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- PDB-2wps: Salmonella enterica SadA 483-523 fused to GCN4 adaptors (SadAK3b-... -

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Basic information

Entry
Database: PDB / ID: 2wps
TitleSalmonella enterica SadA 483-523 fused to GCN4 adaptors (SadAK3b-V2, out-of-register fusion)
ComponentsTRIMERIC AUTOTRANSPORTER ADHESIN FRAGMENT
KeywordsMEMBRANE PROTEIN / ION COORDINATION / HYDROPHOBIC CORE / TRIMERIC AUTOTRANSPORTER ADHESIN / TAA / STUTTER / STAMMER / COILED COIL / PROTEIN EXPORT / POLAR CORE RESIDUES
Function / homology
Function and homology information


cell outer membrane / protein transport / cell surface
Similarity search - Function
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 / ESPR domain / Extended Signal Peptide of Type V secretion system / Trimeric autotransporter adhesin YadA-like, C-terminal membrane anchor domain / YadA-like membrane anchor domain / Pilin-like / Serralysin-like metalloprotease, C-terminal ...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 / ESPR domain / Extended Signal Peptide of Type V secretion system / 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 - #170 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Autotransporter adhesin SadA
Similarity search - Component
Biological speciesSALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHartmann, M.D. / Ridderbusch, O. / Lupas, A.N. / Hernandez Alvarez, B.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: A Coiled-Coil Motif that Sequesters Ions to the Hydrophobic Core.
Authors: Hartmann, M.D. / Ridderbusch, O. / Zeth, K. / Albrecht, R. / Testa, O. / Woolfson, D.N. / Sauer, G. / Dunin-Horkawicz, S. / Lupas, A.N. / Alvarez, B.H.
History
DepositionAug 9, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRIMERIC AUTOTRANSPORTER ADHESIN FRAGMENT
B: TRIMERIC AUTOTRANSPORTER ADHESIN FRAGMENT
C: TRIMERIC AUTOTRANSPORTER ADHESIN FRAGMENT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8057
Polymers37,6633
Non-polymers1424
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10580 Å2
ΔGint-118.4 kcal/mol
Surface area17730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.660, 55.850, 168.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
12A
22B
32C
13A
23B
33C
14A
24B
34C
15A
25B
35C
16A
26B
36C
17A
27B
37C

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLNGLNLYSLYS5AA456 - 5533 - 100
211GLNGLNLYSLYS5BB456 - 5533 - 100
311GLNGLNLYSLYS5CC456 - 5533 - 100
112ILEILEILEILE1AA457 - 4614 - 8
212ILEILEILEILE1BB457 - 4614 - 8
312ILEILEILEILE1CC457 - 4614 - 8
122ILEILELEULEU1AA464 - 46511 - 12
222ILEILELEULEU1BB464 - 46511 - 12
322ILEILELEULEU1CC464 - 46511 - 12
132LYSLYSILEILE1AA467 - 46814 - 15
232LYSLYSILEILE1BB467 - 46814 - 15
332LYSLYSILEILE1CC467 - 46814 - 15
113ILEILEALAALA1AA471 - 47618 - 23
213ILEILEALAALA1BB471 - 47618 - 23
313ILEILEALAALA1CC471 - 47618 - 23
123ILEILEILEILE1AA47825
223ILEILEILEILE1BB47825
323ILEILEILEILE1CC47825
133LEULEUILEILE1AA481 - 48228 - 29
233LEULEUILEILE1BB481 - 48228 - 29
333LEULEUILEILE1CC481 - 48228 - 29
114LYSLYSVALVAL1AA484 - 48531 - 32
214LYSLYSVALVAL1BB484 - 48531 - 32
314LYSLYSVALVAL1CC484 - 48531 - 32
124GLNGLNASNASN1AA487 - 50034 - 47
224GLNGLNASNASN1BB487 - 50034 - 47
324GLNGLNASNASN1CC487 - 50034 - 47
115ASNASNMETMET1AA502 - 52449 - 71
215ASNASNMETMET1BB502 - 52449 - 71
315ASNASNMETMET1CC502 - 52449 - 71
116GLNGLNILEILE1AA526 - 52773 - 74
216GLNGLNILEILE1BB526 - 52773 - 74
316GLNGLNILEILE1CC526 - 52773 - 74
126ASPASPASPASP1AA52976
226ASPASPASPASP1BB52976
326ASPASPASPASP1CC52976
136ILEILEILEILE1AA53178
236ILEILEILEILE1BB53178
336ILEILEILEILE1CC53178
117GLUGLUILEILE1AA533 - 53880 - 85
217GLUGLUILEILE1BB533 - 53880 - 85
317GLUGLUILEILE1CC533 - 53880 - 85
127ILEILEILEILE1AA54188
227ILEILEILEILE1BB54188
327ILEILEILEILE1CC54188
137ASNASNALAALA1AA543 - 54690 - 93
237ASNASNALAALA1BB543 - 54690 - 93
337ASNASNALAALA1CC543 - 54690 - 93
147ILEILELYSLYS1AA548 - 54995 - 96
247ILEILELYSLYS1BB548 - 54995 - 96
347ILEILELYSLYS1CC548 - 54995 - 96
157LEULEUILEILE1AA551 - 55298 - 99
257LEULEUILEILE1BB551 - 55298 - 99
357LEULEUILEILE1CC551 - 55298 - 99

