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- PDB-5mll: Structure of HpDprA at 1.9 Angstroms resolution -

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Basic information

Entry
Database: PDB / ID: 5mll
TitleStructure of HpDprA at 1.9 Angstroms resolution
ComponentsDNA processing chain A (DprA)
KeywordsDNA BINDING PROTEIN / HpDprA
Function / homologyDNA recombination-mediator protein A / DNA recombination-mediator protein A / DNA-mediated transformation / Rossmann fold - #450 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / DNA processing chain A (DprA)
Function and homology information
Biological speciesHelicobacter pylori 26695 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLisboa, J. / Quevillon-Cheruel, S.
CitationJournal: FEBS J. / Year: 2019
Title: The C-terminal domain of HpDprA is a DNA-binding Winged Helix domain that does not bind double-stranded DNA.
Authors: Lisboa, J. / Celma, L. / Sanchez, D. / Marquis, M. / Andreani, J. / Guerois, R. / Ochsenbein, F. / Durand, D. / Marsin, S. / Cuniasse, P. / Radicella, J.P. / Quevillon-Cheruel, S.
History
DepositionDec 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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 processing chain A (DprA)
B: DNA processing chain A (DprA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0875
Polymers48,9012
Non-polymers1863
Water2,594144
1
A: DNA processing chain A (DprA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5753
Polymers24,4501
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNA processing chain A (DprA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5122
Polymers24,4501
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.380, 67.580, 159.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA processing chain A (DprA)


Mass: 24450.414 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori 26695 (bacteria) / Gene: HP_0333 / Production host: Escherichia coli (E. coli) / References: UniProt: O25100
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.38 Å3/Da / Density % sol: 48.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 200mM di-ammonium tartrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 35234 / % possible obs: 99.4 % / Redundancy: 4.35 % / Biso Wilson estimate: 29.3 Å2 / Net I/σ(I): 3.2
Reflection shellResolution: 1.9→1.966 Å / Redundancy: 4.35 % / % possible all: 96.98

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UQZ

3uqz


Resolution: 1.9→41.753 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.05
RfactorNum. reflection% reflection
Rfree0.2472 1760 5 %
Rwork0.1953 --
obs0.1979 35196 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→41.753 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3418 0 12 144 3574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073517
X-RAY DIFFRACTIONf_angle_d14758
X-RAY DIFFRACTIONf_dihedral_angle_d13.3581353
X-RAY DIFFRACTIONf_chiral_restr0.041553
X-RAY DIFFRACTIONf_plane_restr0.005611
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8986-1.950.35571290.27032449X-RAY DIFFRACTION96
1.95-2.00730.26461330.24342515X-RAY DIFFRACTION99
2.0073-2.07210.27921320.22352530X-RAY DIFFRACTION100
2.0721-2.14620.27421330.21712538X-RAY DIFFRACTION100
2.1462-2.23210.30491340.20732554X-RAY DIFFRACTION100
2.2321-2.33370.26631350.21382562X-RAY DIFFRACTION100
2.3337-2.45670.28321340.22032542X-RAY DIFFRACTION100
2.4567-2.61060.26461360.21342570X-RAY DIFFRACTION100
2.6106-2.81210.26451350.21742574X-RAY DIFFRACTION100
2.8121-3.0950.26741370.21532594X-RAY DIFFRACTION100
3.095-3.54270.25961370.20052597X-RAY DIFFRACTION100
3.5427-4.46260.21271390.16472645X-RAY DIFFRACTION100
4.4626-41.76320.20061460.16222766X-RAY DIFFRACTION99

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