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- PDB-6d7y: 1.75 Angstrom Resolution Crystal Structure of the Toxic C-Termina... -

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Basic information

Entry
Database: PDB / ID: 6d7y
Title1.75 Angstrom Resolution Crystal Structure of the Toxic C-Terminal Tip of CdiA from Pseudomonas aeruginosa in Complex with Immune Protein
Components
  • Hemagglutinin
  • immune proteinImmunity (medical)
KeywordsTOXIN / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homologyUncharacterized protein / :
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
Enterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsMinasov, G. / Shuvalova, L. / Wawrzak, Z. / Kiryukhina, O. / Allen, J.P. / Hauser, A.R. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: A comparative genomics approach identifies contact-dependent growth inhibition as a virulence determinant.
Authors: Allen, J.P. / Ozer, E.A. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Satchell, K.J.F. / Hauser, A.R.
History
DepositionApr 25, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Mar 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Apr 15, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hemagglutinin
B: immune protein


Theoretical massNumber of molelcules
Total (without water)28,7932
Polymers28,7932
Non-polymers00
Water1,76598
1
A: Hemagglutinin


Theoretical massNumber of molelcules
Total (without water)10,8661
Polymers10,8661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: immune protein


Theoretical massNumber of molelcules
Total (without water)17,9271
Polymers17,9271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.579, 76.579, 61.441
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Hemagglutinin /


Mass: 10866.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: BKN49_19035 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL-21(DE3) magic / References: UniProt: A0A1X0SIL3
#2: Protein immune protein / Immunity (medical)


Mass: 17926.510 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: SAMEA2273162_06031 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-Magic / References: UniProt: A0A157WHH8
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 1.85 Å3/Da / Density % sol: 33.5 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Protein: 6.4mg/ml, 0.5 Sodium chloride, 0.01M Tris pH 8.3; Screen: Clasics II (D6), 0.1M Bis-Tris pH 5.5, 25% (w/v) PEG 3350;

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 20, 2017
RadiationMonochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. obs: 20855 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 27.7 Å2 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.032 / Rrim(I) all: 0.082 / Rsym value: 0.075 / Χ2: 1.803 / Net I/σ(I): 30.7
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.799 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1035 / CC1/2: 0.722 / Rpim(I) all: 0.34 / Rrim(I) all: 0.868 / Rsym value: 0.799 / Χ2: 1.006 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.75→29.18 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / SU B: 7.205 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.13 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22364 1012 4.9 %RANDOM
Rwork0.18302 ---
obs0.185 19733 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 37.575 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å2-0.42 Å20 Å2
2---0.84 Å20 Å2
3---2.73 Å2
Refinement stepCycle: 1 / Resolution: 1.75→29.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1974 0 0 98 2072
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192065
X-RAY DIFFRACTIONr_bond_other_d0.0010.021903
X-RAY DIFFRACTIONr_angle_refined_deg1.5071.9662776
X-RAY DIFFRACTIONr_angle_other_deg0.8834417
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.8715255
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.14224.02102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.37215337
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4491511
X-RAY DIFFRACTIONr_chiral_restr0.0930.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.0230.022336
X-RAY DIFFRACTIONr_gen_planes_other0.0190.02471
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5361.8261011
X-RAY DIFFRACTIONr_mcbond_other1.5281.8241010
X-RAY DIFFRACTIONr_mcangle_it2.5072.7271269
X-RAY DIFFRACTIONr_mcangle_other2.5082.7291270
X-RAY DIFFRACTIONr_scbond_it1.9892.0581054
X-RAY DIFFRACTIONr_scbond_other1.9882.0581054
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1083.0121507
X-RAY DIFFRACTIONr_long_range_B_refined5.21922.3982284
X-RAY DIFFRACTIONr_long_range_B_other5.18322.2132269
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 85 -
Rwork0.288 1442 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.94730.78490.65253.46150.13725.3315-0.0058-0.02740.18670.0332-0.03490.50380.2586-0.44560.04070.0309-0.05890.0050.1242-0.01620.090118.8150.03949.2394
25.23684.58736.26214.22256.03919.9531-0.16030.00450.617-0.1141-0.08630.5678-0.5121-0.32920.24660.24590.06220.12960.2922-0.00820.491418.943160.656515.1102
37.5069-4.9037-2.86448.75423.98896.1155-0.1248-0.20510.08060.46370.2264-0.40920.21520.2644-0.10160.0555-0.0218-0.00660.0960.00560.06439.353156.854513.6825
42.32180.7916-0.27423.9003-0.05563.5898-0.0624-0.11630.17370.1442-0.0890.18110.0192-0.19180.15140.0327-0.00520.00590.0766-0.03370.028930.109457.319313.7823
53.00120.26440.15632.7939-0.44381.1485-0.15610.1493-0.23330.0319-0.02410.32440.5834-0.21150.18020.4324-0.12630.14880.2157-0.06520.120323.412733.04675.7599
61.48950.61880.43378.7836-3.11091.40150.0807-0.20380.11320.07480.00670.37540.029-0.1247-0.08740.1809-0.09980.06050.2296-0.04180.13639.063933.41679.1809
73.45860.40780.84072.90790.00013.2172-0.19670.1936-0.2972-0.0781-0.02960.22250.4878-0.26070.22630.2852-0.14070.06380.1973-0.03490.082519.547234.66594.8941
82.54640.3370.00673.01911.31473.3239-0.07070.2823-0.1418-0.05830.0879-0.23350.4631-0.0342-0.01720.2536-0.00050.04790.1298-0.01390.030134.944838.92952.4586
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3352 - 3390
2X-RAY DIFFRACTION2A3391 - 3406
3X-RAY DIFFRACTION3A3407 - 3417
4X-RAY DIFFRACTION4A3418 - 3443
5X-RAY DIFFRACTION5B1 - 35
6X-RAY DIFFRACTION6B36 - 48
7X-RAY DIFFRACTION7B49 - 96
8X-RAY DIFFRACTION8B97 - 155

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