[English] 日本語
Yorodumi
- PDB-8gm3: Vibrio harveyi Holo HphA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8gm3
TitleVibrio harveyi Holo HphA
ComponentsHemophilin
KeywordsMETAL TRANSPORT / Heme Binding / Hemophore / Type XI Secretion System Cargo / Beta Barrel
Function / homologyHphA N-terminal heme-binding domain / HphA C-terminal domain / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / metal ion binding / HEME B/C / Uncharacterized protein
Function and homology information
Biological speciesVibrio harveyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.727 Å
AuthorsPan, C. / Shah, M. / Moraes, T.F.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-115182 Canada
CitationJournal: J.Bacteriol. / Year: 2024
Title: Prevalence of Slam-dependent hemophilins in Gram-negative bacteria.
Authors: Shin, H.E. / Pan, C. / Curran, D.M. / Bateman, T.J. / Chong, D.H.Y. / Ng, D. / Shah, M. / Moraes, T.F.
History
DepositionMar 24, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 3, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hemophilin
B: Hemophilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6364
Polymers49,3992
Non-polymers1,2372
Water6,449358
1
A: Hemophilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3182
Polymers24,7001
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hemophilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3182
Polymers24,7001
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.438, 81.080, 135.577
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-465-

HOH

21B-495-

HOH

-
Components

#1: Protein Hemophilin / Transferrin-binding protein B C-lobe/N-lobe beta barrel domain-containing protein


Mass: 24699.615 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio harveyi (bacteria) / Gene: AL538_19455 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3A1PTD6
#2: Chemical ChemComp-HEB / HEME B/C / HYBRID BETWEEN B AND C TYPE HEMES (PROTOPORPHYRIN IX CONTAINING FE)


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: The initial crystals of PUF1 were observed from a screen condition containing 25% PEG3350, 0.1 M Bis-Tris pH 5.5 with trypsin added to 3.53 mg/mL PUF1 at a 1:100 mass ratio. Further ...Details: The initial crystals of PUF1 were observed from a screen condition containing 25% PEG3350, 0.1 M Bis-Tris pH 5.5 with trypsin added to 3.53 mg/mL PUF1 at a 1:100 mass ratio. Further optimization was performed to obtain better crystals that formed in 25% PEG3350, 0.1M Bis-Tris pH 5.0, and 20% glycerol with streak seeding, trypsin at 0.06 mg/mL and PUF1 at 6.64mg/mL

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.727→69.586 Å / Num. obs: 46308 / % possible obs: 92.03 % / Redundancy: 2 % / CC1/2: 0.992 / Net I/σ(I): 10.07
Reflection shellResolution: 1.727→1.789 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.41 / Num. unique obs: 4480 / CC1/2: 0.732 / % possible all: 77.61

-
Processing

Software
NameVersionClassification
PHENIX1.13-2998-000refinement
Cootmodel building
XDSdata reduction
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.727→69.586 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.255 1844 4.3 %
Rwork0.2097 --
obs0.2116 42908 92.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.727→69.586 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3221 0 86 358 3665
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073387
X-RAY DIFFRACTIONf_angle_d0.8274615
X-RAY DIFFRACTIONf_dihedral_angle_d12.4671853
X-RAY DIFFRACTIONf_chiral_restr0.054472
X-RAY DIFFRACTIONf_plane_restr0.004616
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.727-1.77370.4171170.29322594X-RAY DIFFRACTION77
1.7737-1.82590.31661250.28762782X-RAY DIFFRACTION83
1.8259-1.88480.33771390.27623017X-RAY DIFFRACTION88
1.8848-1.95220.3831090.34332689X-RAY DIFFRACTION80
1.9522-2.03040.23041440.22733117X-RAY DIFFRACTION92
2.0304-2.12280.2931410.23783157X-RAY DIFFRACTION93
2.1228-2.23470.25821460.20863140X-RAY DIFFRACTION92
2.2347-2.37470.31961470.24463222X-RAY DIFFRACTION94
2.3747-2.55810.27221500.22323358X-RAY DIFFRACTION98
2.5581-2.81550.27181560.21613432X-RAY DIFFRACTION99
2.8155-3.2230.23661530.19543407X-RAY DIFFRACTION99
3.223-4.06050.21711560.17193483X-RAY DIFFRACTION99
4.0605-69.5860.18971610.16373666X-RAY DIFFRACTION100

+
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