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- PDB-7bvz: Crystal structure of MreB5 of Spiroplasma citri bound to ADP -

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Basic information

Entry
Database: PDB / ID: 7bvz
TitleCrystal structure of MreB5 of Spiroplasma citri bound to ADP
ComponentsCell shape determining protein MreB
KeywordsPROTEIN FIBRIL / Cytoskeleton protein / ATPase
Function / homology
Function and homology information


cell morphogenesis / regulation of cell shape / ATP binding / cytoplasm
Similarity search - Function
Cell shape determining protein MreB / : / MreB/Mbl protein / ATPase, nucleotide binding domain
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / : / Cell shape-determining protein MreB
Similarity search - Component
Biological speciesSpiroplasma citri (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPande, V. / Bagde, S.R. / 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 1.1Oct 21, 2020Group: Derived calculations / Category: pdbx_struct_oper_list
Item: _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation ..._pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[2]
Revision 1.2Dec 23, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Nov 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)40,1604
Polymers39,6701
Non-polymers4913
Water3,045169
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)120,48112
Polymers119,0093
Non-polymers1,4729
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_645x+1,y-1,z1
crystal symmetry operation1_465x-1,y+1,z1
Unit cell
Length a, b, c (Å)37.950, 41.150, 56.360
Angle α, β, γ (deg.)82.340, 74.010, 80.420
Int Tables number1
Space group name H-MP1

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Components

#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
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.09 Å3/Da / Density % sol: 41.26 % / Description: Thin needle like crystals
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.15M Na-K phosphate. 16% PEG 3350, pH 7.8, 2mM ADP, 2mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→40.4 Å / Num. obs: 12584 / % possible obs: 87.9 % / Redundancy: 2.1 % / Biso Wilson estimate: 23.2 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.11 / Net I/σ(I): 6.1
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1233 / CC1/2: 0.48 / Rpim(I) all: 0.52 / % possible all: 86.2

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
Aimlessdata scaling
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4czi

4czi


Resolution: 2.3→36.142 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 27.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2757 657 5.22 %
Rwork0.228 11923 -
obs0.2303 12580 87.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85 Å2 / Biso mean: 27.9296 Å2 / Biso min: 11.57 Å2
Refinement stepCycle: final / Resolution: 2.3→36.142 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2492 0 29 173 2694
Biso mean--17.81 26.94 -
Num. residues----329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022552
X-RAY DIFFRACTIONf_angle_d0.5133451
X-RAY DIFFRACTIONf_chiral_restr0.042409
X-RAY DIFFRACTIONf_plane_restr0.002439
X-RAY DIFFRACTIONf_dihedral_angle_d15.4521555
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3001-2.47760.33271290.283234686
2.4776-2.72690.34011460.2725235887
2.7269-3.12130.28921490.2559235988
3.1213-3.93170.29841050.2162241589
3.9317-36.1420.20481280.1879244590

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