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- PDB-7bnk: Crystal structure of ParB from Myxococcus xanthus bound to CDP an... -

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Basic information

Entry
Database: PDB / ID: 7bnk
TitleCrystal structure of ParB from Myxococcus xanthus bound to CDP and Monothiophosphate
ComponentsParB family protein
KeywordsDNA BINDING PROTEIN / DNA-binding protein / CTP / Myxococcus / DNA-segregation
Function / homology
Function and homology information


chromosome segregation / DNA binding
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
CYTIDINE-5'-DIPHOSPHATE / DI(HYDROXYETHYL)ETHER / Monothiophosphate / ParB family protein
Similarity search - Component
Biological speciesMyxococcus xanthus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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)48,59412
Polymers47,1002
Non-polymers1,49410
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7490 Å2
ΔGint-47 kcal/mol
Surface area18150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.243, 80.706, 143.380
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

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Protein , 1 types, 2 molecules AB

#1: Protein ParB family protein


Mass: 23550.010 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

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Non-polymers , 6 types, 169 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-TS6 / Monothiophosphate / phosphorothioic O,O,S-acid / Thiophosphate


Mass: 114.061 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H3O3PS / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CDP / CYTIDINE-5'-DIPHOSPHATE / Cytidine diphosphate


Mass: 403.176 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N3O11P2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.95 Å3/Da / Density % sol: 58.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 10% (v/v) Glycerol 0.2M MgCl2, 0.1M Tris pH 8.5, 25 % (v/v) 1,2-Propanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.9→42.28 Å / Num. obs: 41375 / % possible obs: 99.87 % / Redundancy: 7.3 % / Biso Wilson estimate: 32.36 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.1961 / Net I/σ(I): 9.21
Reflection shellResolution: 1.9→1.968 Å / Rmerge(I) obs: 2.221 / Mean I/σ(I) obs: 0.83 / Num. unique obs: 4071 / 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: 6SDK

