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- PDB-7e1c: Structure of MreB3 from Spiroplasma eriocheiris -

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Basic information

Entry
Database: PDB / ID: 7e1c
TitleStructure of MreB3 from Spiroplasma eriocheiris
ComponentsCell shape-determining protein MreB
KeywordsSTRUCTURAL PROTEIN / Cytoskeleton / actin homolog
Function / homology
Function and homology information


cell morphogenesis / regulation of cell shape / ATP binding / cytoplasm
Similarity search - Function
Cell shape determining protein MreB / Heat shock hsp70 proteins family signature 1. / Heat shock protein 70, conserved site / ATPase, nucleotide binding domain
Similarity search - Domain/homology
ACETATE ION / Cell shape-determining protein MreB
Similarity search - Component
Biological speciesSpiroplasma eriocheiris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsTakahashi, D. / Miyata, M. / Imada, K.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP17H01544 Japan
Japan Science and TechnologyJPMJCR19S5 Japan
CitationJournal: Open Biology / Year: 2022
Title: ATP-dependent polymerization dynamics of bacterial actin proteins involved in Spiroplasma swimming.
Authors: Takahashi, D. / Fujiwara, I. / Sasajima, Y. / Narita, A. / Imada, K. / Miyata, M.
History
DepositionFeb 1, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 8, 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: 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
A: Cell shape-determining protein MreB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0523
Polymers38,9521
Non-polymers992
Water5,999333
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area270 Å2
ΔGint-10 kcal/mol
Surface area15930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.420, 68.090, 54.570
Angle α, β, γ (deg.)90.000, 91.730, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
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: 38952.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spiroplasma eriocheiris (bacteria) / Gene: mreB3, mreB, SERIO_v1c12260 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3XJK5
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 2.5 Å3/Da / Density % sol: 50.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 20% (w/v) PEG 8000, 0.1 M MES-NaOH pH 6.0, 200 mM Ca(OAc)2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 26, 2019
RadiationMonochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→54.54 Å / Num. obs: 30343 / % possible obs: 100 % / Redundancy: 5.3 % / Biso Wilson estimate: 22.84 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.045 / Net I/σ(I): 9.8
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1962 / CC1/2: 0.866 / Rpim(I) all: 0.263 / % possible all: 100

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Processing

Software
NameVersionClassification
BSSdata collection
PHENIX1.15.2_3472refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4czl

4czl


Resolution: 1.9→54.54 Å / SU ML: 0.2152 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.9178
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2213 2001 6.6 %
Rwork0.1854 28311 -
obs0.1878 30312 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.46 Å2
Refinement stepCycle: LAST / Resolution: 1.9→54.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2511 0 5 333 2849
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00392533
X-RAY DIFFRACTIONf_angle_d0.61373447
X-RAY DIFFRACTIONf_chiral_restr0.0469408
X-RAY DIFFRACTIONf_plane_restr0.0031428
X-RAY DIFFRACTIONf_dihedral_angle_d14.2548969
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.2811270.2542032X-RAY DIFFRACTION99.86
1.95-20.2941460.23471985X-RAY DIFFRACTION100
2-2.060.24051480.22582001X-RAY DIFFRACTION99.63
2.06-2.130.29241440.21282013X-RAY DIFFRACTION99.91
2.13-2.20.24991440.20092008X-RAY DIFFRACTION99.95
2.2-2.290.23951530.19952013X-RAY DIFFRACTION100
2.29-2.390.25581430.19452013X-RAY DIFFRACTION99.95
2.39-2.520.21921360.19422018X-RAY DIFFRACTION99.86
2.52-2.680.23271450.18831999X-RAY DIFFRACTION100
2.68-2.880.20411450.19042030X-RAY DIFFRACTION100
2.88-3.170.21051330.18012042X-RAY DIFFRACTION100
3.17-3.630.20651440.16642038X-RAY DIFFRACTION100
3.63-4.580.18311420.15232047X-RAY DIFFRACTION100
4.58-54.540.20861510.18442072X-RAY DIFFRACTION99.91

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