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- PDB-4ljl: Structural insights into the unique single-stranded DNA binding m... -

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Basic information

Entry
Database: PDB / ID: 4ljl
TitleStructural insights into the unique single-stranded DNA binding mode of DNA processing protein A from Helicobacter pylori
ComponentsDNA processing chain A (DprA)
KeywordsDNA BINDING PROTEIN / DNA processing A domain / Rossmann fold / ssDNA binding / complex / natural recombination mediating protein
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWang, W.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Structural insights into the unique single-stranded DNA-binding mode of Helicobacter pylori DprA.
Authors: Wang, W. / Ding, J. / Zhang, Y. / Hu, Y. / Wang, D.C.
History
DepositionJul 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Database references
Revision 1.2Apr 2, 2014Group: Database references
Revision 1.3Nov 12, 2014Group: Structure summary
Revision 1.4Sep 20, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA processing chain A (DprA)
A: DNA processing chain A (DprA)


Theoretical massNumber of molelcules
Total (without water)51,4462
Polymers51,4462
Non-polymers00
Water5,783321
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-11 kcal/mol
Surface area19990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.090, 107.860, 37.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein DNA processing chain A (DprA)


Mass: 25722.783 Da / Num. of mol.: 2 / Fragment: UNP residues 5-225
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: HP0333, HP_0333 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O25100
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 3.36 Å3/Da / Density % sol: 63.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 25% PEG3350, 100 mM Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.2→45.62 Å / Num. all: 36288 / Num. obs: 34651 / % possible obs: 95.9 %

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
PHENIX(phenix.refine: 1.7_650)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4LJK

4ljk


Resolution: 2.2→39.76 Å / SU ML: 0.26 / σ(F): 0 / Phase error: 21.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.213 1690 4.97 %random
Rwork0.1696 ---
obs0.1718 34008 93.74 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.005 Å2 / ksol: 0.336 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--13.0833 Å20 Å2-0 Å2
2--18.5093 Å20 Å2
3----5.426 Å2
Refinement stepCycle: LAST / Resolution: 2.2→39.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3430 0 0 321 3751
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063504
X-RAY DIFFRACTIONf_angle_d0.9764742
X-RAY DIFFRACTIONf_dihedral_angle_d13.6431350
X-RAY DIFFRACTIONf_chiral_restr0.066553
X-RAY DIFFRACTIONf_plane_restr0.005607
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.26470.25741100.18781949X-RAY DIFFRACTION71
2.2647-2.33780.23951230.1962333X-RAY DIFFRACTION81
2.3378-2.42140.27021360.19472542X-RAY DIFFRACTION91
2.4214-2.51830.23471440.17722636X-RAY DIFFRACTION93
2.5183-2.63290.25411330.18412724X-RAY DIFFRACTION96
2.6329-2.77170.2591290.18512752X-RAY DIFFRACTION97
2.7717-2.94530.26451420.19132798X-RAY DIFFRACTION98
2.9453-3.17260.2261340.18982868X-RAY DIFFRACTION99
3.1726-3.49170.23491630.18422834X-RAY DIFFRACTION100
3.4917-3.99660.19081620.1592879X-RAY DIFFRACTION100
3.9966-5.03360.1741430.12912937X-RAY DIFFRACTION100
5.0336-39.76680.17041710.16363066X-RAY DIFFRACTION99
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)
10.0063-0.00110.0060.0438-0.03120.1079-0.0633-0.2179-0.10440.07620.00660.0470.02530.0903-0.01170.17080.10530.04420.32630.08550.1485-75.826137.0003-8.7904
20.0755-0.0229-0.05530.02250.03660.08390.06720.1167-0.1253-0.03130.01120.1004-0.00450.10430.03130.19850.22730.00920.3207-0.0390.2831-59.933525.2869-20.7296
30.2211-0.06-0.050.0412-0.00980.13330.0380.1242-0.1368-0.0642-0.10130.0692-0.02130.1652-0.01450.16960.07290.00030.2022-0.03320.1606-70.967635.8755-19.7679
40.0483-0.02580.010.05660.02320.0357-0.0426-0.0935-0.0164-0.0036-0.0534-0.04970.01480.1575-0.01350.12580.16360.02470.34810.0140.1481-57.246535.0564-10.6645
50.0215-0.0029-0.00780.01660.00810.01640.00430.00870.0143-0.01730.02280.0172-0.00020.02660.0090.16670.2512-0.03480.4559-0.01090.3075-45.414828.1802-16.1584
60.0012-0.00480.00320.0134-0.00920.006-0.0174-0.0017-0.03940.01560.00660.00410.02910.01190.00410.56220.17910.01060.3640.19120.6737-60.523213.6089-10.8117
70.0793-0.02390.02390.2211-0.06850.0893-0.0038-0.0642-0.0380.04010.0106-0.0526-0.0558-0.0517-0.00740.18160.02610.00680.2342-0.01520.1663-8.633110.9444-20.425
80.09330.00390.05990.0379-0.01980.07660.0810.1310.0539-0.03220.01020.0205-0.053-0.13840.04270.27150.18190.00120.32580.00610.1703-27.229624.3756-24.8704
90.0418-0.057-0.01490.12270.05390.03050.07250.12130.0339-0.1601-0.0237-0.0145-0.1007-0.16990.01090.22920.0714-0.00580.21620.01050.1324-16.524614.1623-28.9734
100.0646-0.0264-0.05980.16650.05920.0651-0.0856-0.0287-0.0049-0.0798-0.07950.0339-0.099-0.2027-0.00690.1830.0943-0.01190.27750.00030.1322-27.579213.0397-16.7029
110.0041-0.0026-0.00460.0059-0.00160.0046-0.0107-0.0172-0.0278-0.011-0.00040.03870.0044-0.0143-0.00520.11350.34620.00440.46540.01590.2073-40.199120.0001-17.7049
120.01370.0032-0.0040.01980.01040.00790.0062-0.00650.0220.0142-0.0009-0.0093-0.0425-0.0097-0.0030.50180.1848-0.02670.3041-0.1130.2855-24.172133.4126-12.7962
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resseq 5:41)
2X-RAY DIFFRACTION2chain 'B' and (resseq 42:71)
3X-RAY DIFFRACTION3chain 'B' and (resseq 72:136)
4X-RAY DIFFRACTION4chain 'B' and (resseq 137:182)
5X-RAY DIFFRACTION5chain 'B' and (resseq 183:206)
6X-RAY DIFFRACTION6chain 'B' and (resseq 207:223)
7X-RAY DIFFRACTION7chain 'A' and (resseq 5:41)
8X-RAY DIFFRACTION8chain 'A' and (resseq 42:71)
9X-RAY DIFFRACTION9chain 'A' and (resseq 72:138)
10X-RAY DIFFRACTION10chain 'A' and (resseq 139:182)
11X-RAY DIFFRACTION11chain 'A' and (resseq 183:206)
12X-RAY DIFFRACTION12chain 'A' and (resseq 207:223)

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