[English] 日本語
Yorodumi
- PDB-4i84: The crystal structure of the Haemophilus influenzae HxuA secretio... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4i84
TitleThe crystal structure of the Haemophilus influenzae HxuA secretion domain involved in the two-partner secretion pathway
ComponentsHeme/hemopexin-binding protein
KeywordsPROTEIN TRANSPORT / beta-helix / TWO-PARTNER SECRETION PATHWAY / HxuB
Function / homology
Function and homology information


extracellular region
Similarity search - Function
: / Filamentous haemagglutinin FhaB/tRNA nuclease CdiA-like, TPS domain / TPS secretion domain / haemagglutination activity domain / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold / Pectin lyase fold/virulence factor / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
Heme/hemopexin-binding protein
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsBaelen, S. / Dewitte, F. / Clantin, B. / Villeret, V.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Structure of the secretion domain of HxuA from Haemophilus influenzae.
Authors: Baelen, S. / Dewitte, F. / Clantin, B. / Villeret, V.
History
DepositionDec 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Heme/hemopexin-binding protein
B: Heme/hemopexin-binding protein


Theoretical massNumber of molelcules
Total (without water)65,9352
Polymers65,9352
Non-polymers00
Water7,728429
1
A: Heme/hemopexin-binding protein


Theoretical massNumber of molelcules
Total (without water)32,9681
Polymers32,9681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Heme/hemopexin-binding protein


Theoretical massNumber of molelcules
Total (without water)32,9681
Polymers32,9681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.990, 70.840, 104.980
Angle α, β, γ (deg.)90.00, 98.10, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Heme/hemopexin-binding protein / Heme:hemopexin utilization protein A


Mass: 32967.695 Da / Num. of mol.: 2 / Fragment: UNP residues 24-324
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Strain: ATCC 51907 / DSM 11121 / KW20 / Rd / Gene: HI_0264, hxuA, KW20 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)omp5 / References: UniProt: P44602
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 429 / 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: 2.18 Å3/Da / Density % sol: 43.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.095M TRI SODIUM CITRATE pH 5.6, 5% GLYCEROL, 19% ISOPROPANOL, 12% PEG4000, 0.5M IMIDAZOLE pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 29, 2011
RadiationMonochromator: CHANNEL CUT CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.5→41.9 Å / Num. all: 89861 / Num. obs: 89775 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.5→1.59 Å

-
Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0109refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ODL

2odl


Resolution: 1.5→41.9 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.648 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.083 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21027 4489 5 %RANDOM
Rwork0.159 ---
obs0.16154 85287 100 %-
all-89815 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.866 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0.08 Å2
2--0.01 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.5→41.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4278 0 0 429 4707
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0224513
X-RAY DIFFRACTIONr_angle_refined_deg2.2361.9486127
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1975617
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.00327.5196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.64315837
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.897159
X-RAY DIFFRACTIONr_chiral_restr0.1560.2725
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023369
X-RAY DIFFRACTIONr_mcbond_it2.8641.52933
X-RAY DIFFRACTIONr_mcangle_it4.24624772
X-RAY DIFFRACTIONr_scbond_it6.0931580
X-RAY DIFFRACTIONr_scangle_it9.2174.51342
X-RAY DIFFRACTIONr_rigid_bond_restr3.18634513
LS refinement shellResolution: 1.5→1.538 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 318 -
Rwork0.232 6044 -
obs--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