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- PDB-7bvy: Crystal structure of MreB 5 of Spiroplasma citri bound to AMPPNP -

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Basic information

Entry
Database: PDB / ID: 7bvy
TitleCrystal structure of MreB 5 of Spiroplasma citri bound to AMPPNP
ComponentsCell shape determining protein MreB
KeywordsPROTEIN FIBRIL / ATPase
Function / homology
Function and homology information


cell morphogenesis / regulation of cell shape / ATP binding / cytoplasm
Similarity search - Function
Cell shape determining protein MreB / ATPase, nucleotide binding domain
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / : / PHOSPHATE ION / Cell shape-determining protein MreB
Similarity search - Component
Biological speciesSpiroplasma citri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsPande, V. / Gayathri, P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/07/IYBA/2013/06 India
CitationJournal: Curr.Biol. / Year: 2020
Title: MreB5 Is a Determinant of Rod-to-Helical Transition in the Cell-Wall-less Bacterium Spiroplasma.
Authors: Harne, S. / Duret, S. / Pande, V. / Bapat, M. / Beven, L. / Gayathri, P.
History
DepositionApr 12, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)40,3345
Polymers39,6701
Non-polymers6654
Water1,964109
1
A: Cell shape determining protein MreB
hetero molecules

A: Cell shape determining protein MreB
hetero molecules

A: Cell shape determining protein MreB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,00315
Polymers119,0093
Non-polymers1,99412
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation1_455x-1,y,z1
Unit cell
Length a, b, c (Å)51.121, 54.083, 138.800
Angle α, β, γ (deg.)90.000, 98.180, 90.000
Int Tables number5
Space group name H-MI121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cell shape determining protein MreB / MreB5 / Rod shape-determining protein


Mass: 39669.770 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: cell wall less bacteria / Source: (gene. exp.) Spiroplasma citri (bacteria) / Gene: mreB5, FRX96_09810, SCITRI_001914, SPICI01A_049 / Variant: GII3 / Plasmid: pHis17 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): AI / References: UniProt: Q8VQG1

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Non-polymers , 5 types, 113 molecules

#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.39 Å3/Da / Density % sol: 48.62 % / Description: Thin Needle- like crystals in a bunch
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 0.15M Na-K phosphate, 16% PEG 3350, pH 7.8, 2mM AMPPNP, 2mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Oct 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.5→49.838 Å / Num. obs: 13181 / % possible obs: 98.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 26.47 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.12 / Net I/σ(I): 7
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1461 / CC1/2: 0.82 / Rpim(I) all: 0.54 / % possible all: 98.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHASERphasing
PHENIX1.11.1_2575refinement
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7BVZ

7bvz


Resolution: 2.5→49.838 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 0.26 / Phase error: 26.62
RfactorNum. reflection% reflection
Rfree0.2426 1322 5.29 %
Rwork0.1903 --
obs0.1931 13181 98.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 76.22 Å2 / Biso mean: 32.1149 Å2 / Biso min: 14.34 Å2
Refinement stepCycle: final / Resolution: 2.5→49.838 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2498 0 51 109 2658
Biso mean--24.76 33.06 -
Num. residues----333
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022575
X-RAY DIFFRACTIONf_angle_d0.4543496
X-RAY DIFFRACTIONf_chiral_restr0.043419
X-RAY DIFFRACTIONf_plane_restr0.002442
X-RAY DIFFRACTIONf_dihedral_angle_d15.261556
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5001-2.60020.31661420.2592265698
2.6002-2.71860.26861680.2363261699
2.7186-2.86190.29961530.2287263799
2.8619-3.04120.27361780.2058259698
3.0412-3.27590.25981170.2029267199
3.2759-3.60550.22411350.1783267398
3.6055-4.1270.24391300.1663263498
4.127-5.19870.21761510.1568250794
5.1987-49.8380.19891480.18182683100

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