100
7.1392-48.33940.14311610.1312969100
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)
13.9281-0.74230.38834.59150.65121.6944-0.26080.21010.5429-0.2654-0.0743-0.0429-0.3115-0.18360.2870.42150.0207-0.11910.3553-0.06360.552624.317133.974240.1577
21.7520.02020.27871.7381-0.96444.291-0.1320.0198-0.19420.06010.0731-0.52510.10.1250.07540.3953-0.0118-0.02590.3438-0.07760.71337.925618.853450.613
34.8021-1.5909-0.45224.2046-0.46423.1608-0.2146-0.68170.1862-0.10820.23150.19270.242-0.98010.01280.3654-0.12480.02780.8363-0.18150.46613.040115.497546.03
41.6599-0.6953-1.1413.87862.64974.12650.26170.40750.3224-0.6328-0.06110.3545-0.4514-0.9281-0.17590.83380.0178-0.00280.75110.08670.5972-18.60798.24319.5849
54.32160.07040.65073.93870.79714.680.20180.18150.40160.02070.04030.2217-0.6162-0.858-0.27330.91980.05740.12190.71890.08410.6101-16.262712.785714.5816
64.0759-0.834-0.43592.2347-0.49321.90740.147-0.039-0.0727-0.6241-0.00140.3250.3454-0.4794-0.11021.0631-0.1569-0.08340.8360.01340.5671-11.7914-2.4011-4.3068
77.78352.2426-0.81793.1107-1.27644.4890.0259-0.73480.4564-0.1956-0.1671-0.0607-0.47270.66140.1690.9351-0.0856-0.00070.8876-0.01120.57279.71191.116710.1257
85.44341.5826-1.75472.2487-1.04971.47740.14940.10190.27860.104-0.1605-0.02020.68330.0608-0.03871.1816-0.01050.090.7248-0.09770.60135.0442-11.06445.9554
92.5868-0.34760.73223.994-0.01055.5314-0.1007-0.0767-0.1537-0.30920.00240.0930.7763-0.5410.11790.7693-0.2590.09870.68020.01460.5807-15.6172-9.133433.2497
103.84351.16470.59233.4428-2.63213.5934-0.0993-0.672-0.43130.3438-0.12820.01090.0732-0.10420.17540.49340.05250.10760.5931-0.06960.616414.06878.762157.5431
112.68981.91960.14034.974-1.43752.3608-0.0479-0.3782-0.4830.04480.0208-0.43240.5099-0.5797-0.01690.5233-0.08070.06530.7191-0.02850.477515.70882.319762.6865
125.3195-5.259-0.27225.33560.80676.41080.2610.0059-0.1749-0.3443-0.4928-0.38290.42940.09420.18730.8769-0.12620.09410.54790.11120.6833-7.9478-3.609220.9461
137.9894-4.3044-1.10417.6398-3.2214.3320.19250.681-0.27610.5482-0.7858-0.2185-0.87490.31510.57871.12770.0372-0.15970.74030.04150.65576.6236-28.284130.7395
141.0982-3.03321.58088.9836-4.51442.50230.39610.3769-0.33180.094-0.43250.8245-0.15640.55950.01260.95840.09470.0590.64750.03570.69270.6352-16.860422.9996
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 82 )
2X-RAY DIFFRACTION2chain 'A' and (resid 83 through 242 )
3X-RAY DIFFRACTION3chain 'A' and (resid 243 through 339 )
4X-RAY DIFFRACTION4chain 'B' and (resid 3 through 42 )
5X-RAY DIFFRACTION5chain 'B' and (resid 43 through 82 )
6X-RAY DIFFRACTION6chain 'B' and (resid 83 through 182 )
7X-RAY DIFFRACTION7chain 'B' and (resid 183 through 202 )
8X-RAY DIFFRACTION8chain 'B' and (resid 203 through 242 )
9X-RAY DIFFRACTION9chain 'B' and (resid 243 through 339 )
10X-RAY DIFFRACTION10(chain 'V' and (resid 18 through 34 )) or (chain 'W' and resid 37)
11X-RAY DIFFRACTION11chain 'W' and (resid 38 through 54 )
12X-RAY DIFFRACTION12chain 'C' and (resid 18 through 27 )
13X-RAY DIFFRACTION13(chain 'C' and (resid 28 through 34 )) or (chain 'D' and (resid 39 through 40))
14X-RAY DIFFRACTION14chain 'D' and (resid 41 through 54 )

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