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- PDB-6t1f: Crystal structure of the C-terminally truncated chromosome-partit... -

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Basic information

Entry
Database: PDB / ID: 6t1f
TitleCrystal structure of the C-terminally truncated chromosome-partitioning protein ParB from Caulobacter crescentus complexed to the centromeric parS site
Components
  • Chromosome-partitioning protein ParB
  • DNA (5'-D(*GP*GP*AP*TP*GP*TP*TP*TP*CP*AP*CP*GP*TP*GP*AP*AP*AP*CP*AP*TP*CP*C)-3')
KeywordsDNA BINDING PROTEIN / chromosome segregation / chromosome maintenance / protein-DNA recognition
Function / homology
Function and homology information


chromosome segregation / 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
DNA / DNA (> 10) / Chromosome-partitioning protein ParB
Similarity search - Component
Biological speciesCaulobacter vibrioides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsJalal, A.S.B. / Pastrana, C.L. / Tran, N.T. / Stevenson, C.E.M. / Lawson, D.M. / Moreno-Herrero, F. / Le, T.B.K.
Funding support United Kingdom, 5items
OrganizationGrant numberCountry
Royal SocietyUF140053 United Kingdom
Royal SocietyRG150448 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/P018165/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBBS/E/J/000C0683 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/P012523/1 United Kingdom
CitationJournal: Elife / Year: 2021
Title: A CTP-dependent gating mechanism enables ParB spreading on DNA.
Authors: Jalal, A.S. / Tran, N.T. / Stevenson, C.E. / Chimthanawala, A. / Badrinarayanan, A. / Lawson, D.M. / Le, T.B.
History
DepositionOct 4, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / diffrn_source / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _diffrn_source.pdbx_synchrotron_site / _struct_ncs_dom_lim.beg_auth_comp_id ..._diffrn_source.pdbx_synchrotron_site / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chromosome-partitioning protein ParB
B: Chromosome-partitioning protein ParB
C: Chromosome-partitioning protein ParB
D: Chromosome-partitioning protein ParB
E: DNA (5'-D(*GP*GP*AP*TP*GP*TP*TP*TP*CP*AP*CP*GP*TP*GP*AP*AP*AP*CP*AP*TP*CP*C)-3')
F: DNA (5'-D(*GP*GP*AP*TP*GP*TP*TP*TP*CP*AP*CP*GP*TP*GP*AP*AP*AP*CP*AP*TP*CP*C)-3')
G: DNA (5'-D(*GP*GP*AP*TP*GP*TP*TP*TP*CP*AP*CP*GP*TP*GP*AP*AP*AP*CP*AP*TP*CP*C)-3')
H: DNA (5'-D(*GP*GP*AP*TP*GP*TP*TP*TP*CP*AP*CP*GP*TP*GP*AP*AP*AP*CP*AP*TP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)139,1058
Polymers139,1058
Non-polymers00
Water0
1
A: Chromosome-partitioning protein ParB
B: Chromosome-partitioning protein ParB
E: DNA (5'-D(*GP*GP*AP*TP*GP*TP*TP*TP*CP*AP*CP*GP*TP*GP*AP*AP*AP*CP*AP*TP*CP*C)-3')
F: DNA (5'-D(*GP*GP*AP*TP*GP*TP*TP*TP*CP*AP*CP*GP*TP*GP*AP*AP*AP*CP*AP*TP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)69,5524
Polymers69,5524
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6310 Å2
ΔGint-41 kcal/mol
Surface area25210 Å2
MethodPISA
2
C: Chromosome-partitioning protein ParB
D: Chromosome-partitioning protein ParB
G: DNA (5'-D(*GP*GP*AP*TP*GP*TP*TP*TP*CP*AP*CP*GP*TP*GP*AP*AP*AP*CP*AP*TP*CP*C)-3')
H: DNA (5'-D(*GP*GP*AP*TP*GP*TP*TP*TP*CP*AP*CP*GP*TP*GP*AP*AP*AP*CP*AP*TP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)69,5524
Polymers69,5524
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6060 Å2
ΔGint-43 kcal/mol
Surface area25430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.250, 172.928, 72.852
Angle α, β, γ (deg.)90.000, 90.540, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D
17E
27F
18E
28G
19E
29H
110F
210G
111F
211H
112G
212H

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERASNASNAA44 - 23834 - 228
21SERSERASNASNBB44 - 23834 - 228
12SERSERASNASNAA44 - 23834 - 228
22SERSERASNASNCC44 - 23834 - 228
13SERSERALAALAAA44 - 23634 - 226
23SERSERALAALADD44 - 23634 - 226
14SERSERASNASNBB44 - 23834 - 228
24SERSERASNASNCC44 - 23834 - 228
15SERSERLYSLYSBB44 - 23534 - 225
25SERSERLYSLYSDD44 - 23534 - 225
16SERSERALAALACC44 - 23634 - 226
26SERSERALAALADD44 - 23634 - 226
17DGDGDCDCEE1 - 221 - 22
27DGDGDCDCFF1 - 221 - 22
18DGDGDCDCEE1 - 221 - 22
28DGDGDCDCGG1 - 221 - 22
19DGDGDCDCEE1 - 221 - 22
29DGDGDCDCHH1 - 221 - 22
110DGDGDCDCFF1 - 221 - 22
210DGDGDCDCGG1 - 221 - 22
111DGDGDCDCFF1 - 221 - 22
211DGDGDCDCHH1 - 221 - 22
112DGDGDCDCGG1 - 221 - 22
212DGDGDCDCHH1 - 221 - 22

