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- PDB-7o0n: Crystal structure of a ParB E93A mutant from Myxococcus xanthus b... -

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Basic information

Entry
Database: PDB / ID: 7o0n
TitleCrystal structure of a ParB E93A mutant from Myxococcus xanthus bound to CDP and monothiophosphate
ComponentsParB family protein
KeywordsHYDROLASE / Myxococcus / ParB / DNA-segregation / CTPase
Function / homology
Function and homology information


positive regulation of sporulation resulting in formation of a cellular spore / chromosome segregation / chromosome / nucleotide binding / DNA binding / metal ion 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 / Chromosome-partitioning protein ParB
Similarity search - Component
Biological speciesMyxococcus xanthus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsAltegoer, F. / Bange, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: 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.
History
DepositionMar 26, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: 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_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2Oct 13, 2021Group: Data collection / Category: pdbx_database_proc
Revision 1.3Oct 20, 2021Group: Data collection / Database references / Category: citation / pdbx_database_proc / Item: _citation.journal_volume / _citation.page_first
Revision 1.4Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)48,24311
Polymers46,8702
Non-polymers1,3739
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7190 Å2
ΔGint-55 kcal/mol
Surface area19030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.120, 80.370, 136.830
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
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: 23434.924 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myxococcus xanthus (strain DK1622) (bacteria)
Strain: DK1622 / Gene: MXAN_7476 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q1CVJ4

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Non-polymers , 6 types, 69 molecules

#2: Chemical ChemComp-CDP / CYTIDINE-5'-DIPHOSPHATE


Mass: 403.176 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N3O11P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-TS6 / Monothiophosphate / phosphorothioic O,O,S-acid


Mass: 114.061 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H3O3PS / Feature type: SUBJECT OF INVESTIGATION
#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: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.78 Å3/Da / Density % sol: 55.75 %
Crystal growTemperature: 294 K / Method: vapor diffusion / Details: 0.1 M Phosphate-citrate pH 4.2; 40% (v/v) PEG 300

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.89→41.99 Å / Num. obs: 39707 / % possible obs: 99.7 % / Redundancy: 12.3 % / Biso Wilson estimate: 39.42 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 14.18
Reflection shellResolution: 1.89→1.95 Å / Rmerge(I) obs: 1.938 / Mean I/σ(I) obs: 1.09 / Num. unique obs: 3794 / CC1/2: 0.578

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XSCALEdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7BNK

