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- PDB-4dez: Structure of MsDpo4 -

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Basic information

Entry
Database: PDB / ID: 4dez
TitleStructure of MsDpo4
ComponentsDNA polymerase IV 1
KeywordsTRANSFERASE / Y-Family / DNA Polymerase
Function / homology
Function and homology information


SOS response / error-prone translesion synthesis / DNA-templated DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / magnesium ion binding / cytosol
Similarity search - Function
DNA polymerase IV / 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 polymerase IV / 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 / 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
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsNair, D.T. / Sharma, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: The PAD region in the mycobacterial DinB homologue MsPolIV exhibits positional heterogeneity.
Authors: Sharma, A. / Subramanian, V. / Nair, D.T.
History
DepositionJan 22, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA polymerase IV 1


Theoretical massNumber of molelcules
Total (without water)38,5361
Polymers38,5361
Non-polymers00
Water2,414134
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: DNA polymerase IV 1

A: DNA polymerase IV 1


Theoretical massNumber of molelcules
Total (without water)77,0722
Polymers77,0722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Buried area1210 Å2
ΔGint-10 kcal/mol
Surface area22350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.230, 125.230, 142.520
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein DNA polymerase IV 1 / Pol IV 1


Mass: 38535.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: MC2 155 / Gene: dinB, dinB1, MSMEG_1014, MSMEG_2294 / Plasmid: PGEX4P1 / Production host: Escherichia coli (E. coli) / Strain (production host): C41DE3 / References: UniProt: A0QR77, DNA-directed DNA polymerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 4.19 Å3/Da / Density % sol: 70.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 2.4 M NaCl with 0.1 M Na/K phosphate (pH=6.2), VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.96 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 20393 / % possible obs: 100 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 23.49
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 4.5 / Num. unique all: 1996 / % possible all: 100

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Processing

Software
NameVersionClassification
MxCuBEdata collection
SHELXSphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.6→50 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1041 -RANDOM
Rwork0.211 ---
all-20888 --
obs-20354 97.4 %-
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1738 0 0 134 1872

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