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- PDB-6xi1: Crystal structure of tetra-tandem repeat in extending RTX adhesin... -

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Basic information

Entry
Database: PDB / ID: 6xi1
TitleCrystal structure of tetra-tandem repeat in extending RTX adhesin from Aeromonas hydrophila
ComponentsFlagellin hook IN motif family
KeywordsMETAL BINDING PROTEIN / Beta-sandwich domains / Bacterial adhesin / RTX protein / Adhesion protein / calcium binding protein / VCBS-repeat
Function / homology
Function and homology information


calcium ion binding
Similarity search - Function
VCBS repeat / Type I secretion C-terminal target domain, VC_A0849 subclass / RapA2, cadherin-like domain / Bacterial cadherin-like domain / Bacterial Ig-like domain 13 / Bacterial Ig-like domain / CalX-like domain superfamily / Hemolysin-type calcium-binding conserved site / Hemolysin-type calcium-binding region signature. / RTX calcium-binding nonapeptide repeat ...VCBS repeat / Type I secretion C-terminal target domain, VC_A0849 subclass / RapA2, cadherin-like domain / Bacterial cadherin-like domain / Bacterial Ig-like domain 13 / Bacterial Ig-like domain / CalX-like domain superfamily / Hemolysin-type calcium-binding conserved site / Hemolysin-type calcium-binding region signature. / RTX calcium-binding nonapeptide repeat / RTX calcium-binding nonapeptide repeat (4 copies) / Serralysin-like metalloprotease, C-terminal / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Flagellin hook IN motif family
Similarity search - Component
Biological speciesAeromonas hydrophila subsp. hydrophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsYe, Q. / Vance, T.D.R. / Conroy, B. / Davies, P.L.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2016-04810 Canada
CitationJournal: J Struct Biol X / Year: 2020
Title: Essential role of calcium in extending RTX adhesins to their target.
Authors: Vance, T.D.R. / Ye, Q. / Conroy, B. / Davies, P.L.
History
DepositionJun 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Flagellin hook IN motif family
BBB: Flagellin hook IN motif family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,00945
Polymers90,5822
Non-polymers2,42743
Water17,547974
1
AAA: Flagellin hook IN motif family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,42322
Polymers45,2911
Non-polymers1,13221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
BBB: Flagellin hook IN motif family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,58623
Polymers45,2911
Non-polymers1,29522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.670, 50.370, 124.600
Angle α, β, γ (deg.)97.555, 98.244, 101.719
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AAABBB

#1: Protein Flagellin hook IN motif family


Mass: 45291.234 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeromonas hydrophila subsp. hydrophila (strain ATCC 7966 / DSM 30187 / JCM 1027 / KCTC 2358 / NCIMB 9240) (bacteria)
Strain: ATCC 7966 / DSM 30187 / JCM 1027 / KCTC 2358 / NCIMB 9240
Gene: AHA_3491 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0KNW4

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Non-polymers , 6 types, 1017 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 974 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.15 Å3/Da / Density % sol: 61.02 %
Crystal growTemperature: 294 K / Method: microbatch / pH: 4.6 / Details: PEG 20,000, sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Feb 12, 2016 / Details: ultra-low expansion titanium siliicate flat mirror
RadiationMonochromator: DCM, Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.75→48.64 Å / Num. obs: 108730 / % possible obs: 97.3 % / Redundancy: 3.9 % / Biso Wilson estimate: 21.075 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.048 / Rrim(I) all: 0.094 / Χ2: 0.91 / Net I/σ(I): 10
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 4 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 5282 / CC1/2: 0.859 / Rpim(I) all: 0.483 / Rrim(I) all: 0.96 / Χ2: 0.9 / % possible all: 95.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
PHENIXmodel building
BUCCANEERmodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.75→48.638 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.802 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.099
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2098 5436 5.001 %
Rwork0.1812 103270 -
all0.183 --
obs-108706 97.26 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 25.274 Å2
Baniso -1Baniso -2Baniso -3
1-0.474 Å2-1.677 Å2-1.366 Å2
2---1.162 Å2-2.253 Å2
3---2.643 Å2
Refinement stepCycle: LAST / Resolution: 1.75→48.638 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6012 0 114 974 7100
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0136151
X-RAY DIFFRACTIONr_bond_other_d0.0030.0175439
X-RAY DIFFRACTIONr_angle_refined_deg1.5741.6468415
X-RAY DIFFRACTIONr_angle_other_deg1.5391.57112675
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4025849
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.50827.885227
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.4515875
X-RAY DIFFRACTIONr_chiral_restr0.0680.2933
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027041
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021043
X-RAY DIFFRACTIONr_nbd_refined0.2480.21125
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1950.24984
X-RAY DIFFRACTIONr_nbtor_refined0.1520.23091
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.22667
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2772
X-RAY DIFFRACTIONr_metal_ion_refined0.1260.2117
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2160.28
X-RAY DIFFRACTIONr_nbd_other0.1820.242
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.150.236
X-RAY DIFFRACTIONr_mcbond_it2.1472.5493402
X-RAY DIFFRACTIONr_mcbond_other2.1452.5483401
X-RAY DIFFRACTIONr_mcangle_it2.8763.8134249
X-RAY DIFFRACTIONr_mcangle_other2.8763.8144250
X-RAY DIFFRACTIONr_scbond_it2.9912.822749
X-RAY DIFFRACTIONr_scbond_other2.9912.8212750
X-RAY DIFFRACTIONr_scangle_it4.3834.124166
X-RAY DIFFRACTIONr_scangle_other4.3824.124167
X-RAY DIFFRACTIONr_lrange_it6.05832.747026
X-RAY DIFFRACTIONr_lrange_other5.59431.9196697
X-RAY DIFFRACTIONr_ncsr_local_group_10.0780.0512403
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.75-1.7950.3153940.31574850.31582660.6050.60995.31820.285
1.795-1.8440.293860.27873330.27980540.7720.76495.84060.25
1.844-1.8980.2713770.24771530.24978430.8430.84296.00920.221
1.898-1.9560.263640.22569170.22775560.8640.8896.36050.202
1.956-2.020.2453580.20968050.21174240.8950.90896.48440.19
2.02-2.0910.2453450.20565550.20771440.9030.91196.58450.185
2.091-2.170.2223330.18763380.18868750.9230.93597.03270.171
2.17-2.2580.2123210.18760950.18866080.9260.93697.09440.17
2.258-2.3580.2343090.18458720.18763370.9170.93897.53830.171
2.358-2.4730.2172970.17756370.17960720.9360.94697.72730.165
2.473-2.6070.2232820.18153600.18357630.9260.94497.90040.173
2.607-2.7640.2272670.17650780.17854490.9320.94998.09140.173
2.764-2.9540.2182550.17848300.1851790.940.94798.1850.18
2.954-3.190.1772340.15544550.15647560.960.96298.59120.161
3.19-3.4930.1922160.17741000.17843750.9510.95498.65140.189
3.493-3.9030.1941970.16237540.16440040.9510.9698.67630.18
3.903-4.5020.1621740.14632970.14734940.9660.97299.34170.172
4.502-5.5020.1781470.15328020.15429690.9680.97199.32640.181
5.502-7.7310.1861150.16221790.16323070.9630.9799.43650.192
7.731-48.6380.175650.16212250.16212920.9710.96899.84520.194

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