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- PDB-3r9v: Cocrystal Structure of Proteolytically Truncated Form of IpaD fro... -

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Basic information

Entry
Database: PDB / ID: 3r9v
TitleCocrystal Structure of Proteolytically Truncated Form of IpaD from Shigella flexneri Bound to Deoxycholate
ComponentsInvasin ipaD
KeywordsCELL INVASION / type III secretion system / tip protein / deoxycholate
Function / homology
Function and homology information


effector-mediated activation of programmed cell death in host / extracellular region
Similarity search - Function
IpaD-like / IpaD-like / Type III secretion systems tip complex components / BipD-like superfamily / Type III secretion systems tip complex components / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBarta, M.L. / Dickenson, N.E. / Picking, W.L. / Picking, W.D. / Geisbrecht, B.V.
CitationJournal: Proteins / Year: 2012
Title: Identification of the bile salt binding site on IpaD from Shigella flexneri and the influence of ligand binding on IpaD structure.
Authors: Barta, M.L. / Guragain, M. / Adam, P. / Dickenson, N.E. / Patil, M. / Geisbrecht, B.V. / Picking, W.L. / Picking, W.D.
History
DepositionMar 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Invasin ipaD
B: Invasin ipaD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3807
Polymers63,3192
Non-polymers1,0615
Water4,071226
1
A: Invasin ipaD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9364
Polymers31,6591
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Invasin ipaD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4453
Polymers31,6591
Non-polymers7852
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-12 kcal/mol
Surface area20240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.974, 43.719, 93.757
Angle α, β, γ (deg.)90.00, 97.42, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Invasin ipaD / 36 kDa membrane antigen


Mass: 31659.391 Da / Num. of mol.: 2 / Fragment: unp residues 39-322
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: ipaD, CP0126 / Production host: Escherichia coli (E. coli) / References: UniProt: P18013
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-DXC / (3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID / DEOXYCHOLIC ACID / Deoxycholic acid


Mass: 392.572 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H40O4 / Comment: detergent*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.02 Å3/Da / Density % sol: 39.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.02M magnesium chloride hexahydrate, 0.1M HEPES, 22% (w/v) Poly(acrylic acid sodium salt) 5100, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 6, 2010
RadiationMonochromator: double crystal - liquid nitrogen cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→45 Å / Num. all: 40352 / Num. obs: 39424 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Rsym value: 0.072 / Net I/σ(I): 21.1
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 2.47 / Rsym value: 0.451 / % possible all: 82.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J0O

2j0o


Resolution: 1.9→25.283 Å / SU ML: 0.23 / σ(F): 1.35 / Phase error: 26.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2482 1999 5.08 %
Rwork0.2276 --
obs0.2287 39374 97.13 %
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.141 Å2 / ksol: 0.336 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.9545 Å2-0 Å2-4.7283 Å2
2--3.9624 Å2-0 Å2
3----10.9168 Å2
Refinement stepCycle: LAST / Resolution: 1.9→25.283 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2823 0 74 226 3123
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072944
X-RAY DIFFRACTIONf_angle_d1.1353986
X-RAY DIFFRACTIONf_dihedral_angle_d13.9561069
X-RAY DIFFRACTIONf_chiral_restr0.066451
X-RAY DIFFRACTIONf_plane_restr0.003502
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8966-1.94410.33051060.30561986X-RAY DIFFRACTION74
1.9441-1.99660.33591350.27872515X-RAY DIFFRACTION91
1.9966-2.05530.27661400.24782622X-RAY DIFFRACTION98
2.0553-2.12160.28351460.23232727X-RAY DIFFRACTION99
2.1216-2.19740.24921450.23122720X-RAY DIFFRACTION100
2.1974-2.28530.29951450.24982707X-RAY DIFFRACTION100
2.2853-2.38930.28191470.23212726X-RAY DIFFRACTION99
2.3893-2.51510.25251450.22632739X-RAY DIFFRACTION100
2.5151-2.67260.23581470.22842732X-RAY DIFFRACTION100
2.6726-2.87860.27111470.23642740X-RAY DIFFRACTION100
2.8786-3.16780.28151480.23942775X-RAY DIFFRACTION100
3.1678-3.62510.24961470.2252762X-RAY DIFFRACTION100
3.6251-4.56280.19731490.20052778X-RAY DIFFRACTION100
4.5628-25.28510.22031520.21932846X-RAY DIFFRACTION99

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