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- PDB-8aam: Crystal structure of MreB from Geobacillus stearothermophilus ATCC7953 -

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Basic information

Entry
Database: PDB / ID: 8aam
TitleCrystal structure of MreB from Geobacillus stearothermophilus ATCC7953
ComponentsCell shape-determining protein MreB
KeywordsSTRUCTURAL PROTEIN / BACTERIAL ACTIN / BACTERIAL CYTOSKELETON
Function / homology
Function and homology information


cell morphogenesis / regulation of cell shape / GTP binding / ATP binding / cytoplasm
Similarity search - Function
Cell shape determining protein MreB / : / MreB/Mbl protein / ATPase, nucleotide binding domain
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Cell shape-determining protein MreB
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsLi de la Sierra-Gallay, I.
Funding support France, 1items
OrganizationGrant numberCountry
French Infrastructure for Integrated Structural Biology (FRISBI)ANR-10-INBS-05 France
CitationJournal: To Be Published
Title: Polymerization cycle of an actin homolog MreB from a Gram-positive bacterium
Authors: Mao, W. / Conilleau, C. / Li de la Sierra-Gallay, I. / Ah-Seng, Y. / van Tilbeurgh, H. / Renner, L. / Nessler, S. / Bertin, A. / Chastanet, A. / Carballido-Lopes, R.
History
DepositionJul 1, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
M: Cell shape-determining protein MreB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8722
Polymers36,4451
Non-polymers4271
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-8 kcal/mol
Surface area15270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.670, 61.710, 51.010
Angle α, β, γ (deg.)90.000, 112.170, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Cell shape-determining protein MreB


Mass: 36445.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: mreB, B4109_2230, B4114_2117, GS458_2390 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A150MJ77
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 1.87 Å3/Da / Density % sol: 34.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 5.5 / Details: PEG 300, 2-(N-morpholino)ethanesulfonic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978565 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 2.29→47.24 Å / Num. obs: 12172 / % possible obs: 94.4 % / Redundancy: 6.89 % / Biso Wilson estimate: 51.76 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.11 / Net I/σ(I): 12.17
Reflection shellResolution: 2.29→2.43 Å / Num. unique obs: 1938 / CC1/2: 0.62 / Rrim(I) all: 1.49

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: D_1292122438

Resolution: 2.29→47.24 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 33.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2739 608 5 %
Rwork0.2024 11558 -
obs0.2062 12166 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.15 Å2 / Biso mean: 57.6584 Å2 / Biso min: 36.23 Å2
Refinement stepCycle: final / Resolution: 2.29→47.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2387 0 27 7 2421
Biso mean--54.56 47.01 -
Num. residues----319
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.29-2.520.33891500.27032840299099
2.52-2.880.33281510.255628823033100
2.88-3.630.32851530.221428993052100
3.63-47.240.22961540.17429373091100

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