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- PDB-3s6l: Crystal structure of a YadA-like head domain of the trimeric auto... -

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Basic information

Entry
Database: PDB / ID: 3s6l
TitleCrystal structure of a YadA-like head domain of the trimeric autotransporter adhesin BoaA from Burkholderia pseudomallei solved by iodide ion SAD phasing
ComponentsHep_Hag family
KeywordsCELL ADHESION / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / trimeric autotransporter adhesin / TAA / BoaA / BoaB / BpaA / YadA / collagen / left handed beta-roll / cell surface / iodide ion / SAD phasing / melioidosis / respiratory track / epithelial cells
Function / homology
Function and homology information


: / cell outer membrane / metal ion binding
Similarity search - Function
Trimeric autotransporter adhesin YadA-like, head domain / YadA head domain repeat (2 copies) / Serralysin-like metalloprotease, C-terminal / 2 Solenoid / Alkaline Protease, subunit P, domain 1 / 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 / Serralysin-like metalloprotease, C-terminal / Mainly Beta
Similarity search - Domain/homology
IODIDE ION / Hep_Hag family
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.3 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of a YadA-like head domain of the trimeric autotransporter adhesin BoaA from Burkholderia pseudomallei
Authors: Edwards, T.E. / Gardberg, A.S. / Lafontaine, E.R. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionMay 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 20, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.3Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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_ref_seq_dif.details / _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: Hep_Hag family
B: Hep_Hag family
C: Hep_Hag family
D: Hep_Hag family
E: Hep_Hag family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,779100
Polymers81,0555
Non-polymers8,72495
Water5,945330
1
A: Hep_Hag family
B: Hep_Hag family
C: Hep_Hag family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,64656
Polymers48,6333
Non-polymers5,01453
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Hep_Hag family
hetero molecules

D: Hep_Hag family
hetero molecules

D: Hep_Hag family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,39360
Polymers48,6333
Non-polymers4,76057
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x+1/2,-y+1/21
crystal symmetry operation11_455y-1/2,-z+1/2,-x1
3
E: Hep_Hag family
hetero molecules

E: Hep_Hag family
hetero molecules

E: Hep_Hag family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,00572
Polymers48,6333
Non-polymers6,37269
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Unit cell
Length a, b, c (Å)144.000, 144.000, 144.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11D-203-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: MET / End label comp-ID: MET / Refine code: 4 / Auth seq-ID: 11 - 157 / Label seq-ID: 16 - 162

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE

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Components

#1: Protein
Hep_Hag family


Mass: 16210.981 Da / Num. of mol.: 5 / Fragment: UNP Residues 1381-1553
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710b / Gene: BURPS1710b_A2381 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3JFX2
#2: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 53 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Zn
#4: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 3.07 Å3/Da / Density % sol: 59.93 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: BupsA.01663.c.A9 at 22.5 mg/mL against JCSG+ screen E7 focus screen, 6% isopropanol, 0.1 M Na cacodylate pH 6.9, 0.2 M ZnCl2 soaked with 6% isopropanol, 0.1 M Na cacodylate pH 7.5, 0.2 M ...Details: BupsA.01663.c.A9 at 22.5 mg/mL against JCSG+ screen E7 focus screen, 6% isopropanol, 0.1 M Na cacodylate pH 6.9, 0.2 M ZnCl2 soaked with 6% isopropanol, 0.1 M Na cacodylate pH 7.5, 0.2 M ZnCl2, 0.7 M NaI, 22% ethylene glycol for 1 minute, crystal tracking ID 218438h2, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Apr 6, 2011 / Details: VariMax
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNumber: 1425650 / Rmerge(I) obs: 0.176 / D res high: 2.5 Å / Num. obs: 66772 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
11.1828.871894.110.038
7.9111.18136810010.082
6.467.91177310010.073
5.596.46209099.710.111
55.59239210010.124
4.565262110010.07
4.234.56286099.710.078
3.954.23306410010.115
3.733.95329510010.12
3.543.73340810010.145
3.373.54365910010.175
3.233.37376010010.222
3.13.23400099.910.241
2.993.1410410010.248
2.892.99429510010.309
2.82.89436299.910.387
2.712.8455610010.423
2.642.71470010010.431
2.572.64483910010.489
2.52.57490810010.628
ReflectionResolution: 2.3→50 Å / Num. all: 44378 / Num. obs: 44337 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 12.1 % / Biso Wilson estimate: 31.861 Å2 / Rmerge(I) obs: 0.125 / Net I/σ(I): 17.43
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
2.3-2.3612.10.6334.663920532523251100
2.36-2.420.5765.0238331316599.9
2.42-2.490.5285.33370053054100
2.49-2.570.4156.61368353027100
2.57-2.660.3038.72351282878100
2.66-2.750.2659.66346192831100
2.75-2.850.24910.05331052700100
2.85-2.970.19412.35321632620100
2.97-3.10.1416.39307932503100
3.1-3.250.13317.1298022421100
3.25-3.430.11519.59283652304100
3.43-3.640.08725.6626685216199.8
3.64-3.890.06831.42250862040100
3.89-4.20.06932.29232831901100
4.2-4.60.05241.0721366176799.9
4.6-5.140.05439.63191201604100
5.14-5.940.07930.89167451414100
5.94-7.270.0638.11135711217100
7.27-10.290.06136.3510075953100
10.290.0445.99489152694.3

