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- PDB-7zpu: Crystal structure of MreB from Geobacillus stearothermophilus ATC... -

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Basic information

Entry
Database: PDB / ID: 7zpu
TitleCrystal structure of MreB from Geobacillus stearothermophilus ATCC7953 in complex with ATP
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'-TRIPHOSPHATE / Cell shape-determining protein MreB
Similarity search - Component
Biological speciesGeobacillus stearothermophilus ATCC 7953 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 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 1.1Nov 22, 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
Revision 1.3Aug 14, 2024Group: Database references / Category: pdbx_database_related

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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)36,9522
Polymers36,4451
Non-polymers5071
Water86548
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-4 kcal/mol
Surface area15040 Å2
Unit cell
Length a, b, c (Å)46.220, 61.600, 50.970
Angle α, β, γ (deg.)90.000, 111.530, 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 ATCC 7953 (bacteria)
Gene: mreB, B4109_2230, B4114_2117, GS458_2390 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A150MJ77
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG 300, 2-(N-morpholino)ethanesulfonic acid / PH range: 5.5

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Data collection

DiffractionMean temperature: 291 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 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 1.96→47.42 Å / Num. obs: 19153 / % possible obs: 99.4 % / Redundancy: 6.96 % / Biso Wilson estimate: 42.12 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.09 / Net I/σ(I): 10.56
Reflection shellResolution: 1.96→2.08 Å / Mean I/σ(I) obs: 0.86 / Num. unique obs: 2999 / CC1/2: 0.6 / Rrim(I) all: 1.35

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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: 1.96→47.41 Å / SU ML: 0.2342 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.575
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2445 957 5 %RANDOM
Rwork0.1942 18181 --
obs0.1967 19138 99.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.98 Å2
Refinement stepCycle: LAST / Resolution: 1.96→47.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2388 0 31 48 2467
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00782448
X-RAY DIFFRACTIONf_angle_d0.9833321
X-RAY DIFFRACTIONf_chiral_restr0.0609398
X-RAY DIFFRACTIONf_plane_restr0.0109422
X-RAY DIFFRACTIONf_dihedral_angle_d6.5442345
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.060.34321320.28422514X-RAY DIFFRACTION97.28
2.06-2.190.28221360.24382597X-RAY DIFFRACTION99.67
2.19-2.360.28941360.20272573X-RAY DIFFRACTION99.85
2.36-2.60.23731370.20112599X-RAY DIFFRACTION99.89
2.6-2.970.23991380.20612620X-RAY DIFFRACTION100
2.97-3.750.2351370.20122610X-RAY DIFFRACTION100
3.75-47.410.23391410.17312668X-RAY DIFFRACTION99.86

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