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- PDB-7e1g: Structure of MreB3 from Spiroplasma eriocheiris -

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Basic information

Entry
Database: PDB / ID: 7e1g
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Cell shape-determining protein MreB
Similarity search - Component
Biological speciesSpiroplasma eriocheiris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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

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Assembly

Deposited unit
A: Cell shape-determining protein MreB
B: Cell shape-determining protein MreB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,3996
Polymers78,3382
Non-polymers1,0614
Water13,745763
1
A: Cell shape-determining protein MreB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6993
Polymers39,1691
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-14 kcal/mol
Surface area16420 Å2
MethodPISA
2
B: Cell shape-determining protein MreB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6993
Polymers39,1691
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-14 kcal/mol
Surface area15800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.290, 56.270, 120.531
Angle α, β, γ (deg.)90.00, 90.56, 90.00
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: 39168.836 Da / Num. of mol.: 2
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 763 / 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: 2.18 Å3/Da / Density % sol: 43.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 30% (w/v) PEG 4000, 0.1 M Acetate-NaOH pH 4.6, 200 mM NH4Ac, 5 mM AMPPNP, 5mM MgCl2

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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: Nov 29, 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: 1.75→56.3 Å / Num. obs: 66116 / % possible obs: 97.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 18.86 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.065 / Net I/σ(I): 6.8
Reflection shellResolution: 1.75→1.78 Å / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3545 / CC1/2: 0.658 / Rpim(I) all: 0.372

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
BSSdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7E1C

7e1c


Resolution: 1.75→50.987 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2135 2006 3.04 %
Rwork0.1744 --
obs0.1756 66020 96.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→50.987 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5115 0 64 763 5942
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065231
X-RAY DIFFRACTIONf_angle_d0.8917187
X-RAY DIFFRACTIONf_dihedral_angle_d5.4164270
X-RAY DIFFRACTIONf_chiral_restr0.053842
X-RAY DIFFRACTIONf_plane_restr0.004879
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.79380.25341480.22834479X-RAY DIFFRACTION96
1.7938-1.84230.29931290.23124431X-RAY DIFFRACTION95
1.8423-1.89650.28021450.23154502X-RAY DIFFRACTION96
1.8965-1.95770.27681440.21624519X-RAY DIFFRACTION96
1.9577-2.02770.24841440.19654514X-RAY DIFFRACTION96
2.0277-2.10890.22681440.18574518X-RAY DIFFRACTION96
2.1089-2.20480.2591370.18144559X-RAY DIFFRACTION97
2.2048-2.32110.20241480.17494556X-RAY DIFFRACTION97
2.3211-2.46650.19921400.17414585X-RAY DIFFRACTION97
2.4665-2.65690.23661450.17364604X-RAY DIFFRACTION97
2.6569-2.92430.2281390.17424604X-RAY DIFFRACTION97
2.9243-3.34740.19241450.1674668X-RAY DIFFRACTION98
3.3474-4.2170.19291440.14674696X-RAY DIFFRACTION98
4.217-50.9870.17311540.16024779X-RAY DIFFRACTION98

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