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- PDB-3lt6: A transition from strong right-handed to canonical left-handed su... -

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Basic information

Entry
Database: PDB / ID: 3lt6
TitleA transition from strong right-handed to canonical left-handed supercoiling in a conserved coiled coil segment of trimeric autotransporter adhesins - the Mutant 4 structure
ComponentsAdhesin yadA
KeywordsCELL ADHESION / YADA / TRIMERIC AUTOTRANSPORTER / CORE RESIDUES / Cell membrane / Cell outer membrane / Membrane / Virulence
Function / homology
Function and homology information


protein secretion by the type V secretion system / collagen binding / cell outer membrane / protein transport / cell adhesion / cell surface
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2280 / Outer membrane adhesion, Yersinia / Trimeric autotransporter adhesin YadA-like, head domain / YadA head domain repeat (2 copies) / Trimeric autotransporter adhesin YadA-like, stalk domain / Coiled stalk of trimeric autotransporter adhesin / Trimeric autotransporter adhesin YadA-like, C-terminal membrane anchor domain / YadA-like membrane anchor domain / Pilin-like / Serralysin-like metalloprotease, C-terminal ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2280 / Outer membrane adhesion, Yersinia / Trimeric autotransporter adhesin YadA-like, head domain / YadA head domain repeat (2 copies) / Trimeric autotransporter adhesin YadA-like, stalk domain / Coiled stalk of trimeric autotransporter adhesin / Trimeric autotransporter adhesin YadA-like, C-terminal membrane anchor domain / YadA-like membrane anchor domain / Pilin-like / Serralysin-like metalloprotease, C-terminal / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Adhesin YadA / Adhesin YadA
Similarity search - Component
Biological speciesYersinia enterocolitica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsZeth, K. / Hernandez-Alvarez, B. / Lupas, A.N.
CitationJournal: J.Struct.Biol. / Year: 2010
Title: A transition from strong right-handed to canonical left-handed supercoiling in a conserved coiled-coil segment of trimeric autotransporter adhesins.
Authors: Alvarez, B.H. / Gruber, M. / Ursinus, A. / Dunin-Horkawicz, S. / Lupas, A.N. / Zeth, K.
History
DepositionFeb 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adhesin yadA
B: Adhesin yadA
C: Adhesin yadA
D: Adhesin yadA
E: Adhesin yadA
F: Adhesin yadA


Theoretical massNumber of molelcules
Total (without water)44,0236
Polymers44,0236
Non-polymers00
Water1,17165
1
A: Adhesin yadA
B: Adhesin yadA
C: Adhesin yadA


Theoretical massNumber of molelcules
Total (without water)22,0123
Polymers22,0123
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6740 Å2
ΔGint-57 kcal/mol
Surface area10780 Å2
MethodPISA
2
D: Adhesin yadA
E: Adhesin yadA
F: Adhesin yadA


Theoretical massNumber of molelcules
Total (without water)22,0123
Polymers22,0123
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6900 Å2
ΔGint-58 kcal/mol
Surface area11050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.000, 115.760, 48.080
Angle α, β, γ (deg.)90.00, 89.93, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

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Components

#1: Protein
Adhesin yadA


Mass: 7337.171 Da / Num. of mol.: 6 / Fragment: TRIMERIC COILED COIL
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia enterocolitica (bacteria) / Gene: yadA, invA, yop1, yopA / Plasmid: PET / Production host: Escherichia coli (E. coli) / References: UniProt: P31489, UniProt: P0C2W0*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.53 Å3/Da / Density % sol: 51.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.76
11h,-k,-l20.24
ReflectionResolution: 1.8→20 Å / Num. obs: 37715 / % possible obs: 98.36 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.3
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.43 / Num. unique all: 2005

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Processing

Software
NameVersionClassification
MAR345data collection
SHELXSphasing
REFMAC5.5.0063refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.8→19.3 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.902 / SU B: 8.971 / SU ML: 0.114 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26619 2005 5 %RANDOM
Rwork0.22739 ---
obs0.22935 37715 98.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.536 Å2
Baniso -1Baniso -2Baniso -3
1--9.46 Å20 Å21.12 Å2
2--28.32 Å20 Å2
3----18.85 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2834 0 0 65 2899
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0212885
X-RAY DIFFRACTIONr_angle_refined_deg2.0031.9643875
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9565358
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.86924.72125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.46115604
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6651518
X-RAY DIFFRACTIONr_chiral_restr0.140.2470
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022022
X-RAY DIFFRACTIONr_mcbond_it1.3381.51789
X-RAY DIFFRACTIONr_mcangle_it2.04122886
X-RAY DIFFRACTIONr_scbond_it3.61331096
X-RAY DIFFRACTIONr_scangle_it5.614.5986
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 403 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Aloose positional0.865
Bloose positional0.925
Cloose positional0.975
Dloose positional0.935
Eloose positional0.885
Floose positional0.895
Aloose thermal4.810
Bloose thermal3.1410
Cloose thermal3.4910
Dloose thermal3.7110
Eloose thermal2.8110
Floose thermal2.7810
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 132 -
Rwork0.225 2589 -
obs--92.84 %
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)
10.4605-0.36650.23212.51793.93269.59130.1224-0.0254-0.0521-0.1021-0.13970.07380.0281-0.6950.01740.0318-0.0058-0.00460.11630.00670.13126.495-3.01-22.584
20.3178-0.01930.00992.18053.02636.2230.06650.0179-0.12430.17880.0737-0.05030.61650.0877-0.14010.1138-0.0067-0.0020.09780.02020.15931.113-11.145-20.176
30.3949-0.0099-0.19743.57525.591711.08850.0281-0.0233-0.0362-0.09080.0317-0.0296-0.17680.1592-0.05990.0046-0.00310.00030.01390.00910.034535.54-4.904-24.701
40.4631-0.11870.10343.77755.979312.04930.0435-0.0107-0.0310.10180.0293-0.01120.34740.227-0.07270.01770.0121-0.00530.02450.00110.023455.483-3.404-27.956
50.2850.0692-0.51722.04823.661911.08040.03460.05240.01070.0704-0.06480.02060.116-0.27710.03030.00730.00440.00160.0456-0.00050.023346.358-4.2-28.171
60.2429-0.0673-0.22562.69664.26689.19010.1003-0.02940.0767-0.19710.028-0.061-0.48990.0396-0.12840.07880.0142-0.00090.10340.01320.155251.0783.47-31.61
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-5 - 46
2X-RAY DIFFRACTION2B-4 - 50
3X-RAY DIFFRACTION3C-4 - 50
4X-RAY DIFFRACTION4D-5 - 50
5X-RAY DIFFRACTION5E-5 - 49
6X-RAY DIFFRACTION6F-5 - 50

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