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- PDB-8ab4: Crystal structure of MreB from Geobacillus stearothermophilus ATC... -

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Basic information

Entry
Database: PDB / ID: 8ab4
TitleCrystal structure of MreB from Geobacillus stearothermophilus ATCC7953 in complex with GTP
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
GUANOSINE-5'-TRIPHOSPHATE / Cell shape-determining protein MreB
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 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 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 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)36,9682
Polymers36,4451
Non-polymers5231
Water1086
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-7 kcal/mol
Surface area14920 Å2
Unit cell
Length a, b, c (Å)46.140, 61.410, 50.920
Angle α, β, γ (deg.)90.000, 111.820, 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-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 1.84 Å3/Da / Density % sol: 33.06 %
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: 2.22→47.27 Å / Num. obs: 13182 / % possible obs: 99.5 % / Redundancy: 6.9 % / Biso Wilson estimate: 53.43 Å2 / CC1/2: 1 / Rrim(I) all: 0.09 / Net I/σ(I): 12.74
Reflection shellResolution: 2.22→2.35 Å / Num. unique obs: 2073 / CC1/2: 0.6 / Rrim(I) all: 1.61 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ZPT

7zpt


Resolution: 2.22→42.83 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 33.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2463 657 4.99 %
Rwork0.2078 12502 -
obs0.2101 13159 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.8 Å2 / Biso mean: 64.0333 Å2 / Biso min: 40.23 Å2
Refinement stepCycle: final / Resolution: 2.22→42.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2363 0 32 6 2401
Biso mean--61.73 46.49 -
Num. residues----316
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.22-2.390.34181260.31192425255198
2.39-2.630.31161320.263724942626100
2.63-3.010.29731320.235924982630100
3.01-3.790.28741320.216825252657100
3.79-42.830.20311350.179625602695100

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