[English] 日本語
Yorodumi
- PDB-3la9: Crystal structure of the trimeric autotransporter adhesin head do... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3la9
TitleCrystal structure of the trimeric autotransporter adhesin head domain BpaA from Burkholderia pseudomallei, iodide phased
ComponentsHaemagglutinin family protein
KeywordsTRANSPORT PROTEIN / NIAID / Seattle Structural Genomics Center for Infectious Disease / autotransporter / iodide phased / collagen binding / melioidosis / SSGCID
Function / homology
Function and homology information


cell outer membrane / cell surface
Similarity search - Function
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 / 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 / 2 Solenoid / Alkaline Protease, subunit P, domain 1 / 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 / Mainly Beta
Similarity search - Domain/homology
IODIDE ION / Haemagluttinin family protein
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SAD / MAD / Resolution: 2.05 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Plos One / Year: 2010
Title: Structure of a Burkholderia pseudomallei trimeric autotransporter adhesin head.
Authors: Edwards, T.E. / Phan, I. / Abendroth, J. / Dieterich, S.H. / Masoudi, A. / Guo, W. / Hewitt, S.N. / Kelley, A. / Leibly, D. / Brittnacher, M.J. / Staker, B.L. / Miller, S.I. / Van Voorhis, W. ...Authors: Edwards, T.E. / Phan, I. / Abendroth, J. / Dieterich, S.H. / Masoudi, A. / Guo, W. / Hewitt, S.N. / Kelley, A. / Leibly, D. / Brittnacher, M.J. / Staker, B.L. / Miller, S.I. / Van Voorhis, W.C. / Myler, P.J. / Stewart, L.J.
History
DepositionJan 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 27, 2017Group: Data collection / Category: pdbx_diffrn_reflns_shell / Item: _pdbx_diffrn_reflns_shell.percent_possible_obs
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: Haemagglutinin family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,51110
Polymers19,3691
Non-polymers1,1429
Water2,972165
1
A: Haemagglutinin family protein
hetero molecules

A: Haemagglutinin family protein
hetero molecules

A: Haemagglutinin family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,53330
Polymers58,1063
Non-polymers3,42627
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area22130 Å2
ΔGint-137 kcal/mol
Surface area15400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.780, 50.780, 135.660
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-188-

IOD

21A-224-

HOH

31A-301-

HOH

-
Components

#1: Protein Haemagglutinin family protein


Mass: 19368.803 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710b / Gene: BURPS1710b_A0459, xadA / Production host: Escherichia coli (E. coli) / References: UniProt: Q3JLD6
#2: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 1.737879 Å3/Da / Density % sol: 29.224056 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4
Details: Original hit: PACT B1, 0.1 M MIB buffer pH 4.0, 25% PEG 1500; soaked into 0.1 M MIB buffer pH 4.0, 1.0 M KI, 35% PEG 1500 for 1 hour; crystal tracking ID 203140b1, 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: Nov 13, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNumber: 88646 / Rmerge(I) obs: 0.025 / D res high: 2.05 Å / Num. obs: 16334 / % possible obs: 99.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
6.489.1734210010.025
5.296.4842810010.022
4.585.2951410010.02
4.14.5859210010.019
3.744.164299.710.018
3.473.7470199.910.02
3.243.4777010010.022
3.063.2479210010.022
2.93.0685410010.022
2.762.991210010.024
2.652.7686410010.027
2.542.6598410010.03
2.452.54101010010.031
2.372.45107399.910.036
2.292.37107210010.035
2.222.29115210010.034
2.162.22111210010.038
2.12.16115899.810.042
2.052.111969610.039
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.802
11K, H, -L20.198
ReflectionResolution: 2.05→50 Å / Num. obs: 8173 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 5.43 % / Biso Wilson estimate: 13.559 Å2 / Rmerge(I) obs: 0.025 / Net I/σ(I): 53.75
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 3.62 % / Rmerge(I) obs: 0.039 / Mean I/σ(I) obs: 31 / Num. measured obs: 4329 / Num. unique all: 1196 / Num. unique obs: 1196 / % possible all: 96

-
Phasing

PhasingMethod: MAD
Phasing MADD res high: 2.05 Å / D res low: 18.45 Å / FOM : 0.486 / FOM acentric: 0.487 / FOM centric: 0 / Reflection: 8175 / Reflection acentric: 8157 / Reflection centric: 0
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.53-18.450.460.4601591590
5.56-7.530.5220.52202382380
4.61-5.560.4960.49603093090
4.03-4.610.5550.55503733730
3.62-4.030.5050.50503963960
3.31-3.620.5370.53804674660
3.08-3.310.520.5204784780
2.88-3.080.5010.50105245240
2.72-2.880.50.505575570
2.58-2.720.530.5305995990
2.47-2.580.4980.49806086080
2.36-2.470.4470.44806476460
2.27-2.360.480.4806826820
2.19-2.270.4660.46606876870
2.12-2.190.4360.43607007000
2.05-2.120.4160.42107517350

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.05→45.22 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.919 / WRfactor Rfree: 0.157 / WRfactor Rwork: 0.117 / Occupancy max: 1 / Occupancy min: 0.19 / FOM work R set: 0.874 / SU B: 3.362 / SU ML: 0.094 / SU R Cruickshank DPI: 0.036 / SU Rfree: 0.028 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.036 / ESU R Free: 0.028 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.154 377 4.6 %RANDOM
Rwork0.115 ---
obs0.117 8173 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 55.35 Å2 / Biso mean: 7.779 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20 Å20 Å2
2--0.73 Å20 Å2
3----1.46 Å2
Refinement stepCycle: LAST / Resolution: 2.05→45.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1124 0 9 165 1298
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221153
X-RAY DIFFRACTIONr_angle_refined_deg1.1421.9231587
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9245169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.47126.05338
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.1115137
X-RAY DIFFRACTIONr_dihedral_angle_4_deg29.368152
X-RAY DIFFRACTIONr_chiral_restr0.0780.2198
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021888
X-RAY DIFFRACTIONr_mcbond_it0.541.5826
X-RAY DIFFRACTIONr_mcangle_it0.91921316
X-RAY DIFFRACTIONr_scbond_it1.2363327
X-RAY DIFFRACTIONr_scangle_it1.9134.5269
LS refinement shellResolution: 2.05→2.102 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.185 19 -
Rwork0.103 569 -
all-588 -
obs--96.08 %

+
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