6sdk


Resolution: 1.9→42.28 Å / SU ML: 0.2755 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.6499
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2366 2071 5 %
Rwork0.2034 39347 -
obs0.2051 41372 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.41 Å2
Refinement stepCycle: LAST / Resolution: 1.9→42.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3005 0 89 159 3253
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00553160
X-RAY DIFFRACTIONf_angle_d0.84194273
X-RAY DIFFRACTIONf_chiral_restr0.0493491
X-RAY DIFFRACTIONf_plane_restr0.0053554
X-RAY DIFFRACTIONf_dihedral_angle_d7.9081446
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.940.38641300.38092464X-RAY DIFFRACTION95.33
1.94-1.990.36651350.33562579X-RAY DIFFRACTION99.82
1.99-2.040.33351360.29882590X-RAY DIFFRACTION99.93
2.04-2.10.35561380.29412619X-RAY DIFFRACTION99.75
2.1-2.170.29811350.26112568X-RAY DIFFRACTION99.96
2.17-2.250.26471380.2372621X-RAY DIFFRACTION99.93
2.25-2.340.27491360.2242591X-RAY DIFFRACTION99.89
2.34-2.450.24561380.22272607X-RAY DIFFRACTION100
2.45-2.570.26731370.2092611X-RAY DIFFRACTION100
2.57-2.740.25691380.20342622X-RAY DIFFRACTION99.89
2.74-2.950.23721390.19722646X-RAY DIFFRACTION100
2.95-3.240.21641390.20422636X-RAY DIFFRACTION100
3.24-3.710.20761410.17882670X-RAY DIFFRACTION99.96
3.71-4.670.19691410.15912686X-RAY DIFFRACTION99.93
4.68-42.280.20821500.18382837X-RAY DIFFRACTION99.67
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)
13.351247172020.3119231746590.9562965711043.109465176070.9553009800456.507692049550.010522694260.09077906646350.305603063553-0.3618349346770.03831013506380.128106436578-0.3255679596250.00536428754334-0.09265188446440.285085468961-0.00603910047883-0.009847766031430.2239320525980.02596568103720.298022348276-9.12529.117-37.367
24.028070640223.772226694975.957948473163.786674882665.662876631058.735664391340.1305597827450.372815222041-0.292282480556-0.2293465543310.154762861974-0.5680304881970.1569751841640.656684984249-0.2039076980280.2721574032570.04894935632790.02402281507670.2932180882050.002229383795290.351885956197-2.63215.017-34.948
34.792950569770.146113978217-1.224508320251.1399680455-1.369572584384.868510650290.0706979916910.5833279767380.448628143133-0.02878923805070.2821528758340.476935930839-0.491117076112-0.18481388579-0.2862537330390.2731166442040.0107732237131-0.01699495815660.2420109526410.02727360397880.247354110382-16.45226.513-38.515
45.17309406604-2.62986532136-0.5002697251465.631286446820.1126811458221.291416448720.1997512896280.1979687534090.136775788583-0.592260996648-0.110886512888-0.040544997863-0.142524533367-0.00476482824538-0.0658295405760.279487263881-0.00978227409656-0.02972222787330.2400466194120.04606970045310.214106547856-12.55826.05-39.406
52.07462507624-1.315341928740.6223140632863.57328493954-0.4374213115681.26203257401-0.044249811242-0.148839676255-0.04742583157460.3138325250960.0156937899002-0.06368233413230.01255850388740.04348601253590.04017968734270.215401352476-0.00557819096135-0.001596196980360.2709343768260.03202120903850.237868851148-11.81717.32-23.121
63.17949497523-0.9813344047070.5940698453575.11624047865-0.7649686669797.420676653770.07154846410260.062445415374-0.3433795236370.036366882362-0.126424121786-0.6064210531420.2044085660450.5795392495130.06175330951770.2431762686440.0215851924085-0.03863704152240.2360750285370.03104440175340.410558492835-1.8662.343-26.816
72.0415344219-0.460154298297-1.080405667923.918791967752.899427882762.61271022751-0.285934072408-0.474457114034-0.4815492799780.3930964278110.100842047489-0.0276505628907-0.7107638688370.3546773520730.1541521079690.599561196963-0.00158145774562-0.07788085010060.5979051709710.1205660021390.3670974447321.2556.501-8.317
89.807026964131.345647613150.006863894458412.341489194231.803397873021.91205774994-0.0528511957894-1.38816239088-0.6139046911272.23966668329-0.112224658711-0.118046691743-0.4761546870481.325658319930.03147564473330.993034120711-0.0352211213876-0.08873328529880.9435895442610.1605686222010.4516292119343.6385.3150.116
