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- PDB-6z63: FtsE structure from Streptococus pneumoniae in complex with ADP a... -

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Basic information

Entry
Database: PDB / ID: 6z63
TitleFtsE structure from Streptococus pneumoniae in complex with ADP at 1.57 A resolution (spacegroup P 21)
ComponentsCell division ATP-binding protein FtsE
KeywordsCELL CYCLE / Cell division / divisome / FtsEX / ATP-binding protein
Function / homology
Function and homology information


transmembrane transporter activity / transmembrane transport / cell cycle / cell division / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
Cell division protein FtsE, ATP-binding / ABC transporter, lipoprotein release, LolD / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Cell division ATP-binding protein FtsE / Cell division ATP-binding protein FtsE
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsAlcorlo, M. / Straume, D. / Havarstein, L.S. / Hermoso, J.A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesBFU2017-90030-P Spain
CitationJournal: Mbio / Year: 2020
Title: Structural Characterization of the Essential Cell Division Protein FtsE and Its Interaction with FtsX in Streptococcus pneumoniae.
Authors: Alcorlo, M. / Straume, D. / Lutkenhaus, J. / Havarstein, L.S. / Hermoso, J.A.
History
DepositionMay 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2021Group: Database references / Category: citation / citation_author
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
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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 ATP-binding protein FtsE
B: Cell division ATP-binding protein FtsE
C: Cell division ATP-binding protein FtsE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,4188
Polymers77,2823
Non-polymers2,1365
Water11,620645
1
A: Cell division ATP-binding protein FtsE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6153
Polymers25,7611
Non-polymers8542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cell division ATP-binding protein FtsE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1882
Polymers25,7611
Non-polymers4271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cell division ATP-binding protein FtsE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6153
Polymers25,7611
Non-polymers8542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.047, 118.541, 82.372
Angle α, β, γ (deg.)90.000, 97.550, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cell division ATP-binding protein FtsE


Mass: 25760.676 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria)
Gene: ftsE_1, ftsE, ftsE_2, AZJ28_05890, AZJ96_05755, AZK21_09500, AZK39_08795, CWI64_10710, ERS003549_00229, ERS019159_00859, ERS019166_00608, ERS019258_00545, ERS019260_01795, ERS019499_01745, ...Gene: ftsE_1, ftsE, ftsE_2, AZJ28_05890, AZJ96_05755, AZK21_09500, AZK39_08795, CWI64_10710, ERS003549_00229, ERS019159_00859, ERS019166_00608, ERS019258_00545, ERS019260_01795, ERS019499_01745, ERS020087_02007, ERS020408_00564, ERS020474_01891, ERS020873_00605, ERS021072_00923, ERS021218_01619, ERS021243_01290, ERS043879_00383, ERS050419_00449, ERS232443_01143, ERS232484_01031, ERS368006_01003, ERS409062_02036, ERS409277_00646, NCTC12140_01748, SAMEA104035134_02097, SAMEA104035170_01887, SAMEA104154666_00013, SAMEA2052026_00651, SAMEA2203388_01270, SAMEA2203858_01390, SAMEA2335963_01162, SAMEA2335976_01110, SAMEA2341322_01915, SAMEA2521606_00082, SAMEA2521861_00196, SAMEA2696310_01884, SAMEA2696394_01822, SAMEA2696492_00847, SAMEA2696596_00644, SAMEA2796717_01437, SAMEA2796719_00990, SAMEA3171064_02197, SAMEA3172940_00439, SAMEA3173021_00704, SAMEA3207192_00670, SAMEA3207204_00699, SAMEA3232645_02031, SAMEA3309623_00023, SAMEA3353431_01338, SAMEA3353605_01219, SAMEA3353631_01406, SAMEA3354309_00922, SAMEA3381574_01396, SAMEA3389847_01128, SAMEA3390019_01763, SAMEA3506052_00474, SAMEA3714202_02061, SAMEA3714261_01293, SAMEA3714340_00855, SAMEA4038883_00064, SAMEA4388199_00912, SpnNT_00739
Production host: Escherichia coli (E. coli) / References: UniProt: A0A064BZ20, UniProt: Q8DQH4*PLUS
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 645 / Source method: isolated from a natural source / Formula: H2O
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: 2.06 Å3/Da / Density % sol: 40.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.15 M NaF and 16% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.96862 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96862 Å / Relative weight: 1
ReflectionResolution: 1.57→47.97 Å / Num. obs: 86937 / % possible obs: 99.5 % / Redundancy: 5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.081 / Net I/σ(I): 11.7
Reflection shellResolution: 1.57→1.6 Å / Rmerge(I) obs: 0.817 / Num. unique obs: 4252 / CC1/2: 0.56

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OUK

2ouk


Resolution: 1.57→47.967 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2152 4228 4.87 %
Rwork0.1828 82669 -
obs0.1844 86897 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.27 Å2 / Biso mean: 22.972 Å2 / Biso min: 3.1 Å2
Refinement stepCycle: final / Resolution: 1.57→47.967 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5395 0 195 645 6235
Biso mean--35.04 30.37 -
Num. residues----686
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.57-1.58780.31521420.2659270799
1.5878-1.60650.31361560.2512709100
1.6065-1.62610.27131380.24172799100
1.6261-1.64670.27511310.24732802100
1.6467-1.66840.30331510.24912705100
1.6684-1.69120.29951120.2391276799
1.6912-1.71540.26131380.24182766100
1.7154-1.7410.31461540.2362278299
1.741-1.76820.28781480.2395265099
1.7682-1.79720.26081420.23292785100
1.7972-1.82820.27561540.2152275499
1.8282-1.86140.25341620.20072702100
1.8614-1.89720.23181280.197274499
1.8972-1.9360.23481400.1879279699
1.936-1.97810.22771460.1837271399
1.9781-2.02410.23091460.18762720100
2.0241-2.07470.24691210.18492827100
2.0747-2.13080.21141320.17922730100
2.1308-2.19350.21081530.17762810100
2.1935-2.26430.25141590.18642692100
2.2643-2.34520.2341420.18622810100
2.3452-2.43910.20581390.18792718100
2.4391-2.55010.20031220.182281399
2.5501-2.68450.20921310.18282754100
2.6845-2.85270.22451200.18682786100
2.8527-3.07290.20621410.17852789100
3.0729-3.38210.2111440.1773276099
3.3821-3.87130.17921540.1565273299
3.8713-4.87670.15431600.1358275299
4.8767-47.9670.18641220.1688279598

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