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- PDB-6z67: FtsE structure of Streptococcus pneumoniae in complex with AMPPNP... -

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Basic information

Entry
Database: PDB / ID: 6z67
TitleFtsE structure of Streptococcus pneumoniae in complex with AMPPNP at 2.4 A resolution
ComponentsCell division ATP-binding protein FtsE
KeywordsCELL CYCLE / FtsE / cell division / divisome / FtsEX / FtsX / ATP-binding protein
Function / homology
Function and homology information


transmembrane transporter activity / transmembrane transport / 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 / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / 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: 2.4 Å
AuthorsAlcorlo, M. / Straume, D. / Havarstein, L.S. / Hermoso, j.A.
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 28, 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

Downloads & links

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Assembly

Deposited unit
C: Cell division ATP-binding protein FtsE
B: Cell division ATP-binding protein FtsE
E: Cell division ATP-binding protein FtsE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,7226
Polymers77,2823
Non-polymers1,4403
Water93752
1
C: 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
2
B: Cell division ATP-binding protein FtsE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2672
Polymers25,7611
Non-polymers5061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Cell division ATP-binding protein FtsE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2672
Polymers25,7611
Non-polymers5061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.068, 117.901, 81.484
Angle α, β, γ (deg.)90.000, 98.110, 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


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.03 Å3/Da / Density % sol: 39.38 %
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: 0.97934 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.4→47.6 Å / Num. obs: 23969 / % possible obs: 99 % / Redundancy: 5.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.6
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.55 / Num. unique obs: 2528 / CC1/2: 0.91

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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: 2.4→47.596 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 30.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2523 1188 4.96 %
Rwork0.1886 22751 -
obs0.1919 23939 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.68 Å2 / Biso mean: 51.2369 Å2 / Biso min: 16.79 Å2
Refinement stepCycle: final / Resolution: 2.4→47.596 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5358 0 127 52 5537
Biso mean--65.56 43.62 -
Num. residues----681
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4-2.50930.35051220.25892888100
2.5093-2.64150.29751440.2436282699
2.6415-2.8070.27961670.2437284899
2.807-3.02370.35441620.2308280498
3.0237-3.32790.28441460.2223279998
3.3279-3.80930.25551430.1815281598
3.8093-4.79860.19341440.1442288199
4.7986-47.5960.21691600.16492890100
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)
11.0440.91140.14351.3180.07820.97020.00050.23270.0734-0.2804-0.05420.1242-0.1037-0.05810.00040.20040.02720.03090.2510.02330.18448.1574-30.277712.8719
21.4087-0.43940.26390.9750.62690.8938-0.0579-0.07370.2458-0.044-0.01010.0525-0.0529-0.17750.00080.14920.01590.02770.1801-0.0310.22382.9481-20.986435
31.3619-0.0565-0.28881.21290.08380.31510.0684-0.01610.2003-0.1097-0.0523-0.107-0.16740.205-0.00070.1837-0.01550.05420.29350.0030.342620.491-20.23121.0869
41.0090.36460.09930.57760.1930.87740.05820.2002-0.0277-0.147-0.04170.0112-0.1292-0.04950.00050.3020.0816-0.01160.342-0.02220.2681.004320.312912.4244
50.4212-0.47820.11490.4143-0.39350.29010.28420.18330.0646-0.3965-0.3814-0.41060.51990.3580.00150.36520.0317-0.02110.43630.00230.486911.196413.122125.8972
60.37160.10650.2240.3664-0.33740.5640.1529-0.15780.17580.1168-0.13480.2232-0.2418-0.04710.00010.3920.0110.00440.3591-0.06280.364710.537114.844840.3304
71.4304-0.86220.58040.5559-0.65450.91370.0026-0.1799-0.38090.0198-0.0716-0.0407-0.0106-0.1391-0.00030.1749-0.0116-0.0050.2112-0.00590.3332-0.62356.826230.2974
80.4997-0.0212-0.0538-0.0042-0.16960.31770.07980.048-0.0054-0.4586-0.07760.5489-0.0170.07780.00020.33110.0787-0.05340.3713-0.06110.4052-12.752512.155913.6146
90.267-0.0659-0.17310.51540.52960.44010.31220.1066-0.1401-0.098-0.18120.15340.30510.11450.00650.38990.074-0.08680.2066-0.04640.19572.5246-4.4609-27.2302
100.5919-0.0924-0.10440.05430.23650.18620.0723-0.0366-0.27410.25460.18130.05670.75080.2555-0.00020.67990.0752-0.14860.3578-0.03840.348211.7752-12.2722-22.0825
110.18450.1249-0.25530.48330.10860.3624-0.2066-0.3658-0.8433-0.42460.36470.20990.196-0.03270.00120.67930.056-0.07770.35730.0430.55997.1759-8.3485-1.7215
121.2094-0.1488-0.34721.0651-0.00591.656-0.0468-0.11070.06630.29660.05740.0296-0.09420.14560.00190.34490.03220.00010.2378-0.01740.1867.05792.6449-6.2301
130.2362-0.1041-0.32580.27160.08360.39570.26920.12670.2274-0.3576-0.1391-0.28050.3762-0.59220.00030.42290.0391-0.00610.32790.01850.2506-1.46857.1626-27.5877
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 1 through 86 )C1 - 86
2X-RAY DIFFRACTION2chain 'C' and (resid 87 through 171 )C87 - 171
3X-RAY DIFFRACTION3chain 'C' and (resid 172 through 229 )C172 - 229
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 72 )B1 - 72
5X-RAY DIFFRACTION5chain 'B' and (resid 73 through 97 )B73 - 97
6X-RAY DIFFRACTION6chain 'B' and (resid 98 through 127 )B98 - 127
7X-RAY DIFFRACTION7chain 'B' and (resid 128 through 204 )B128 - 204
8X-RAY DIFFRACTION8chain 'B' and (resid 205 through 229 )B205 - 229
9X-RAY DIFFRACTION9chain 'E' and (resid 1 through 50 )E1 - 50
10X-RAY DIFFRACTION10chain 'E' and (resid 51 through 86 )E51 - 86
11X-RAY DIFFRACTION11chain 'E' and (resid 87 through 112 )E87 - 112
12X-RAY DIFFRACTION12chain 'E' and (resid 113 through 204 )E113 - 204
13X-RAY DIFFRACTION13chain 'E' and (resid 205 through 228 )E205 - 228

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