90.8895222904760.712295791550.04306239376940.702968049299-0.4866335776471.912948126970.387067596899-0.4895616929640.4783587563610.777847528919-0.634113229457-0.176295418429-0.1479142065761.007578201080.1314194905750.723841623364-0.162012935231-0.1717833539660.7917936998140.002245818338380.2074246843174.36113.793-11.445
107.11455256332-0.7644256569742.511275260733.496429175410.516638930633.54295499401-0.0288337351649-0.304969807146-0.6169281081340.252232142408-0.02084829354310.1438516733090.128528532848-0.3361508670550.04816717581840.249604935539-0.03589469256650.04095076618510.3058227807520.05122221499460.375253301719-24.30110.507-22.566
118.71334637347-4.06592666483.263050559983.4337638144-3.069352744973.09664899065-0.239254018659-0.6279816273920.08545902401570.1109040104530.09199471523180.161193631610.101088878899-0.3562668068580.06452770914210.2767348101910.016196987293-0.01367970954920.314921514725-0.02892458229360.255355688811-22.51924.78-16.32
123.97176458151.76892182718-0.3268296590841.067643832390.3988406656994.43600142318-0.1911001825030.114013310482-0.755614153513-0.4442883702310.0763936066579-0.459857744290.333822860567-0.2275919884120.05651252422130.23395273193-0.000181684782535-0.003422452165510.279065292214-0.04421097618430.454403334379-25.01812.933-30.033
131.2172765468-0.02736380967810.1880181804993.870907765842.624126811835.107453362370.0337065160897-0.10371203691-0.3238800262310.0155840699593-0.1286514214210.4453543876310.0978144814199-0.3248286212130.1379336448180.165644741289-0.0244881544769-0.02427706318460.2310932690760.00610593355090.343501291825-26.11213.329-26.302
141.35649610338-0.3927613643660.2444087934924.487301822141.215718381491.36426548348-0.0502344496891-0.1771762174910.1766834711450.1823851153730.09696475357-0.107013253819-0.1115027736020.0570997816022-0.02718314715790.234766112154-0.00894087315857-0.004815513618520.269486499906-0.014952412840.242305709468-13.08827.965-22.642
155.954640216964.149453917220.669273410165.02171681705-1.97273321042.95654158966-0.127007628933-1.319149671990.2232407298270.538500056739-0.120069632789-0.169174943398-0.4341913104720.1573591207050.1182612786630.4356361513580.0219178874314-0.06335784236910.46076256711-0.1956278374870.311897372617-9.35537.095-11.355
165.51465191136-1.09720053220.1534391728819.867966124711.169876027129.37839470738-0.25699537354-0.6597001719520.285841115470.6362410662450.4410505748770.6392219885680.210929891473-0.0538927350012-0.1133663870820.2965904338960.00933259629851-0.02039125111780.601104055685-0.09741486835960.4108601311392.94934.398-10.758
172.91319719992-0.728176323587-2.775262178012.457625250933.280086337076.05806732039-0.181908837394-0.9357459542251.198333124980.3113675009710.622866561752-1.5314311807-0.1648650029861.35827186946-0.3454506491190.461606078382-0.103697356614-0.06481097960530.984819126041-0.2700397748210.76820172866310.83535.92-7.82
184.057206055251.9281551554-2.306979901954.890577365162.832884764515.302396481140.415886290341-2.257162142-0.8687583042081.044627509360.0616572772085-0.3677724423720.745292486794-0.976319971637-0.4925430084940.7379854777930.0559953944066-0.1842834430791.3651776040.02113754150230.4141842242897.12429.7970.065
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 37:58 )A37 - 58
2X-RAY DIFFRACTION2( CHAIN A AND RESID 59:72 )A59 - 72
3X-RAY DIFFRACTION3( CHAIN A AND RESID 73:85 )A73 - 85
4X-RAY DIFFRACTION4( CHAIN A AND RESID 86:115 )A86 - 115
5X-RAY DIFFRACTION5( CHAIN A AND RESID 116:147 )A116 - 147
6X-RAY DIFFRACTION6( CHAIN A AND RESID 148:175 )A148 - 175
7X-RAY DIFFRACTION7( CHAIN A AND RESID 176:202 )A176 - 202
8X-RAY DIFFRACTION8( CHAIN A AND RESID 203:215 )A203 - 215
9X-RAY DIFFRACTION9( CHAIN A AND RESID 216:230 )A216 - 230
10X-RAY DIFFRACTION10( CHAIN B AND RESID 37:58 )B37 - 58
11X-RAY DIFFRACTION11( CHAIN B AND RESID 59:72 )B59 - 72
12X-RAY DIFFRACTION12( CHAIN B AND RESID 73:85 )B73 - 85
13X-RAY DIFFRACTION13( CHAIN B AND RESID 86:115 )B86 - 115
14X-RAY DIFFRACTION14( CHAIN B AND RESID 116:163 )B116 - 163
15X-RAY DIFFRACTION15( CHAIN B AND RESID 164:175 )B164 - 175
16X-RAY DIFFRACTION16( CHAIN B AND RESID 176:202 )B176 - 202
17X-RAY DIFFRACTION17( CHAIN B AND RESID 203:215 )B203 - 215
18X-RAY DIFFRACTION18( CHAIN B AND RESID 216:229 )B216 - 229

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