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- PDB-7dsg: Crystal structure of Brucella abortus PhiA -

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Basic information

Entry
Database: PDB / ID: 7dsg
TitleCrystal structure of Brucella abortus PhiA
ComponentsBrucella Abortus PhiA
KeywordsUNKNOWN FUNCTION / T4SS / lysozyme inhibitor / PliC
Function / homologyC-type lysozyme inhibitor superfamily / MliC domain-containing protein
Function and homology information
Biological speciesBrucella abortus biovar 1 (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHyun, Y. / Ha, N.-C.
CitationJournal: To Be Published
Title: Crystal structure of Brucella abortus PhiA
Authors: Hyun, Y. / Ha, N.-C.
History
DepositionDec 31, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 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: Brucella Abortus PhiA


Theoretical massNumber of molelcules
Total (without water)12,2001
Polymers12,2001
Non-polymers00
Water27015
1
A: Brucella Abortus PhiA

A: Brucella Abortus PhiA

A: Brucella Abortus PhiA

A: Brucella Abortus PhiA


Theoretical massNumber of molelcules
Total (without water)48,7984
Polymers48,7984
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
crystal symmetry operation3_455-x-1,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area4340 Å2
ΔGint-33 kcal/mol
Surface area17300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.020, 62.100, 68.280
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Brucella Abortus PhiA


Mass: 12199.530 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella abortus biovar 1 (strain 9-941) (bacteria)
Strain: 9-941 / Gene: BruAb1_0102 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q57FR6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

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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: 2.3 Å3/Da / Density % sol: 46.6 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 287.15 K / Method: vapor diffusion, hanging drop
Details: 2% Tacsimate pH 6.5, 0.1 M BIS-TRIS pH 6.5, 24% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 298.15 K / Serial crystal experiment: N
Diffraction sourceSource: FREE ELECTRON LASER / Site: PAL-XFEL / Beamline: NCI / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: May 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→45.95 Å / Num. obs: 17157 / % possible obs: 100 % / Redundancy: 108.3 % / Biso Wilson estimate: 38.63 Å2 / CC star: 0.99 / R split: 0.1716 / Net I/σ(I): 3.7
Reflection shellResolution: 1.9→1.97 Å / Num. unique obs: 5214 / CC star: 0.92 / R split: 0.7431

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
CrystFELdata reduction
CrystFELdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MIR

4mir


Resolution: 1.9→45.94 Å / SU ML: 0.2668 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.9499
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2609 1714 10 %
Rwork0.2385 15430 -
obs0.2409 17144 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.9 Å2
Refinement stepCycle: LAST / Resolution: 1.9→45.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms686 0 0 15 701
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092699
X-RAY DIFFRACTIONf_angle_d0.9523949
X-RAY DIFFRACTIONf_chiral_restr0.0579108
X-RAY DIFFRACTIONf_plane_restr0.0049121
X-RAY DIFFRACTIONf_dihedral_angle_d16.3974254
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.37891300.33541200X-RAY DIFFRACTION93.73
1.95-2.020.26921450.29991277X-RAY DIFFRACTION99.72
2.02-2.090.32311440.2861290X-RAY DIFFRACTION100
2.09-2.170.36491330.26811280X-RAY DIFFRACTION99.93
2.17-2.270.31081500.27331313X-RAY DIFFRACTION99.86
2.27-2.390.33941450.26831286X-RAY DIFFRACTION99.86
2.39-2.540.36371430.26061315X-RAY DIFFRACTION100
2.54-2.730.27691430.27011270X-RAY DIFFRACTION100
2.74-3.010.31941410.23641297X-RAY DIFFRACTION100
3.01-3.440.23331510.22121301X-RAY DIFFRACTION100
3.45-4.340.2091420.20421300X-RAY DIFFRACTION100
4.34-45.940.24241470.23681301X-RAY DIFFRACTION100

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