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- PDB-5z2w: Crystal structure of the bacterial cell division protein FtsQ and FtsB -

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Basic information

Entry
Database: PDB / ID: 5z2w
TitleCrystal structure of the bacterial cell division protein FtsQ and FtsB
Components
  • Cell division protein FtsB
  • Cell division protein FtsQ
KeywordsCELL CYCLE / Cell division
Function / homology
Function and homology information


FtsBL complex / FtsQBL complex / cell septum assembly / divisome complex / cell septum / FtsZ-dependent cytokinesis / division septum assembly / cell division site / plasma membrane => GO:0005886 / cell division ...FtsBL complex / FtsQBL complex / cell septum assembly / divisome complex / cell septum / FtsZ-dependent cytokinesis / division septum assembly / cell division site / plasma membrane => GO:0005886 / cell division / identical protein binding / plasma membrane
Similarity search - Function
Cell division protein FtsQ/DivIB / Septum formation initiator FtsL/DivIC / Cell division protein FtsB / Septum formation initiator / Cell division protein FtsQ, C-terminal / Cell division protein FtsQ / Cell division protein FtsQ/DivIB, C-terminal / POTRA domain, FtsQ-type / Cell division protein FtsQ/DivIB, C-terminal / POTRA domain, FtsQ-type ...Cell division protein FtsQ/DivIB / Septum formation initiator FtsL/DivIC / Cell division protein FtsB / Septum formation initiator / Cell division protein FtsQ, C-terminal / Cell division protein FtsQ / Cell division protein FtsQ/DivIB, C-terminal / POTRA domain, FtsQ-type / Cell division protein FtsQ/DivIB, C-terminal / POTRA domain, FtsQ-type / membrane protein fhac / POTRA domain / POTRA domain profile. / Ubiquitin-like (UB roll) / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Cell division protein FtsB / Cell division protein FtsQ / Cell division protein FtsQ / Cell division protein FtsB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsChoi, Y. / Yoon, H.J. / Lee, H.H.
CitationJournal: Sci Rep / Year: 2018
Title: Structural Insights into the FtsQ/FtsB/FtsL Complex, a Key Component of the Divisome.
Authors: Choi, Y. / Kim, J. / Yoon, H.J. / Jin, K.S. / Ryu, S. / Lee, H.H.
History
DepositionJan 4, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 2, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell division protein FtsQ
B: Cell division protein FtsB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0504
Polymers28,0022
Non-polymers492
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-16 kcal/mol
Surface area14270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.557, 39.306, 73.191
Angle α, β, γ (deg.)90.000, 94.770, 90.000
Int Tables number3
Space group name H-MP121

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Components

#1: Protein Cell division protein FtsQ


Mass: 24045.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ftsQ / Production host: Escherichia coli (E. coli) / References: UniProt: J7Q602, UniProt: P06136*PLUS
#2: Protein/peptide Cell division protein FtsB


Mass: 3956.361 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ftsB, AWP75_20790 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Q6B6Y5, UniProt: P0A6S5*PLUS
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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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: 3.26 Å3/Da / Density % sol: 62.23 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 15% PEG6000, 0.2M magnesium chloride, 0.1M Tris-HCl pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.03
ReflectionResolution: 2.92→50 Å / Num. obs: 8124 / % possible obs: 100 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.047 / Rrim(I) all: 0.088 / Χ2: 1.563 / Net I/σ(I): 9.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allΧ2% possible allRrim(I) all
2.92-2.9740.984090.7040.5531.542100
2.97-3.0240.9533890.7380.5321.697100
3.02-3.084.10.7423950.8580.4121.6891000.85
3.08-3.154.10.6363950.8840.3541.5871000.73
3.15-3.214.10.4544090.8990.2531.5031000.521
3.21-3.294.20.4214100.930.2321.7241000.482
3.29-3.374.10.3333900.9570.1831.5641000.381
3.37-3.464.10.2484010.9780.1371.6341000.284
3.46-3.564.10.1974150.9830.1091.6971000.226
3.56-3.684.10.173780.990.0951.8681000.195
3.68-3.814.10.1264120.9910.071.7191000.145
3.81-3.964.10.0954220.9960.0531.6461000.109
3.96-4.144.10.0793940.9970.0441.6211000.091
4.14-4.364.10.0624110.9980.0351.681000.072
4.36-4.634.10.0483970.9980.0271.5391000.056
4.63-4.994.10.0434150.9990.0241.3981000.05
4.99-5.494.10.054050.9970.0281.3341000.057
5.49-6.2940.0484230.9970.0271.2731000.055
6.29-7.9240.0344150.9990.0191.1571000.039
7.92-503.70.034390.9980.0181.39899.10.035

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→36.469 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2745 749 10.04 %
Rwork0.2074 --
obs0.2141 7463 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 172.47 Å2 / Biso mean: 84.5849 Å2 / Biso min: 43.83 Å2
Refinement stepCycle: final / Resolution: 3→36.469 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1966 0 2 0 1968
Biso mean--62.88 --
Num. residues----244

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