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12

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Components

#1: Protein
Chromosome-partitioning protein ParB


Mass: 28024.861 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: The expressed protein comprised residues 11-254 of the wild-type sequence with a C-terminal nickel affinity tag of sequence KLAAALEHHHHHH from the pET21b expression plasmid
Source: (gene. exp.) Caulobacter vibrioides (strain NA1000 / CB15N) (bacteria)
Strain: NA1000 / CB15N / Gene: parB, CCNA_03868 / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta / Variant (production host): Solu / References: UniProt: B8GW30
#2: DNA chain
DNA (5'-D(*GP*GP*AP*TP*GP*TP*TP*TP*CP*AP*CP*GP*TP*GP*AP*AP*AP*CP*AP*TP*CP*C)-3')


Mass: 6751.378 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: Palindromic DNA sequence similar to the parS sequence from Caulobacter vibriodes without 5' phosphates.
Source: (synth.) Caulobacter vibrioides (bacteria)

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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: 2.46 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: NULL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.916 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.916 Å / Relative weight: 1
ReflectionResolution: 2.9→172.93 Å / Num. obs: 29654 / % possible obs: 99.7 % / Redundancy: 6.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.057 / Rrim(I) all: 0.146 / Net I/σ(I): 8.7 / Num. measured all: 198135 / Scaling rejects: 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.9-3.087.11.5263388847750.6770.6141.6461.4100
8.7-172.9360.057675511300.9960.0250.06226.599.4

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Processing

Software
NameVersionClassification
XDSNov11-2017data reduction
Aimless0.7.2data scaling
REFMAC5.8.0230refinement
PDB_EXTRACT3.24data extraction
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UMK

4umk


Resolution: 2.9→72.96 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.926 / SU B: 50.975 / SU ML: 0.405 / SU R Cruickshank DPI: 0.3707 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.391
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2626 1466 4.9 %RANDOM
Rwork0.2395 ---
obs0.2407 28155 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 150.93 Å2 / Biso mean: 84.719 Å2 / Biso min: 49.77 Å2
Baniso -1Baniso -2Baniso -3
1--3.39 Å20 Å2-0.64 Å2
2--0.18 Å20 Å2
3---3.23 Å2
Refinement stepCycle: final / Resolution: 2.9→72.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5371 1792 0 0 7163
Num. residues----851
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0137443
X-RAY DIFFRACTIONr_bond_other_d0.0010.0185771
X-RAY DIFFRACTIONr_angle_refined_deg1.0451.51510510
X-RAY DIFFRACTIONr_angle_other_deg0.9941.87613430
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6995756
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.73721.377247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.73815788
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3421546
X-RAY DIFFRACTIONr_chiral_restr0.0530.21057
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027427
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021309
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A45810.12
12B45810.12
21A52310.1
22C52310.1
31A44560.1
32D44560.1
41B47940.12
42C47940.12
51B46730.07
52D46730.07
61C46120.12
62D46120.12
71E20400.02
72F20400.02
81E20420.02
82G20420.02
91E20400.02
92H20400.02
101F20370.02
102G20370.02
111F20500.01
112H20500.01
121G20340.02
122H20340.02
LS refinement shellResolution: 2.9→2.975 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 102 -
Rwork0.366 2083 -
all-2185 -
obs--99.82 %
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)
15.5677-0.4871.53392.3044-0.42822.00020.1155-0.3044-0.57190.05710.0052-0.14330.11680.0996-0.12080.6567-0.0320.0520.70410.01140.2398-25.0317-4.6892110.5387
20.7506-1.0937-0.33953.92921.06060.63420.0920.0636-0.1726-0.0846-0.0652-0.65190.30260.1724-0.02680.83930.07130.01540.9192-0.02180.4396-17.4133-3.8680.4248
35.3468-0.5298-1.41632.5270.362.36850.0874-0.15590.84320.0344-0.00350.144-0.1308-0.1082-0.08390.5374-0.0618-0.01580.5773-0.02370.1888-59.342942.413382.7239
41.7886-2.29421.05973.2169-1.26671.60110.13040.0423-0.0934-0.1906-0.03310.4909-0.1385-0.1968-0.09731.0852-0.06810.02111.16820.02990.5378-65.754242.125652.2747
51.33290.4242-1.38861.6506-0.91444.79610.1509-0.02690.1555-0.06980.08870.1534-0.3915-0.3872-0.23960.49320.02460.01270.6736-0.03080.0285-33.07549.325993.8821
61.08110.1082-0.13221.2765-0.91166.76590.1276-0.08020.1012-0.02060.07550.1458-0.0289-0.2516-0.20310.4930.02020.03430.604-0.05860.034-33.69259.001492.5701
70.77990.15071.09991.05730.58037.18920.17870.0666-0.1165-0.13190.1661-0.13350.46380.0778-0.34470.65090.00050.04530.76540.0090.0409-50.585927.799665.8392
81.4722-0.05680.13021.37540.11146.16450.23210.051-0.0713-0.19920.1066-0.15030.30260.1845-0.33870.61040.0280.00040.634-0.02860.0372-50.009428.066264.5586
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A44 - 238
2X-RAY DIFFRACTION2B44 - 239
3X-RAY DIFFRACTION3C44 - 238
4X-RAY DIFFRACTION4D44 - 236
5X-RAY DIFFRACTION5E1 - 22
6X-RAY DIFFRACTION6F1 - 22
7X-RAY DIFFRACTION7G1 - 22
8X-RAY DIFFRACTION8H1 - 22

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