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- PDB-7zpt: Crystal structure of MreB from Geobacillus stearothermophilus ATCC7953 -

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Basic information

Entry
Database: PDB / ID: 7zpt
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
Cell shape-determining protein MreB
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLi de la Sierra-Gallay, I. / Mao, W.
Funding support France, 1items
OrganizationGrant numberCountry
French Infrastructure for Integrated Structural Biology (FRISBI)ANR-10-INBS-05 France
CitationJournal: Elife / Year: 2023
Title: On the role of nucleotides and lipids in the polymerization of the actin homolog MreB from a Gram-positive bacterium.
Authors: Mao, W. / Renner, L.D. / Cornilleau, C. / Li de la Sierra-Gallay, I. / Afensiss, S. / Benlamara, S. / Ah-Seng, Y. / Van Tilbeurgh, H. / Nessler, S. / Bertin, A. / Chastanet, A. / Carballido-Lopez, R.
History
DepositionApr 28, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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 1.2Feb 7, 2024Group: Refinement description / Category: 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)36,6832
Polymers36,4451
Non-polymers2381
Water2,288127
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area420 Å2
ΔGint-3 kcal/mol
Surface area16410 Å2
Unit cell
Length a, b, c (Å)47.190, 62.010, 50.910
Angle α, β, γ (deg.)90.000, 112.980, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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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-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.88 Å3/Da / Density % sol: 34.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.7 / 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: 1.8→46.87 Å / Num. obs: 25002 / % possible obs: 99.5 % / Redundancy: 6.95 % / Biso Wilson estimate: 29.96 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.15 / Net I/σ(I): 7.21
Reflection shellResolution: 1.8→1.9 Å / Num. unique obs: 3960 / CC1/2: 0.76

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CZJ

4czj


Resolution: 1.8→46.87 Å / SU ML: 0.2221 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.1971
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2338 1249 5 %RANDOM
Rwork0.1909 23719 --
obs0.1931 24968 99.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.99 Å2
Refinement stepCycle: LAST / Resolution: 1.8→46.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2497 0 16 127 2640
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00762541
X-RAY DIFFRACTIONf_angle_d0.96493432
X-RAY DIFFRACTIONf_chiral_restr0.0627410
X-RAY DIFFRACTIONf_plane_restr0.0112441
X-RAY DIFFRACTIONf_dihedral_angle_d5.8268372
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.870.33611360.3052573X-RAY DIFFRACTION97.03
1.87-1.960.31171370.23992618X-RAY DIFFRACTION99.78
1.96-2.060.28511380.20992621X-RAY DIFFRACTION99.96
2.06-2.190.26841380.20622610X-RAY DIFFRACTION99.85
2.19-2.360.25791400.19382663X-RAY DIFFRACTION100
2.36-2.60.26861380.19362629X-RAY DIFFRACTION100
2.6-2.980.22521400.20922652X-RAY DIFFRACTION99.96
2.98-3.750.22911390.18632643X-RAY DIFFRACTION99.96
3.75-46.870.19761430.16582710X-RAY DIFFRACTION99.93

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