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- PDB-8onw: Crystal structure of the hetero-dimeric complex from Archaeoglobu... -

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Basic information

Entry
Database: PDB / ID: 8onw
TitleCrystal structure of the hetero-dimeric complex from Archaeoglobus fulgidus PRC1 and PRC2 domains
Components(PRC-barrel domain-containing protein) x 3
KeywordsCELL CYCLE / ftsz / cell division / divisome / archeae
Function / homologyPRC-barrel domain / PRC-barrel domain / PRC-barrel-like superfamily / PRC-barrel domain-containing protein / PRC-barrel domain-containing protein
Function and homology information
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsCiziene, D. / Bellini, D. / Lowe, J.Y.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: Nat Microbiol / Year: 2024
Title: Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division.
Authors: Nussbaum, P. / Kureisaite-Ciziene, D. / Bellini, D. / van der Does, C. / Kojic, M. / Taib, N. / Yeates, A. / Tourte, M. / Gribaldo, S. / Loose, M. / Lowe, J. / Albers, S.V.
History
DepositionApr 4, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PRC-barrel domain-containing protein
H: PRC-barrel domain-containing protein
B: PRC-barrel domain-containing protein
C: PRC-barrel domain-containing protein
D: PRC-barrel domain-containing protein
E: PRC-barrel domain-containing protein
F: PRC-barrel domain-containing protein
G: PRC-barrel domain-containing protein


Theoretical massNumber of molelcules
Total (without water)72,7018
Polymers72,7018
Non-polymers00
Water724
1
A: PRC-barrel domain-containing protein
H: PRC-barrel domain-containing protein


Theoretical massNumber of molelcules
Total (without water)19,1792
Polymers19,1792
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-15 kcal/mol
Surface area10380 Å2
MethodPISA
2
B: PRC-barrel domain-containing protein
C: PRC-barrel domain-containing protein


Theoretical massNumber of molelcules
Total (without water)19,1792
Polymers19,1792
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-14 kcal/mol
Surface area10290 Å2
MethodPISA
3
D: PRC-barrel domain-containing protein
E: PRC-barrel domain-containing protein


Theoretical massNumber of molelcules
Total (without water)17,1712
Polymers17,1712
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-14 kcal/mol
Surface area8700 Å2
MethodPISA
4
F: PRC-barrel domain-containing protein
G: PRC-barrel domain-containing protein


Theoretical massNumber of molelcules
Total (without water)17,1712
Polymers17,1712
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-13 kcal/mol
Surface area8990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.086, 102.633, 112.323
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 PRC-barrel domain-containing protein


Mass: 10536.238 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: XD40_0572 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A117KMF0
#2: Protein
PRC-barrel domain-containing protein


Mass: 8643.102 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: XD40_0428 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A117KMK3
#3: Protein PRC-barrel domain-containing protein


Mass: 8527.935 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: XD40_0572 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A117KMF0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.29 Å3/Da / Density % sol: 46.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 5% MPD, 40 mM magnesium chloride, 50 mM sodium cacodylate pH 6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.29→39.02 Å / Num. obs: 30556 / % possible obs: 89 % / Redundancy: 6 % / CC1/2: 0.5 / Rrim(I) all: 0.048 / Net I/σ(I): 11.3
Reflection shellResolution: 2.29→2.37 Å / Num. unique obs: 463 / CC1/2: 0.5

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Processing

Software
NameVersionClassification
REFMACv5.0refinement
PHENIXv1.7refinement
DIALSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.29→39.02 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.28 --
Rwork0.23 --
obs-30556 89 %
Displacement parametersBiso mean: 68.23 Å2
Refinement stepCycle: LAST / Resolution: 2.29→39.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5079 0 0 4 5083
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00775152
X-RAY DIFFRACTIONf_angle_d1.03586952
X-RAY DIFFRACTIONf_chiral_restr0.0619833
X-RAY DIFFRACTIONf_plane_restr0.0068868
X-RAY DIFFRACTIONf_dihedral_angle_d9.02131949

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