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- PDB-6umk: Structure of E. coli FtsZ(L178E)-GDP complex -

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Basic information

Entry
Database: PDB / ID: 6umk
TitleStructure of E. coli FtsZ(L178E)-GDP complex
ComponentsCell division protein FtsZ
KeywordsCELL CYCLE / FtsZ / E. coli / model system / closed state
Function / homology
Function and homology information


divisome complex / FtsZ-dependent cytokinesis / division septum assembly / cell division site / protein polymerization / cell division / GTPase activity / GTP binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Tubulin-like protein FtsZ/CetZ / Cell division protein FtsZ / Cell division protein FtsZ, conserved site / Cell division protein FtsZ, C-terminal / FtsZ family, C-terminal domain / FtsZ protein signature 1. / FtsZ protein signature 2. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal ...Tubulin-like protein FtsZ/CetZ / Cell division protein FtsZ / Cell division protein FtsZ, conserved site / Cell division protein FtsZ, C-terminal / FtsZ family, C-terminal domain / FtsZ protein signature 1. / FtsZ protein signature 2. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Cell division protein FtsZ / Cell division protein FtsZ
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.35 Å
AuthorsSchumacher, M.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM130290 United States
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: High-resolution crystal structures of Escherichia coli FtsZ bound to GDP and GTP.
Authors: Schumacher, M.A. / Ohashi, T. / Corbin, L. / Erickson, H.P.
History
DepositionOct 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.2Oct 11, 2023Group: 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 protein FtsZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1922
Polymers31,7491
Non-polymers4431
Water5,909328
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.427, 85.189, 41.398
Angle α, β, γ (deg.)90.000, 106.920, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cell division protein FtsZ /


Mass: 31748.955 Da / Num. of mol.: 1 / Mutation: L178E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ftsZ, D4U49_01465, DNQ92_00675 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3T9KGL2, UniProt: P0A9A6*PLUS
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 1.99 Å3/Da / Density % sol: 38.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: Peg 8000, cacodylate pH 6.5, Calcium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→35.915 Å / Num. obs: 52607 / % possible obs: 96.7 % / Redundancy: 3 % / Biso Wilson estimate: 15.18 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.021 / Rrim(I) all: 0.035 / Rsym value: 0.031 / Net I/σ(I): 23.8
Reflection shellResolution: 1.35→1.38 Å / Mean I/σ(I) obs: 4.7 / Num. unique obs: 3192 / CC1/2: 0.995 / Rpim(I) all: 0.047 / Rsym value: 0.69

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VAW

2vaw


Resolution: 1.35→35.915 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 22.14
RfactorNum. reflection% reflection
Rfree0.2045 1994 3.79 %
Rwork0.1862 --
obs0.1869 52607 96.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 92.2 Å2 / Biso mean: 25.0634 Å2 / Biso min: 9.06 Å2
Refinement stepCycle: final / Resolution: 1.35→35.915 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2176 0 28 328 2532
Biso mean--18.25 33.28 -
Num. residues----303
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.3501-1.38380.30951210.2306307082
1.3838-1.42130.24541410.2296362398
1.4213-1.46310.24961460.2257367899
1.4631-1.51030.22991450.2107365298
1.5103-1.56430.21251450.2083367898
1.5643-1.62690.24451450.1986368099
1.6269-1.7010.22221440.1927366999
1.701-1.79060.21991440.1997365698
1.7906-1.90280.21481430.1932363798
1.9028-2.04970.19181420.1926360996
2.0497-2.2560.21291440.1822363497
2.256-2.58230.20291440.18367098
2.5823-3.25310.18831440.1886366498
3.2531-35.9150.18861460.1679369397
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)
10.04640.0032-0.02730.06360.01960.0346-0.0362-0.1180.00360.1090.03310.13660.0421-0.1233-0.00440.1477-0.00770.01920.1297-0.00670.10610.509-7.6117.019
20.002-0.0013-0-0-0.00210.0035-0.00260.00740.00630.0099-0.02950.00260.0040.0086-00.35650.056-0.11970.4148-0.04470.26429.205-11.63227.665
30.0797-0.0287-0.09360.0713-0.02760.0765-0.04140.0234-0.09670.02190.0447-0.024-0.00150.1048-0.02660.1403-0.0062-0.00050.109-0.02740.121520.755-10.22610.569
40.040.0272-0.02350.0082-0.01050.0302-0.03570.0539-0.067-0.06970.0223-0.1417-0.11210.205-0.00010.1181-0.02370.00790.1546-0.01460.126527.3910.55510.983
50.0050.0261-0.02010.018-0.02540.02790.0493-0.03160.22210.0298-0.04380.0864-0.0153-0.1210.00650.146-0.01090.03050.1196-0.02630.168812.2666.34213.492
60.083-0.01640.08160.1331-0.06460.2068-0.05150.38690.1832-0.05880.21120.14510.02010.07370.07570.1277-0.00720.00180.13930.0940.206510.3177.88-3.285
70.07010.06090.12470.16960.1830.3896-0.24890.22280.2297-0.10390.25480.3783-0.04080.25180.06080.1145-0.0664-0.01860.15040.21610.25519.12310.303-5.461
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 11:64 )A11 - 64
2X-RAY DIFFRACTION2( CHAIN A AND RESID 65:73 )A65 - 73
3X-RAY DIFFRACTION3( CHAIN A AND RESID 74:138 )A74 - 138
4X-RAY DIFFRACTION4( CHAIN A AND RESID 139:169 )A139 - 169
5X-RAY DIFFRACTION5( CHAIN A AND RESID 173:201 )A173 - 201
6X-RAY DIFFRACTION6( CHAIN A AND RESID 202:248 )A202 - 248
7X-RAY DIFFRACTION7( CHAIN A AND RESID 249:316 )A249 - 316

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