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- PDB-4xo1: crystal structure of Se-Met GnsA with double mutations -

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Basic information

Entry
Database: PDB / ID: 4xo1
Titlecrystal structure of Se-Met GnsA with double mutations
ComponentsProtein GnsA
KeywordsPROTEIN BINDING / suppressor
Function / homologyGns / GnsA/GnsB toxin of bacterial toxin-antitoxin system / protein homodimerization activity / identical protein binding / cytosol / Protein GnsA
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.802 Å
AuthorsZhan, L. / Gao, Z. / Dong, Y.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2015
Title: Crystal structure of GnsA from Escherichia coli
Authors: Wei, Y. / Zhan, L. / Gao, Z. / Prive, G.G. / Dong, Y.
History
DepositionJan 16, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein GnsA


Theoretical massNumber of molelcules
Total (without water)7,2371
Polymers7,2371
Non-polymers00
Water79344
1
A: Protein GnsA

A: Protein GnsA


Theoretical massNumber of molelcules
Total (without water)14,4732
Polymers14,4732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area3150 Å2
ΔGint-28 kcal/mol
Surface area7690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.074, 42.539, 72.782
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Protein GnsA


Mass: 7236.585 Da / Num. of mol.: 1 / Mutation: L25M, I36M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: gnsA, yccL, b4517, JW0976 / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AC92
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.4 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M BIS-TRIS pH 5.5, 25%(w/v) Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.9792 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 10526 / % possible obs: 99.9 % / Redundancy: 14.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 60.3
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 14.2 % / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 6.9 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 1.802→28.37 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.01 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2232 466 4.43 %random selection
Rwork0.1946 ---
obs0.196 10526 99.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.802→28.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms483 0 0 44 527
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009495
X-RAY DIFFRACTIONf_angle_d1.22658
X-RAY DIFFRACTIONf_dihedral_angle_d19.46200
X-RAY DIFFRACTIONf_chiral_restr0.09674
X-RAY DIFFRACTIONf_plane_restr0.00384
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8017-2.06240.31891490.21583359X-RAY DIFFRACTION100
2.0624-2.59810.26871560.21863356X-RAY DIFFRACTION100
2.5981-28.37360.1891610.18113345X-RAY DIFFRACTION100

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