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- PDB-7nfu: Crystal structure of C-terminally truncated Geobacillus thermoleo... -

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Basic information

Entry
Database: PDB / ID: 7nfu
TitleCrystal structure of C-terminally truncated Geobacillus thermoleovorans nucleoid occlusion protein Noc
ComponentsNucleoid occlusion protein
KeywordsDNA BINDING PROTEIN / CTP switch / chromosome segregation / protein-DNA recognition / peripheral membrane protein
Function / homology
Function and homology information


nucleoid / division septum assembly / DNA binding / cytoplasm
Similarity search - Function
Nucleoid occlusion protein / 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
Nucleoid occlusion protein
Similarity search - Component
Biological speciesGeobacillus thermoleovorans CCB_US3_UF5 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsJalal, A.S.B. / Tran, N.T. / Wu, L.J. / Ramakrishnan, K. / Rejzek, M. / Stevenson, C.E.M. / Lawson, D.M. / Errington, J. / Le, T.B.K.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Royal SocietyURF-R-201020 United Kingdom
Wellcome Trust209500 United Kingdom
Royal SocietyRG150448 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BBS-E-J-000C0683 United Kingdom
CitationJournal: Mol.Cell / Year: 2021
Title: CTP regulates membrane-binding activity of the nucleoid occlusion protein Noc.
Authors: Jalal, A.S.B. / Tran, N.T. / Wu, L.J. / Ramakrishnan, K. / Rejzek, M. / Gobbato, G. / Stevenson, C.E.M. / Lawson, D.M. / Errington, J. / Le, T.B.K.
History
DepositionFeb 7, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
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.title / _citation.year
Revision 1.2Sep 15, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Jun 19, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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: Nucleoid occlusion protein
B: Nucleoid occlusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,50230
Polymers58,8162
Non-polymers2,68628
Water55831
1
A: Nucleoid occlusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,84516
Polymers29,4081
Non-polymers1,43715
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Nucleoid occlusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,65714
Polymers29,4081
Non-polymers1,24913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)146.790, 146.790, 146.790
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 5 - 225 / Label seq-ID: 5 - 225

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Nucleoid occlusion protein / Noc


Mass: 29408.084 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The expressed protein corresponds to residues 46-284 of UniProtKB - G8N1K9. However, sequence alignments indicate that Met46 in this sequence represents the true start and thus the numbering ...Details: The expressed protein corresponds to residues 46-284 of UniProtKB - G8N1K9. However, sequence alignments indicate that Met46 in this sequence represents the true start and thus the numbering used in this PDB entry reflects this i.e Met46 is now Met1. The C-terminal sequence KLAAALEHHHHHH is a nickel affinity tag from the pET21b expression plasmid.
Source: (gene. exp.) Geobacillus thermoleovorans CCB_US3_UF5 (bacteria)
Gene: noc, GTCCBUS3UF5_39100 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta / References: UniProt: G8N1K9
#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: SO4
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 4.49 Å3/Da / Density % sol: 72.6 % / Description: NULL
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting 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: 0.9119 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9119 Å / Relative weight: 1
ReflectionResolution: 2.5→84.89 Å / Num. obs: 36704 / % possible obs: 100 % / Redundancy: 39.7 % / CC1/2: 1 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.015 / Rrim(I) all: 0.093 / Net I/σ(I): 28.5
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
2.5-2.639.72.65441190.670.4252.688
9.02-84.8935.10.02486610.0040.025

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→84.89 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.934 / SU B: 13.604 / SU ML: 0.149 / SU R Cruickshank DPI: 0.223 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.223 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2399 1794 4.9 %RANDOM
Rwork0.2095 ---
obs0.2111 34834 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 169.64 Å2 / Biso mean: 86 Å2 / Biso min: 48.79 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.5→84.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3416 0 141 31 3588
Biso mean--118.17 70.82 -
Num. residues----434
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133568
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173368
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.6394832
X-RAY DIFFRACTIONr_angle_other_deg1.2821.5737780
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6725431
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.35622.284197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.715661
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4911532
X-RAY DIFFRACTIONr_chiral_restr0.0710.2477
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023833
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02675
Refine LS restraints NCS

Ens-ID: 1 / Number: 6306 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.501→2.566 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 114 -
Rwork0.328 2563 -
all-2677 -
obs--99.81 %
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)
12.37723.3893-1.44945.3188-3.10513.6691-0.0172-0.0241-0.0346-0.10270.13390.18920.337-0.4645-0.11670.0741-0.04670.04340.08770.01790.3733114.4874.324199.2554
23.0135-0.07030.02573.27561.85237.4780.0343-0.2598-0.09610.0861-0.11970.2071-0.0796-0.18770.08540.0054-0.00650.00090.07910.08160.1467119.123410.9117104.9071
35.8761-3.3421-0.89342.72230.63460.6490.0507-0.2466-0.04130.22040.00310.2091-0.1-0.3741-0.05380.17020.0513-0.02990.35140.03750.301393.552725.017693.1422
42.8811.5921-2.03254.61523.04496.95930.0685-0.19770.4187-0.25120.3205-0.4519-0.48511.024-0.38890.1597-0.0455-0.0230.26310.19940.70341.352456.4575102.7322
51.8907-0.31990.41432.2502-0.41457.9062-0.0507-0.05830.16070.05980.0596-0.3409-0.08720.2201-0.00890.02790.015-0.00090.0392-0.06070.192540.227753.6314110.0004
65.4928-3.26080.1133.2681-0.12790.360.0943-0.20980.11210.14390.0494-0.30870.08980.3052-0.14370.21760.10570.05290.3810.00860.325662.035433.540197.1768
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 43
2X-RAY DIFFRACTION2A44 - 104
3X-RAY DIFFRACTION3A105 - 225
4X-RAY DIFFRACTION4B5 - 42
5X-RAY DIFFRACTION5B43 - 108
6X-RAY DIFFRACTION6B109 - 225

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