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- PDB-4nsr: Crystal structure of the Immunity protein -

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Basic information

Entry
Database: PDB / ID: 4nsr
TitleCrystal structure of the Immunity protein
ComponentsImmunity protein
KeywordsPROTEIN BINDING / Helix / peptidoglycan
Function / homologyHelicase, Ruva Protein; domain 3 - #1160 / : / : / Antitoxin TsiV3 / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / Mainly Alpha / identical protein binding / Antitoxin protein TsiV3
Function and homology information
Biological speciesVibrio cholerae O1 biovar El Tor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.795 Å
AuthorsDong, C. / Gao, Z.-Q. / Dong, Y.-H.
CitationJournal: Febs Lett. / Year: 2014
Title: Structural basis for recognition of the type VI spike protein VgrG3 by a cognate immunity protein.
Authors: Zhang, J. / Zhang, H. / Gao, Z. / Hu, H. / Dong, C. / Dong, Y.H.
History
DepositionNov 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1May 21, 2014Group: Database references
Revision 1.2Jun 11, 2014Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Immunity protein
C: Immunity protein
A: Immunity protein
E: Immunity protein
F: Immunity protein
D: Immunity protein


Theoretical massNumber of molelcules
Total (without water)79,6016
Polymers79,6016
Non-polymers00
Water68538
1
B: Immunity protein
A: Immunity protein


Theoretical massNumber of molelcules
Total (without water)26,5342
Polymers26,5342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-11 kcal/mol
Surface area10130 Å2
MethodPISA
2
C: Immunity protein
D: Immunity protein


Theoretical massNumber of molelcules
Total (without water)26,5342
Polymers26,5342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-11 kcal/mol
Surface area10660 Å2
MethodPISA
3
E: Immunity protein
F: Immunity protein


Theoretical massNumber of molelcules
Total (without water)26,5342
Polymers26,5342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-11 kcal/mol
Surface area10170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.984, 78.298, 106.795
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe asymmetric unit of a crystal structure contain three biological units.

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Components

#1: Protein
Immunity protein


Mass: 13266.843 Da / Num. of mol.: 6 / Fragment: UNP residues 26-122
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor (bacteria)
Strain: N16961 / Gene: VC_A0124 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KN41
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 1.94 Å3/Da / Density % sol: 36.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M Ammonium citrate tribasic, 20% w/v Polyethylene glycol monomethyl ether 2000, 0.1M Imidazole pH7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 15, 2013
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.795→50 Å / Num. obs: 15700 / Redundancy: 5.9 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 25
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.401 / Mean I/σ(I) obs: 3 / Num. unique all: 770 / % possible all: 99.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.795→44.115 Å / SU ML: 0.54 / σ(F): 1.36 / Phase error: 30.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2825 777 4.96 %random
Rwork0.224 ---
obs0.2269 15653 98.27 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.282 Å2 / ksol: 0.328 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-12.7573 Å2-0 Å20 Å2
2---16.7469 Å20 Å2
3---4.2928 Å2
Refinement stepCycle: LAST / Resolution: 2.795→44.115 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4361 0 0 38 4399
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134415
X-RAY DIFFRACTIONf_angle_d1.5455931
X-RAY DIFFRACTIONf_dihedral_angle_d10.6041695
X-RAY DIFFRACTIONf_chiral_restr0.074655
X-RAY DIFFRACTIONf_plane_restr0.01777
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7946-2.96970.47321060.35142472X-RAY DIFFRACTION99
2.9697-3.19890.3571230.27632460X-RAY DIFFRACTION99
3.1989-3.52070.3381340.25092464X-RAY DIFFRACTION99
3.5207-4.02990.32711280.21652462X-RAY DIFFRACTION99
4.0299-5.0760.21181610.18022463X-RAY DIFFRACTION98
5.076-44.12070.23791250.20532555X-RAY DIFFRACTION96

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