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 2.5 Å / D res low: 29.41 Å / FOM : 0.618 / FOM acentric: 0.63 / FOM centric: 0.464 / Reflection: 34590 / Reflection acentric: 32105 / Reflection centric: 2483
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
9.67-11.540.5390.5930.31725920851
8.49-9.670.6460.6620.55529525045
7.66-8.490.6310.6520.52233928554
7.03-7.660.6460.670.49136831850
6.54-7.030.630.6690.38238833553
6.14-6.540.6020.6290.40442637650
5.8-6.140.6510.6720.49243838850
5.51-5.80.6320.6480.50546541550
5.26-5.510.6660.6790.54849744651
5.05-5.260.6590.670.55750045149
4.85-5.050.6690.6930.43650746047
4.68-4.850.6460.6640.46156451351
4.53-4.680.660.6810.44555350350
4.39-4.530.6460.6690.40760555154
4.26-4.390.6430.6570.46458253943
4.14-4.260.6070.6320.33763157754
4.03-4.140.60.6210.34662757948
3.93-4.030.5980.6140.41565660650
3.84-3.930.6210.6390.40364559649
3.75-3.840.6070.6290.34169364053
3.67-3.750.6150.6290.43569564451
3.59-3.670.6010.6160.38471666848
3.52-3.590.5870.6030.36170265547
3.46-3.520.5820.5940.42273568550
3.39-3.460.5840.5980.39875470153
3.33-3.390.5780.5890.39877572946
3.27-3.330.5750.5830.44976471846
3.22-3.270.5860.5950.45480175348
3.17-3.220.570.580.43380275151
3.12-3.170.5840.5980.37682176853
3.07-3.120.5780.5870.41181376845
3.03-3.070.5880.5970.45986080852
2.98-3.030.580.5880.44285280151
2.94-2.980.570.5770.43585480945
2.9-2.940.5860.5950.42986381548
2.86-2.90.60.6040.54687481856
2.83-2.860.6170.6240.48288884840
2.79-2.830.610.6150.53491886751
2.76-2.790.6350.6430.4994188754
2.73-2.760.6180.6260.47492888147
2.69-2.730.6410.6480.52593788453
2.66-2.690.6410.6440.57894490143
2.63-2.660.660.6620.62298793255
2.61-2.630.6560.660.5794990247
2.58-2.610.6330.6340.6196892344
2.55-2.580.6370.640.596103297260
2.53-2.550.6970.70.641101997147
2.5-2.530.7190.7230.64598593649

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
StructureStudiodata collection
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.1828 / WRfactor Rwork: 0.1573 / Occupancy max: 1 / Occupancy min: 0.18 / FOM work R set: 0.8828 / SU B: 7.634 / SU ML: 0.104 / SU R Cruickshank DPI: 0.2089 / SU Rfree: 0.1734 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.209 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2072 2222 5 %RANDOM
Rwork0.1748 ---
obs0.1764 44216 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 108.97 Å2 / Biso mean: 24.8705 Å2 / Biso min: 2 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4929 0 95 330 5354
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0214979
X-RAY DIFFRACTIONr_angle_refined_deg1.3461.9116771
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1725772
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.36825.928167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.0915565
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9241519
X-RAY DIFFRACTIONr_chiral_restr0.090.2773
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213945
X-RAY DIFFRACTIONr_mcbond_it0.5971.53755
X-RAY DIFFRACTIONr_mcangle_it1.07125759
X-RAY DIFFRACTIONr_scbond_it2.14331224
X-RAY DIFFRACTIONr_scangle_it3.3634.51012
Refine LS restraints NCS

Ens-ID: 1 / Number: 915 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.190.5
2BMEDIUM POSITIONAL0.430.5
3CMEDIUM POSITIONAL0.220.5
4DMEDIUM POSITIONAL0.210.5
5EMEDIUM POSITIONAL0.260.5
1AMEDIUM THERMAL0.82
2BMEDIUM THERMAL0.872
3CMEDIUM THERMAL0.852
4DMEDIUM THERMAL1.492
5EMEDIUM THERMAL1.112
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 155 -
Rwork0.213 3100 -
all-3255 -
obs--99.72 %
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)
10.48560.2923-0.07431.6527-0.16630.295-0.02340.0272-0.0573-0.06670.0293-0.03950.0086-0.0048-0.00590.04780.01460.02670.0795-0.01090.04094.554640.758239.1765
20.62760.1453-0.061.54470.12160.1561-0.0476-0.05890.00920.02990.02170.12310.0096-0.08490.02590.05850.02810.02420.09650.00080.0202-5.176344.22745.4325
30.92170.4847-0.03761.7620.00350.0742-0.0825-0.1115-0.070.17610.0871-0.1080.0270.0415-0.00460.06560.03590.0020.0933-0.00410.0125.225741.350751.0638
40.5540.3361-0.25510.7546-0.40130.49240.0097-0.1367-0.00750.0512-0.0327-0.00540.02480.03090.0230.0579-0.00350.01630.08080.01920.0303-27.684241.262136.7467
50.8020.48730.75430.72640.61570.9079-0.007-0.02710.11490.0269-0.05160.1014-0.0271-0.03470.05860.03830.02560.03340.03920.01390.058417.809427.118724.2986
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 165
2X-RAY DIFFRACTION2B11 - 163
3X-RAY DIFFRACTION3C11 - 165
4X-RAY DIFFRACTION4D11 - 168
5X-RAY DIFFRACTION5E11 - 166

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