[English] 日本語
Yorodumi
- PDB-3s6l: Crystal structure of a YadA-like head domain of the trimeric auto... -

+
Open data


ID or keywords:

Loading...

-
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 / protein transport / cell surface / 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 / Pilin-like ...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 / Pilin-like / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more