[English] 日本語
Yorodumi
- PDB-6om5: Structure of a haemophore from Haemophilus haemolyticus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6om5
TitleStructure of a haemophore from Haemophilus haemolyticus
Componentshaemophore
KeywordsMETAL TRANSPORT / Haemophilus haemolyticus / haemophore / antimicrobial
Function / homologyHphA N-terminal heme-binding domain / HphA C-terminal domain / C-lobe and N-lobe beta barrels of Tf-binding protein B / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / metal ion binding / PROTOPORPHYRIN IX CONTAINING FE / Polymerase
Function and homology information
Biological speciesHaemophilus haemolyticus M19107 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsTorrado, M. / Walshe, J.L. / Mackay, J.P. / Guss, J.M. / Gell, D.A.
CitationJournal: Mol.Microbiol. / Year: 2020
Title: A heme-binding protein produced by Haemophilus haemolyticus inhibits non-typeable Haemophilus influenzae.
Authors: Latham, R.D. / Torrado, M. / Atto, B. / Walshe, J.L. / Wilson, R. / Guss, J.M. / Mackay, J.P. / Tristram, S. / Gell, D.A.
History
DepositionApr 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Mar 13, 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: haemophore
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,74511
Polymers27,4011
Non-polymers1,34410
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The assembly is confirmed by UV-visible absorption properties of the haem
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.043, 91.043, 97.484
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-303-

SO4

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein haemophore


Mass: 27400.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus haemolyticus M19107 (bacteria)
Strain: M19107 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) Rosetta 2 / References: UniProt: A0A0M3G7Q5*PLUS

-
Non-polymers , 5 types, 180 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 4.28 Å3/Da / Density % sol: 71.25 % / Description: Hexagonal crystals with orange-red colour
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1 M sodium acetate trihydrate pH 4.5, 2 M ammonium sulfate, 30 mM sodium phosphate, 72 mM NaCl

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.45866, 0.95372
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 5, 2017
RadiationMonochromator: Silicon Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.458661
20.953721
ReflectionResolution: 1.6→45.52 Å / Num. obs: 62031 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 1 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.023 / Rrim(I) all: 0.073 / Χ2: 0.97 / Net I/σ(I): 23.2
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 21 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 4 / Num. unique obs: 3086 / CC1/2: 0.909 / Rpim(I) all: 0.25 / Rrim(I) all: 0.82 / Χ2: 0.86 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PARROTphasing
BUCCANEERmodel building
Cootmodel building
Blu-Icedata collection
RefinementMethod to determine structure: SAD / Resolution: 1.6→41.49 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.088 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.059 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.18449 3056 4.9 %RANDOM
Rwork0.17122 ---
obs0.17186 58934 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.667 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å2-0 Å2
2---0.02 Å20 Å2
3---0.06 Å2
Refinement stepCycle: 1 / Resolution: 1.6→41.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1915 0 84 170 2169
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122109
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181943
X-RAY DIFFRACTIONr_angle_refined_deg1.4531.6792858
X-RAY DIFFRACTIONr_angle_other_deg0.4841.5924531
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0085267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.92823.80492
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.95815369
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.193158
X-RAY DIFFRACTIONr_chiral_restr0.0740.2267
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022386
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02427
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_it1.8222.4741047
X-RAY DIFFRACTIONr_mcbond_other1.8112.4711042
X-RAY DIFFRACTIONr_mcangle_it2.5713.7081321
X-RAY DIFFRACTIONr_mcangle_other2.5563.7061318
X-RAY DIFFRACTIONr_scbond_it3.0311062
X-RAY DIFFRACTIONr_scbond_other3.0291063
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6421538
X-RAY DIFFRACTIONr_long_range_B_refined5.7712300
X-RAY DIFFRACTIONr_long_range_B_other5.772301
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 218 -
Rwork0.223 4321 -
obs--99.98 %

+
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