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- PDB-7bnr: Crystal structure of a ParB Q52A mutant from Myxococcus xanthus b... -

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Basic information

Entry
Database: PDB / ID: 7bnr
TitleCrystal structure of a ParB Q52A mutant from Myxococcus xanthus bound to CTPyS
ComponentsParB family protein
KeywordsDNA BINDING PROTEIN / DNA-binding protein / CTP / Myxococcus / DNA-segregation
Function / homology
Function and homology information


chromosome segregation / chromosome / hydrolase activity / nucleotide binding / DNA binding / cytoplasm
Similarity search - Function
ParB/Spo0J, HTH domain / HTH domain found in ParB protein / : / ParB/RepB/Spo0J partition protein / ParB/Sulfiredoxin domain / ParB/Sulfiredoxin / ParB-like nuclease domain / ParB/Sulfiredoxin superfamily
Similarity search - Domain/homology
Cytosine 5'-[gamma-thio]triphosphate / Chromosome-partitioning protein ParB
Similarity search - Component
Biological speciesMyxococcus xanthus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsAltegoer, F. / Bange, G.
Citation
Journal: Mol.Cell / Year: 2021
Title: The CTPase activity of ParB determines the size and dynamics of prokaryotic DNA partition complexes.
Authors: Osorio-Valeriano, M. / Altegoer, F. / Das, C.K. / Steinchen, W. / Panis, G. / Connolley, L. / Giacomelli, G. / Feddersen, H. / Corrales-Guerrero, L. / Giammarinaro, P.I. / Hanssmann, J. / ...Authors: Osorio-Valeriano, M. / Altegoer, F. / Das, C.K. / Steinchen, W. / Panis, G. / Connolley, L. / Giacomelli, G. / Feddersen, H. / Corrales-Guerrero, L. / Giammarinaro, P.I. / Hanssmann, J. / Bramkamp, M. / Viollier, P.H. / Murray, S. / Schafer, L.V. / Bange, G. / Thanbichler, M.
#1: Journal: Biorxiv / Year: 2021
Title: The CTPase activity of ParB acts as a timing mechanism to control the dynamics and function of prokaryotic DNA partition complexes
Authors: Osorio-Valeriano, M. / Altegoer, F. / Das, C.K. / Steinchen, W. / Panis, G. / Connolley, L. / Giacomelli, G. / Feddersen, H. / Corrales-Guerrero, L. / Giammarinaro, P. / Hanssmann, J. / ...Authors: Osorio-Valeriano, M. / Altegoer, F. / Das, C.K. / Steinchen, W. / Panis, G. / Connolley, L. / Giacomelli, G. / Feddersen, H. / Corrales-Guerrero, L. / Giammarinaro, P. / Hanssmann, J. / Bramkamp, M. / Viollier, P.H. / Murray, S. / Schafer, L.V. / Bange, G. / Thanbichler, M.
History
DepositionJan 22, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 20, 2021Group: Data collection / Database references / Category: citation / pdbx_database_proc / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ParB family protein
B: ParB family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0117
Polymers46,8722
Non-polymers1,1395
Water5,513306
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-13 kcal/mol
Surface area18790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.750, 80.870, 135.710
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein ParB family protein


Mass: 23435.908 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myxococcus xanthus (strain DK 1622) (bacteria)
Strain: DK 1622 / Gene: MXAN_7476 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q1CVJ4
#2: Chemical ChemComp-UFQ / Cytosine 5'-[gamma-thio]triphosphate / [[[(2R,3S,4R,5R)-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-sulfanyl-phosphinic acid


Mass: 499.222 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N3O13P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.92 Å3/Da / Density % sol: 36.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris pH 8.5, 20% PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97626 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 1.5→43.39 Å / Num. obs: 56287 / % possible obs: 99.82 % / Redundancy: 12.8 % / Biso Wilson estimate: 25.24 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.67
Reflection shellResolution: 1.5→1.55 Å / Mean I/σ(I) obs: 0.74 / Num. unique obs: 7929 / CC1/2: 0.457

