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- PDB-1q8i: Crystal structure of ESCHERICHIA coli DNA Polymerase II -

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Basic information

Entry
Database: PDB / ID: 1q8i
TitleCrystal structure of ESCHERICHIA coli DNA Polymerase II
ComponentsDNA polymerase II
KeywordsTRANSFERASE / DNA Polymerase II / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


DNA replication proofreading / 3'-5'-DNA exonuclease activity / SOS response / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding
Similarity search - Function
DNA polymerase B, N domain, beta-barrel / B family DNA polymerase, N domain, alpha/beta motif / Helix Hairpins - #1130 / DNA polymerase II, N-terminal / B family DNA polymerase, finger domain / Palm domain of DNA polymerase / B family DNA polymerase, palm domain / DNA polymerase family B, thumb domain / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site ...DNA polymerase B, N domain, beta-barrel / B family DNA polymerase, N domain, alpha/beta motif / Helix Hairpins - #1130 / DNA polymerase II, N-terminal / B family DNA polymerase, finger domain / Palm domain of DNA polymerase / B family DNA polymerase, palm domain / DNA polymerase family B, thumb domain / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Helix Hairpins / Ribonuclease H-like superfamily/Ribonuclease H / Helix non-globular / Special / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Helix Hairpins / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / Alpha-Beta Complex / Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2 Å
AuthorsBrunzelle, J.S. / Muchmore, C.R.A. / Mashhoon, N. / Blair-Johnson, M. / Shuvalova, L. / Goodman, M.F. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of Escherichia Coli DNA Polymerase II
Authors: Brunzelle, J.S. / Muchmore, C.R.A. / Mashhoon, N. / Blair-Johnson, M. / Shuvalova, L. / Goodman, M.F. / Anderson, W.F.
History
DepositionAug 21, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA polymerase II


Theoretical massNumber of molelcules
Total (without water)90,1541
Polymers90,1541
Non-polymers00
Water7,494416
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.383, 116.596, 82.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a monomer

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Components

#1: Protein DNA polymerase II / / Pol II


Mass: 90154.383 Da / Num. of mol.: 1 / Mutation: I428V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: POLB OR DINA OR B0060 / Production host: Escherichia coli (E. coli) / References: UniProt: P21189, DNA-directed DNA polymerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 416 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.7655.15
2
3
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2951vapor diffusion, hanging drop5.3Citrate , PEG3K, DTT, EDTA, Glycerol, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 295K
2952vapor diffusion, hanging drop5.5Citrate , PEG3K, DTT, EDTA, Glycerol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
2953vapor diffusion, hanging drop5.8Citrate , PEG3K, DTT, MgCl2, Glycerol, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31
1,2,31
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 5ID-B11
SYNCHROTRONAPS 5ID-B21
SYNCHROTRONAPS 19-ID31.77
Detector
TypeIDDetector
MARRESEARCH1CCD
CUSTOM-MADE2CCD
3
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
2Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
3Mx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.771
ReflectionResolution: 2→29.7 Å / Num. obs: 60657

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MIRAS / Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.933 / SU ML: 99.357 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23612 3064 5.1 %RANDOM
Rwork0.19672 ---
obs0.19872 57543 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.269 Å2
Baniso -1Baniso -2Baniso -3
1--1.59 Å20 Å20 Å2
2---0.64 Å20 Å2
3---2.23 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5709 0 0 416 6125
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0215886
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6361.9457981
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8163704
X-RAY DIFFRACTIONr_dihedral_angle_2_deg20.633151063
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.472151036
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1510.2846
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.024567
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.240.32813
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.5901
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2390.380
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2830.556
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it3.1711.53523
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.28525680
X-RAY DIFFRACTIONr_scbond_it6.47332363
X-RAY DIFFRACTIONr_scangle_it8.994.52301
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.278 236
Rwork0.186 4118
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)
15.6309-1.04051.51591.2126-0.3641.0429-0.1689-0.41980.2280.0955-0.02250.0174-0.23160.00740.19140.14080.0058-0.04650.0981-0.02560.132642.672698.589957.3773
22.4665-2.59050.718516.157-3.40931.32550.14530.63830.42-1.772-0.3446-2.30990.31720.26030.19940.25240.03370.25140.2321-0.00130.4126.0915116.170333.4208
31.87920.59980.82751.69811.47192.2367-0.02510.24470.138-0.235-0.0131-0.001-0.09290.0510.03820.07670.02170.04680.03950.04410.05739.703274.627332.2737
41.71221.8869-3.28045.0768-5.63756.4035-0.0486-0.5414-0.01740.6110.0007-0.0657-0.50890.15860.04790.35340.1024-0.00550.63270.03790.08834.396984.946-2.1388
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1462 - 146
2X-RAY DIFFRACTION2AA147 - 360147 - 360
3X-RAY DIFFRACTION3AA361 - 600361 - 600
4X-RAY DIFFRACTION4AA601 - 783601 - 783

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