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- PDB-3h7x: A transition from strong right-handed to canonical left-handed su... -

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Basic information

Entry
Database: PDB / ID: 3h7x
TitleA transition from strong right-handed to canonical left-handed supercoiling in a conserved coiled coil segment of trimeric autotransporter adhesins - the wildtype structure
ComponentsAdhesin yadA
KeywordsCELL ADHESION / YadA / Adhesin / Adhesion / Coiled coil / Cell membrane / Cell outer membrane / Membrane / Plasmid / Virulence
Function / homology
Function and homology information


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
Biological speciesYersinia enterocolitica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 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
DepositionApr 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)42,7316
Polymers42,7316
Non-polymers00
Water1,820101
1
A: Adhesin yadA
B: Adhesin yadA
C: Adhesin yadA


Theoretical massNumber of molelcules
Total (without water)21,3653
Polymers21,3653
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6130 Å2
ΔGint-44 kcal/mol
Surface area9900 Å2
MethodPISA
2
D: Adhesin yadA
E: Adhesin yadA
F: Adhesin yadA


Theoretical massNumber of molelcules
Total (without water)21,3653
Polymers21,3653
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6080 Å2
ΔGint-44 kcal/mol
Surface area10190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.825, 105.553, 44.706
Angle α, β, γ (deg.)90.00, 90.02, 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: 7121.828 Da / Num. of mol.: 6 / Fragment: YADA STALK DOMAIN (RESIDUES 299-362)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia enterocolitica (bacteria) / Gene: yadA / Production host: Escherichia coli (E. coli) / References: UniProt: P0C2W0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.2 Å3/Da / Density % sol: 44.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 25% Peg3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.523
11-h,-k,l20.477
ReflectionResolution: 2→34.12 Å / Num. obs: 21317 / % possible obs: 89 % / Observed criterion σ(I): 4 / Redundancy: 1.9 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.057 / Net I/σ(I): 9.9
Reflection shellResolution: 2→2.12 Å / Redundancy: 2 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.95 / Num. unique all: 3666 / Rsym value: 0.197 / % possible all: 90

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Processing

Software
NameVersionClassification
MAR345data collection
SHELXSphasing
REFMAC5.5.0063refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: SAD
Starting model: MODEL FROM SAD

Resolution: 2→34 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.844 / SU B: 8.012 / SU ML: 0.199 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29785 1156 5.1 %RANDOM
Rwork0.24928 ---
obs0.25181 21317 90.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.982 Å2
Baniso -1Baniso -2Baniso -3
1--18.53 Å20 Å24.9 Å2
2--41.01 Å20 Å2
3----22.48 Å2
Refinement stepCycle: LAST / Resolution: 2→34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2526 0 0 101 2627
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0212661
X-RAY DIFFRACTIONr_angle_refined_deg2.4541.9433597
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4265342
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.69524.104134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.25515522
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1771524
X-RAY DIFFRACTIONr_chiral_restr0.1820.2423
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021965
X-RAY DIFFRACTIONr_mcbond_it0.9471.51628
X-RAY DIFFRACTIONr_mcangle_it1.64522641
X-RAY DIFFRACTIONr_scbond_it3.19931033
X-RAY DIFFRACTIONr_scangle_it4.9034.5941
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 341 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Atight positional0.150.05
Btight positional0.140.05
Ctight positional0.140.05
Dtight positional0.150.05
Etight positional0.140.05
Ftight positional0.140.05
Atight thermal0.390.5
Btight thermal0.370.5
Ctight thermal0.380.5
Dtight thermal0.350.5
Etight thermal0.370.5
Ftight thermal0.340.5
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 97 -
Rwork0.35 1514 -
obs--88.32 %

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