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

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Basic information

Entry
Database: PDB / ID: 8azg
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: 2.29 Å
AuthorsLi de la Sierra-Gallay, I. / Mao, W.
Funding support France, 1items
OrganizationGrant numberCountry
French Infrastructure for Integrated Structural Biology (FRISBI)ANR-10-INSB-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
DepositionSep 6, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Database references / Category: 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

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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)38,1895
Polymers37,4051
Non-polymers7834
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-7 kcal/mol
Surface area15400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.740, 169.100, 43.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Cell shape-determining protein MreB


Mass: 37405.078 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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.94 Å3/Da / Density % sol: 58.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: PEG 8000, glycerol, potassium phosphate, magnesium chloride

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Data collection

DiffractionMean temperature: 95 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→43.88 Å / Num. obs: 19996 / % possible obs: 99.7 % / Redundancy: 13.13 % / Biso Wilson estimate: 48.1 Å2 / CC1/2: 1 / Rrim(I) all: 0.146 / Net I/σ(I): 12.41
Reflection shellResolution: 2.29→2.43 Å / Num. unique obs: 3130 / CC1/2: 0.84 / Rrim(I) all: 1.41

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
XDS1.20_4459data reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ZPT

7zpt


Resolution: 2.29→42.47 Å / SU ML: 0.2779 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.9527
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2501 1001 5.01 %
Rwork0.2068 18995 -
obs0.209 19996 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.48 Å2
Refinement stepCycle: LAST / Resolution: 2.29→42.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2450 0 49 81 2580
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00762527
X-RAY DIFFRACTIONf_angle_d0.89553426
X-RAY DIFFRACTIONf_chiral_restr0.0556410
X-RAY DIFFRACTIONf_plane_restr0.0076434
X-RAY DIFFRACTIONf_dihedral_angle_d7.6442362
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.410.35361400.31762647X-RAY DIFFRACTION98.9
2.41-2.570.30591380.25472650X-RAY DIFFRACTION99.75
2.57-2.760.26411420.23382678X-RAY DIFFRACTION99.86
2.76-3.040.28581410.23672670X-RAY DIFFRACTION99.61
3.04-3.480.25711420.20622708X-RAY DIFFRACTION99.82
3.48-4.380.21351460.1852758X-RAY DIFFRACTION99.97
4.39-42.470.23951520.18972884X-RAY DIFFRACTION99.9

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