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- PDB-3lt7: A transition from strong right-handed to canonical left-handed su... -

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Basic information

Entry
Database: PDB / ID: 3lt7
TitleA transition from strong right-handed to canonical left-handed supercoiling in a conserved coiled coil segment of trimeric autotransporter adhesins - the M3 mutant structure
ComponentsAdhesin yadA
KeywordsCELL ADHESION / ADHESION / COILED COIL / TRIMERIC AUTOTRANSPORTER / Cell membrane / Cell outer membrane / Membrane / Plasmid / 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 / MOLECULAR REPLACEMENT / Resolution: 1.5 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: Version format compliance
Revision 1.2Feb 21, 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

Downloads & links

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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)43,8386
Polymers43,8386
Non-polymers00
Water2,612145
1
A: Adhesin yadA
B: Adhesin yadA
C: Adhesin yadA


Theoretical massNumber of molelcules
Total (without water)21,9193
Polymers21,9193
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6780 Å2
ΔGint-55 kcal/mol
Surface area10770 Å2
MethodPISA
2
D: Adhesin yadA
E: Adhesin yadA
F: Adhesin yadA


Theoretical massNumber of molelcules
Total (without water)21,9193
Polymers21,9193
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6840 Å2
ΔGint-58 kcal/mol
Surface area10660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.032, 114.847, 48.188
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D

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Components

#1: Protein
Adhesin yadA


Mass: 7306.254 Da / Num. of mol.: 6
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 / Water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.53 Å3/Da / Density % sol: 51.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.536
11h,-k,-l20.464
ReflectionResolution: 1.5→20 Å / Num. obs: 54137 / % possible obs: 91.2 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 5.71
Reflection shellResolution: 1.5→1.6 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.27 / Rsym value: 0.0266

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0063refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→20 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.887 / SU B: 3.78 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.027 / ESU R Free: 0.021 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26542 2931 5.1 %RANDOM
Rwork0.23356 ---
obs0.23514 54137 82.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.772 Å2
Baniso -1Baniso -2Baniso -3
1--6.49 Å20 Å2-1.35 Å2
2--22.27 Å20 Å2
3----15.78 Å2
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2795 0 0 145 2940
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0212864
X-RAY DIFFRACTIONr_angle_refined_deg1.7921.963856
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4955356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.34924.58131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.76715585
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1161518
X-RAY DIFFRACTIONr_chiral_restr0.1150.2464
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022038
X-RAY DIFFRACTIONr_mcbond_it1.4621.51755
X-RAY DIFFRACTIONr_mcangle_it222833
X-RAY DIFFRACTIONr_scbond_it3.14231109
X-RAY DIFFRACTIONr_scangle_it4.2834.51016
X-RAY DIFFRACTIONr_rigid_bond_restr1.90232864
X-RAY DIFFRACTIONr_sphericity_free5.4213145
X-RAY DIFFRACTIONr_sphericity_bonded2.75132828
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 387 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Aloose positional0.235
Dloose thermal1.5410
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 212 -
Rwork0.322 3941 -
obs--81.18 %

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