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- PDB-2wpq: Salmonella enterica SadA 479-519 fused to GCN4 adaptors (SadAK3, ... -

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Basic information

Entry
Database: PDB / ID: 2wpq
TitleSalmonella enterica SadA 479-519 fused to GCN4 adaptors (SadAK3, in- register fusion)
ComponentsTRIMERIC AUTOTRANSPORTER ADHESIN FRAGMENT
KeywordsMEMBRANE PROTEIN / HYDROPHOBIC CORE / ION COORDINATION / PROTEIN EXPORT / TRIMERIC AUTOTRANSPORTER ADHESIN / TAA / 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) / ESPR domain / Extended Signal Peptide of Type V secretion system / 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 ...Trimeric autotransporter adhesin YadA-like, head domain / YadA head domain repeat (2 copies) / ESPR domain / Extended Signal Peptide of Type V secretion system / 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 - #170 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
NITRATE ION / Autotransporter adhesin SadA
Similarity search - Component
Biological speciesSALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsHartmann, M.D. / Hernandez Alvarez, B. / Albrecht, R. / Zeth, K. / Lupas, A.N.
Citation
#1: Journal: Protein Eng.Des.Sel. / Year: 2008
Title: A New Expression System for Protein Crystallization Using Trimeric Coiled-Coil Adaptors.
Authors: Hernandez Alvarez, B. / Hartmann, M.D. / Albrecht, R. / Lupas, A.N. / Zeth, K. / Linke, D.
History
DepositionAug 9, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 29, 2017Group: Refinement description
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

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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)34,7917
Polymers34,5963
Non-polymers1954
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10890 Å2
ΔGint-101.58 kcal/mol
Surface area17250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.022, 36.967, 178.445
Angle α, β, γ (deg.)90.00, 92.73, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 6 / Auth seq-ID: 450 - 548 / Label seq-ID: 1 - 99

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC

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Components

#1: Protein TRIMERIC AUTOTRANSPORTER ADHESIN FRAGMENT / PUTATIVE INNER MEMBRANE PROTEIN


Mass: 11532.017 Da / Num. of mol.: 3 / Fragment: RESIDUES 479-519 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-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.6 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growDetails: 20% (W/V) PEG 3350, 0.2 M KNO3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.969
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.969 Å / Relative weight: 1
ReflectionResolution: 1.85→34 Å / Num. obs: 29718 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 3.97 % / Biso Wilson estimate: 34.7 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.1
Reflection shellResolution: 1.85→1.96 Å / Redundancy: 3.82 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 1.91 / % possible all: 94

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GCM

1gcm


Resolution: 1.85→34.14 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.918 / SU B: 9.891 / SU ML: 0.13 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RECORD CONTAINS RESIDUAL B FACTORS ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.28831 1470 5.1 %RANDOM
Rwork0.22082 ---
obs0.22422 27627 98.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.788 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å20 Å2-1.33 Å2
2--3.54 Å20 Å2
3----3.16 Å2
Refinement stepCycle: LAST / Resolution: 1.85→34.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2415 0 10 170 2595
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222433
X-RAY DIFFRACTIONr_bond_other_d0.0010.021598
X-RAY DIFFRACTIONr_angle_refined_deg0.8411.963276
X-RAY DIFFRACTIONr_angle_other_deg0.76333998
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8845294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.02727.805123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.60415522
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.308156
X-RAY DIFFRACTIONr_chiral_restr0.0520.2405
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022621
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02369
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.60841491
X-RAY DIFFRACTIONr_mcbond_other0.4524591
X-RAY DIFFRACTIONr_mcangle_it2.83162453
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.3898942
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.5112823
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

Ens-ID: 1 / Number: 1327 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Aloose positional0.775
2Bloose positional0.825
3Cloose positional0.895
1Aloose thermal2.7810
2Bloose thermal2.3110
3Cloose thermal2.5710
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.418 100 -
Rwork0.359 1958 -
obs--97.49 %
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)
10.6530.03631.23330.02430.02782.4387-0.01350.05050.02970.0063-0.01340.0279-0.00180.12510.02690.03940.0120.02170.0233-0.01310.0475-16.79490.203-42.9002
21.23530.12612.00060.01980.17963.3563-0.0037-0.0455-0.0138-0.0117-0.0117-0.00150.051-0.04450.01530.03520.00440.02580.01940.00490.0571-16.6997-0.4335-43.6149
30.62620.03741.3070.01460.08682.9025-0.0220.04530.05070.0073-0.0250.00720.02880.09220.0470.04930.00050.01270.04850.00660.0613-16.58640.1584-43.8715
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A450 - 548
2X-RAY DIFFRACTION2B450 - 548
3X-RAY DIFFRACTION3C450 - 548

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