[English] 日本語
Yorodumi
- PDB-3bgh: Crystal structure of putative neuraminyllactose-binding hemagglut... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3bgh
TitleCrystal structure of putative neuraminyllactose-binding hemagglutinin homolog from Helicobacter pylori
ComponentsPutative neuraminyllactose-binding hemagglutinin homolog
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homologyPutative neuraminyllactose-binding hemagglutinin homolog like domain / Neuraminyllactose-binding hemagglutinin / Neuraminyllactose-binding hemagglutinin superfamily / Neuraminyllactose-binding hemagglutinin precursor (NLBH) / Double Stranded RNA Binding Domain / cell outer membrane / 2-Layer Sandwich / Alpha Beta / Neuraminyllactose-binding hemagglutinin
Function and homology information
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.45 Å
AuthorsBonanno, J.B. / Dickey, J. / Bain, K.T. / McKenzie, C. / Romero, R. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of putative neuraminyllactose-binding hemagglutinin homolog from Helicobacter pylori.
Authors: Bonanno, J.B. / Dickey, J. / Bain, K.T. / McKenzie, C. / Romero, R. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionNov 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative neuraminyllactose-binding hemagglutinin homolog
B: Putative neuraminyllactose-binding hemagglutinin homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2337
Polymers54,7532
Non-polymers4805
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
MethodPISA
2
A: Putative neuraminyllactose-binding hemagglutinin homolog
B: Putative neuraminyllactose-binding hemagglutinin homolog
hetero molecules

A: Putative neuraminyllactose-binding hemagglutinin homolog
B: Putative neuraminyllactose-binding hemagglutinin homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,46614
Polymers109,5054
Non-polymers96110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area6940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.508, 77.508, 177.509
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
DetailsAUTHORS STATE THAT THE DIMERIC ASSEMBLY OF THE BIOLOGICAL UNIT THAT IS SHOWN IN REMARK 350 IS PUTATIVE AT THE TIME OF DEPOSITION.

-
Components

#1: Protein Putative neuraminyllactose-binding hemagglutinin homolog / Protein HpaA


Mass: 27376.371 Da / Num. of mol.: 2 / Fragment: Residues 25-249
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: HP_0410 / Plasmid: modified pET26 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O25166
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.43 Å3/Da / Density % sol: 49.48 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 5.5
Details: 100mM Bis-Tris pH 5.5, 25% PEG 3350, 200mM Lithium sulfate, VAPOR DIFFUSION, temperature 294K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 12, 2007
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 2.45→34.02 Å / Num. all: 20647 / Num. obs: 20647 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.9 % / Biso Wilson estimate: 62.9 Å2 / Rmerge(I) obs: 0.104 / Rsym value: 0.104 / Net I/σ(I): 14.6
Reflection shellResolution: 2.45→2.58 Å / Redundancy: 8 % / Rmerge(I) obs: 0.798 / Mean I/σ(I) obs: 2.3 / Num. unique all: 2968 / Rsym value: 0.798 / % possible all: 100

-
Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT3.004data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXCDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.45→20 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.908 / SU B: 9.544 / SU ML: 0.227 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.387 / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.278 1057 5.1 %RANDOM
Rwork0.236 ---
obs0.238 20582 99.78 %-
all-20627 --
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: 65.893 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å20 Å2
2---0.2 Å20 Å2
3---0.41 Å2
Refinement stepCycle: LAST / Resolution: 2.45→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3043 0 25 26 3094
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223116
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.9784182
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8125369
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.10325.655145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.06815635
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.127159
X-RAY DIFFRACTIONr_chiral_restr0.10.2465
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022241
X-RAY DIFFRACTIONr_nbd_refined0.2240.21214
X-RAY DIFFRACTIONr_nbtor_refined0.3080.22066
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.296
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.27
X-RAY DIFFRACTIONr_mcbond_it0.9421.51923
X-RAY DIFFRACTIONr_mcangle_it1.59423036
X-RAY DIFFRACTIONr_scbond_it2.31931318
X-RAY DIFFRACTIONr_scangle_it3.634.51146
LS refinement shellResolution: 2.45→2.513 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 76 -
Rwork0.258 1393 -
all-1469 -
obs-1393 100 %

+
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