NCS ensembles :
ID
1
2
3
4
5
6
7

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Components

#1: Protein TRIMERIC AUTOTRANSPORTER ADHESIN FRAGMENT


Mass: 12554.290 Da / Num. of mol.: 3 / Fragment: RESIDUES 483-523 FUSED TO GCN4 ADAPTORS
Source method: isolated from a genetically manipulated source
Details: N- AND C-TERMINAL IN-REGISTER FUSION TO GCN4 ADAPTORS
Source: (gene. exp.) SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q8ZL64
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN- AND C-TERMINAL OUT-OF-REGISTER FUSION TO GCN4 ADAPTORS (UNIPROT: P03069)

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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: 2.4 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growDetails: 10% (W/V) PEG 4000, 10% (V/V) ISOPOPANOL, 3% (W/V) 1,5-DIAMINOPENTANE DIHYDROCHLORIDE, 100 MM NA-CITRATE PH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.992
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.992 Å / Relative weight: 1
ReflectionResolution: 2.6→36 Å / Num. obs: 11193 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 3.47 % / Biso Wilson estimate: 35.9 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 7.61
Reflection shellResolution: 2.6→2.75 Å / Redundancy: 3.05 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.01 / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GCM

1gcm


Resolution: 2.6→35.83 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.857 / SU B: 12.427 / SU ML: 0.261 / Cross valid method: THROUGHOUT / ESU R: 1.072 / ESU R Free: 0.413 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.32443 577 5.2 %RANDOM
Rwork0.23786 ---
obs0.24193 10616 98.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.717 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2--4.53 Å20 Å2
3----4.37 Å2
Refinement stepCycle: LAST / Resolution: 2.6→35.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2365 0 4 73 2442
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222374
X-RAY DIFFRACTIONr_bond_other_d0.0020.021548
X-RAY DIFFRACTIONr_angle_refined_deg1.321.9623204
X-RAY DIFFRACTIONr_angle_other_deg0.96733885
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8025291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.20527.876113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.17615510
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.72156
X-RAY DIFFRACTIONr_chiral_restr0.0760.2411
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022531
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02351
X-RAY DIFFRACTIONr_nbd_refined0.2360.2606
X-RAY DIFFRACTIONr_nbd_other0.150.21375
X-RAY DIFFRACTIONr_nbtor_refined0.1930.21174
X-RAY DIFFRACTIONr_nbtor_other0.0910.21280
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.275
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1560.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2310.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2230.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8741642
X-RAY DIFFRACTIONr_mcbond_other0.4454585
X-RAY DIFFRACTIONr_mcangle_it3.9662427
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.3858957
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it9.75812777
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
21A130tight positional0.040.05
22B130tight positional0.030.05
23C130tight positional0.040.05
31A114tight positional0.050.05
32B114tight positional0.040.05
33C114tight positional0.040.05
41A187tight positional0.040.05
42B187tight positional0.060.05
43C187tight positional0.050.05
51A260tight positional0.040.05
52B260tight positional0.040.05
53C260tight positional0.040.05
61A53tight positional0.040.05
62B53tight positional0.040.05
63C53tight positional0.050.05
71A201tight positional0.040.05
72B201tight positional0.040.05
73C201tight positional0.040.05
11A587medium positional0.240.5
12B587medium positional0.250.5
13C587medium positional0.260.5
11A695loose positional0.75
12B695loose positional0.715
13C695loose positional0.655
21A130tight thermal0.110.5
22B130tight thermal0.10.5
23C130tight thermal0.090.5
31A114tight thermal0.120.5
32B114tight thermal0.110.5
33C114tight thermal0.110.5
41A187tight thermal0.150.5
42B187tight thermal0.150.5
43C187tight thermal0.130.5
51A260tight thermal0.140.5
52B260tight thermal0.140.5
53C260tight thermal0.140.5
61A53tight thermal0.140.5
62B53tight thermal0.10.5
63C53tight thermal0.120.5
71A201tight thermal0.10.5
72B201tight thermal0.10.5
73C201tight thermal0.120.5
11A587medium thermal0.542
12B587medium thermal0.452
13C587medium thermal0.632
11A695loose thermal2.0810
12B695loose thermal2.0610
13C695loose thermal2.4710
LS refinement shellResolution: 2.597→2.664 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 50 -
Rwork0.317 732 -
obs--94.9 %

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