7bnk


Resolution: 1.89→41.99 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.96 / SU B: 9.061 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.216 1986 5 %RANDOM
Rwork0.196 ---
obs0.197 37721 99.6 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 157.09 Å2 / Biso mean: 61.86 Å2 / Biso min: 27.86 Å2
Baniso -1Baniso -2Baniso -3
1--2.55 Å20 Å20 Å2
2---1.91 Å20 Å2
3---4.46 Å2
Refinement stepCycle: final / Resolution: 1.89→41.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3052 0 81 60 3193
Biso mean--46.48 51.62 -
Num. residues----388
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0173192
X-RAY DIFFRACTIONr_bond_other_d0.0010.0193208
X-RAY DIFFRACTIONr_angle_refined_deg1.3191.9284310
X-RAY DIFFRACTIONr_angle_other_deg1.1322.6777374
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2915394
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.07221.099182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.13815607
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9451536
X-RAY DIFFRACTIONr_chiral_restr0.1230.2495
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023517
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02701
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.89→1.94 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 139 -
Rwork0.376 2644 -
all-2783 -
obs--95.5 %
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)
15.62681.09232.67165.3901-1.187411.8780.2948-0.23-0.1401-0.1961-0.02940.1840.0466-1.0544-0.26530.4163-0.0501-0.11150.4674-0.0040.0939-3.7316.143.938
29.23586.122-6.02999.2961-1.337712.40930.62790.909-0.33840.4704-0.52141.124-0.4789-1.7538-0.10640.66530.0488-0.13041.61950.00850.6285-15.4386.5074.752
37.0084-2.79590.91977.4097-2.50473.13230.28990.324-0.7454-0.6159-0.0501-0.03170.5072-0.2475-0.23980.189-0.00470.02310.18250.02340.251324.84410.76921.001
44.74493.1592.22156.81743.95099.4913-0.0790.414-0.0371-0.47510.0687-0.06140.09270.11230.01040.14410.04370.01630.11260.02770.09422.12924.74714.619
54.655-2.17340.23917.3054-1.39492.84130.0715-0.0008-0.4626-0.1221-0.1257-0.15560.2340.12570.05420.03810.0168-0.01390.03150.01110.091824.74613.17424.747
60.65411.8060.11087.5849-1.60813.5780.07770.0296-0.10340.3638-0.1019-0.5317-0.20790.23580.02430.06570.0374-0.02550.11490.07180.202227.03114.72228.771
72.7321-5.18050.029613.5495-1.81453.7569-0.00750.011-0.051-0.0562-0.0038-0.14230.17820.04020.01130.0633-0.0336-0.04790.1053-0.01380.097713.0516.86727.68
84.55073.8294-1.43847.4101-3.65462.06040.01020.16970.39240.28660.15870.3769-0.2168-0.1375-0.16890.15150.0687-0.01830.12450.01620.04277.50133.21120.64
910.2693-1.14540.6575.95480.51154.47410.00180.62330.3568-0.35510.0287-0.1957-0.3077-0.05-0.03050.24370.02920.01920.12270.07340.052914.19938.65114.457
107.0440.76572.92538.5534-2.15798.5487-0.05851.20570.3779-0.68060.2620.2368-0.6067-0.3594-0.20350.3350.07-0.04040.71140.14050.2727-6.39236.3368.086
1112.308-0.24776.47937.948-1.05499.89830.60480.29940.4261-2.1341-0.40380.02591.824-0.4789-0.2011.4599-0.04030.24421.1525-0.16610.6225-7.40631.669-1.792
123.17372.0263.87815.49882.00087.32390.1194-0.09170.55550.144-0.1550.2963-0.20920.0260.03560.2408-0.01610.09230.3015-0.03270.26689.19128.6936.969
139.6914-5.10073.83465.2156-2.8183.70880.0492-0.2460.13320.1563-0.01880.32110.1163-0.3406-0.03040.0938-0.02290.01440.15180.00720.14482.28215.44433.477
145.25273.39580.35436.0536-0.40321.71080.2885-0.39680.28060.7643-0.12420.214-0.1736-0.1252-0.16430.1934-0.00090.02720.103-0.02510.038413.60226.31637.655
151.732.29450.23488.40870.29590.9280.00560.0701-0.1052-0.09280.111-0.05510.1177-0.146-0.11660.09480.0093-0.0350.08290.01030.024811.60117.83321.6
163.73160.00750.26494.4090.12467.27860.03470.0181-0.2007-0.06090.09840.38690.4449-0.4823-0.13310.1367-0.0916-0.08270.11420.0430.17121.9632.08525.456
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B176 - 219
2X-RAY DIFFRACTION2B220 - 231
3X-RAY DIFFRACTION3A39 - 58
4X-RAY DIFFRACTION4A59 - 72
5X-RAY DIFFRACTION5A73 - 101
6X-RAY DIFFRACTION6A102 - 115
7X-RAY DIFFRACTION7A116 - 128
8X-RAY DIFFRACTION8A129 - 147
9X-RAY DIFFRACTION9A148 - 175
10X-RAY DIFFRACTION10A176 - 215
11X-RAY DIFFRACTION11A216 - 231
12X-RAY DIFFRACTION12B38 - 58
13X-RAY DIFFRACTION13B59 - 72
14X-RAY DIFFRACTION14B73 - 115
15X-RAY DIFFRACTION15B116 - 147
16X-RAY DIFFRACTION16B148 - 175

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