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7BNK

7bnk


Resolution: 1.7→43.35 Å / SU ML: 0.1834 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.0597
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2107 2811 5 %RANDOM
Rwork0.1823 53458 --
obs0.1837 56269 99.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.38 Å2
Refinement stepCycle: LAST / Resolution: 1.7→43.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3006 0 66 306 3378
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00683187
X-RAY DIFFRACTIONf_angle_d1.25344331
X-RAY DIFFRACTIONf_chiral_restr0.0621501
X-RAY DIFFRACTIONf_plane_restr0.0056563
X-RAY DIFFRACTIONf_dihedral_angle_d9.4156485
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.730.26451390.25942629X-RAY DIFFRACTION99.96
1.73-1.760.30541390.25192650X-RAY DIFFRACTION100
1.76-1.790.26441360.24012607X-RAY DIFFRACTION99.89
1.79-1.830.26721400.21752650X-RAY DIFFRACTION99.89
1.83-1.870.21251370.19742608X-RAY DIFFRACTION99.96
1.87-1.910.2391410.18852667X-RAY DIFFRACTION99.96
1.91-1.960.22771370.18792624X-RAY DIFFRACTION99.82
1.96-2.020.20381390.18772653X-RAY DIFFRACTION100
2.02-2.070.24921400.1922663X-RAY DIFFRACTION99.93
2.07-2.140.20831380.19152624X-RAY DIFFRACTION100
2.14-2.220.20541400.18052667X-RAY DIFFRACTION99.96
2.22-2.310.18751410.17962667X-RAY DIFFRACTION99.96
2.31-2.410.21731400.18582659X-RAY DIFFRACTION100
2.41-2.540.24981400.19312667X-RAY DIFFRACTION99.93
2.54-2.70.23211410.19592689X-RAY DIFFRACTION100
2.7-2.910.20421410.19292679X-RAY DIFFRACTION99.96
2.91-3.20.23081420.18752689X-RAY DIFFRACTION100
3.2-3.660.21021430.17352727X-RAY DIFFRACTION100
3.66-4.610.16081450.15042751X-RAY DIFFRACTION100
4.61-43.350.20731520.17792888X-RAY DIFFRACTION99.77
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)
11.69670165055-0.00907990790335-0.187210389256.194729711140.2596422491711.551860579-0.01023637284570.09512408860870.0655171192461-0.3164054653630.0208492430534-0.182825129699-0.04954401107930.0766978311732-0.02157411107860.176196596467-0.01317217669670.01739260511020.1828762770630.01823391568010.133727240441-10.086732693425.3697885281-37.0148742475
21.57463235261-1.140835182370.1778779196212.52813253899-0.5190130621960.593909685199-0.0494707808266-0.169734880294-0.0800730468050.08116821495010.0689762300714-0.06014378877190.05686349305130.07073428106740.004244348730230.183518964343-0.00897030217414-0.01557822475990.2298432420880.001605368254660.183798810999-7.3010700390712.5254017989-24.4058414141
35.877714481510.9210183084451.222225955614.24397965314-0.3590695799044.797897509570.322889842893-0.2805455505070.04748412388670.679862332855-0.37483141923-0.361303653313-0.3977919098021.166230813110.1045373122480.551927210571-0.15708819631-0.07383748145440.7889128743030.07324712910460.36579324737610.14086752376.88187268723-4.90298406997
42.118876511090.687807772376-0.1884974423254.464835483451.640532038172.533115695960.0479759374938-0.233984656996-0.1065022924690.321744434029-0.01167221804310.1711471607160.125806183975-0.0302612810098-0.01756853480330.17933487016-0.007977990282920.0171564621470.2196901302490.009316927032790.217028221519-24.028904920614.543862529-21.7893842982
55.018051671141.869831346122.359100374912.202041224113.726873916376.712381963120.1537609868130.00949717266358-0.03577761867190.148812988026-0.09959167845970.01810455858240.183091272054-0.1755059838420.05357348811220.2027982250730.01269976500680.004137174447070.2134754491990.02771365305670.211752082915-13.49564473846.51659307621-28.2532149813
61.903546954650.6401265071430.6158368318322.598413303860.6527192881051.97960657522-0.0629321622457-0.2422807649720.2457105104280.4380539491190.0448475231728-0.213270297745-0.2024837202990.1578331196050.01187425906810.267585353065-0.0229806403882-0.04587482035910.235164569741-0.0374703203380.206360422824-7.6059788778735.8477703895-17.2118090438
76.99396638382-2.569210796530.2481392092037.85082801654-2.479529325249.05559466512-0.22472204004-0.2043151886360.2617558647770.4496876501870.247963443311-1.072053138310.07291923701781.400398912630.06829805960250.5454380049190.124681435625-0.05662260117050.874684879766-0.06135513844990.4689015030838.3432051234935.2434188529-6.35721665507
82.871407965424.038204769384.221117130195.940368028626.295079780446.70152970988-0.0713452346238-0.978119818580.09038410861150.4906158815450.430782113909-0.2630714256530.2453509057730.807308351681-0.2214601446230.9072560241150.134924021916-0.157478138391.107061537430.0591208383850.7137713499677.8384109571235.30432372372.50260401219
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 37 through 101 )AA37 - 1011 - 69
22chain 'A' and (resid 102 through 190 )AA102 - 19070 - 165
33chain 'A' and (resid 191 through 231 )AA191 - 231166 - 206
44chain 'B' and (resid 38 through 115 )BD38 - 1151 - 84
55chain 'B' and (resid 116 through 128 )BD116 - 12885 - 99
66chain 'B' and (resid 129 through 190 )BD129 - 190100 - 163
77chain 'B' and (resid 191 through 219 )BD191 - 219164 - 192
88chain 'B' and (resid 220 through 233 )BD220 - 233193 - 206

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