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- PDB-5dol: Crystal structure of YabA amino-terminal domain from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 5dol
TitleCrystal structure of YabA amino-terminal domain from Bacillus subtilis
ComponentsInitiation-control protein YabA
KeywordsREPLICATION / YabA / DnaA / DnaN / Zinc finger / initiation control
Function / homologyInitiation control protein YabA / Initiation control protein YabA / regulation of DNA-templated DNA replication initiation / DNA replication / DNA damage response / identical protein binding / Initiation-control protein YabA
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 2.7 Å
AuthorsCherrier, M.V. / Bazin, A. / Jameson, K.H. / Wilkinson, A.J. / Noirot-Gros, M.F. / Terradot, L.
Funding support France, 1items
OrganizationGrant numberCountry
Region Rhone-AlpesCIBLE 2011 France
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Tetramerization and interdomain flexibility of the replication initiation controller YabA enables simultaneous binding to multiple partners.
Authors: Felicori, L. / Jameson, K.H. / Roblin, P. / Fogg, M.J. / Garcia-Garcia, T. / Ventroux, M. / Cherrier, M.V. / Bazin, A. / Noirot, P. / Wilkinson, A.J. / Molina, F. / Terradot, L. / Noirot-Gros, M.F.
History
DepositionSep 11, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1May 8, 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: Initiation-control protein YabA
B: Initiation-control protein YabA


Theoretical massNumber of molelcules
Total (without water)15,0032
Polymers15,0032
Non-polymers00
Water724
1
A: Initiation-control protein YabA
B: Initiation-control protein YabA

A: Initiation-control protein YabA
B: Initiation-control protein YabA


Theoretical massNumber of molelcules
Total (without water)30,0064
Polymers30,0064
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_467y-1,x+1,-z+21
Buried area9880 Å2
ΔGint-88 kcal/mol
Surface area15600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.480, 83.480, 64.710
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
SymmetryPoint symmetry: (Schoenflies symbol: C2 (2 fold cyclic))

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Components

#1: Protein Initiation-control protein YabA


Mass: 7501.492 Da / Num. of mol.: 2 / Fragment: UNP residues 1-62
Source method: isolated from a genetically manipulated source
Details: Amino-terminal domain of the protein (residus 1-62)
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Gene: yabA, BSU00330 / Plasmid: PET151/D-TOPO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P37542
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 4.34 Å3/Da / Density % sol: 71.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 3350 (W/V), 100 mM Bis-Tris propane pH 6.5, 200 mM potassium thiocyanate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93222 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93222 Å / Relative weight: 1
ReflectionRedundancy: 21.2 % / Number: 45757 / Rsym value: 0.141 / D res high: 4.002 Å / D res low: 71.908 Å / Num. obs: 2157 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsRsym valueRedundancy
12.6541.5210.0570.05715.2
8.9412.6510.050.0518.6
7.38.9410.1010.10120.2
6.327.310.180.1821.2
5.666.3210.3720.37220.5
5.165.6610.4270.42722.2
4.785.1610.380.3822.3
4.474.7810.6860.68620.7
4.224.4710.940.9422.5
44.2211.451.4523
ReflectionResolution: 2.7→36.1 Å / Num. obs: 7306 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 21.2 % / Biso Wilson estimate: 90.05 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.036 / Rrim(I) all: 0.079 / Rsym value: 0.072 / Χ2: 0.991 / Net I/av σ(I): 2 / Net I/σ(I): 17.98 / Num. measured all: 51889
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured allNum. measured obsNum. possibleNum. unique allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.7-2.8230.5372.6261.23683455627532977520.3092.8321.452.699.9
2.8-2.922.50.6861.5662.09635846466292826290.2041.680.944.2100
2.9-320.70.8010.9853.35567642045712745710.1531.0570.6865.4100
3-3.122.30.8850.7194.59554837065072495070.0830.7710.388.7100
3.1-3.222.20.9040.5735.87521733424522354520.0930.6140.4277.8100
3.2-3.320.50.9380.4147.93444227723812173810.0850.4440.3727.9100
3.3-421.20.9960.11318.17421012818176519917650.0420.1210.1813.7100
4-620.20.9990.03937.26337811137162316716200.0260.0420.10122.999.8
6-1018.610.02642.26266633955601435450.0180.0290.0536.497.3
10-41.51615.20.9980.02544.72142830717694840.0180.0290.05742.547.7

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Phasing

Phasing
Method
SAD
molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.12 Å36.15 Å
Translation4.12 Å36.15 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PHASER2.5.6phasing
SOLVEphasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.7→36.1 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2701 728 9.97 %
Rwork0.2223 6573 -
obs0.227 7301 98.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 249.42 Å2 / Biso mean: 125.3684 Å2 / Biso min: 42.62 Å2
Refinement stepCycle: final / Resolution: 2.7→36.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1042 0 0 4 1046
Biso mean---92.81 -
Num. residues----123
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051081
X-RAY DIFFRACTIONf_angle_d0.6161448
X-RAY DIFFRACTIONf_chiral_restr0.023156
X-RAY DIFFRACTIONf_plane_restr0.002191
X-RAY DIFFRACTIONf_dihedral_angle_d14.831432
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7002-2.90850.39111430.3461301X-RAY DIFFRACTION100
2.9085-3.20110.34721460.28481325X-RAY DIFFRACTION100
3.2011-3.66390.33131460.24861311X-RAY DIFFRACTION100
3.6639-4.61460.24881500.1911341X-RAY DIFFRACTION100
4.6146-36.10.24141430.21061295X-RAY DIFFRACTION93
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)
13.7408-3.57481.72423.7235-0.28751.83840.3047-1.2845-0.8663-0.20950.19480.13330.1370.3364-0.42370.47980.050.04211.15590.04570.8872.2596107.058170.1872
25.5022-6.62582.92756.2092-2.0883.5117-0.5536-1.4007-0.02510.33270.7924-0.1292-0.6438-0.5547-0.35440.76010.00550.17270.81030.03050.8637-32.7307129.369466.2272
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 62 )A0
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 62 )B0

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