[English] 日本語
Yorodumi
- PDB-8ki0: Crystal structure of the hemophore HasA from Pseudomonas protegen... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ki0
TitleCrystal structure of the hemophore HasA from Pseudomonas protegens Pf-5 capturing Fe-tetraphenylporphyrin
ComponentsHeme acquisition protein HasAp
KeywordsTRANSPORT PROTEIN / HEME ACQUISITION PROTEIN
Function / homologyHaem-binding HasA / Haem-binding HasA superfamily / Heme-binding protein A (HasA) / metal ion binding / Chem-MQP / Heme acquisition protein HasAp
Function and homology information
Biological speciesPseudomonas protegens Pf-5 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsShisaka, Y. / Inaba, H. / Sugimoto, H. / Shoji, O.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP18H02084 Japan
Japan Society for the Promotion of Science (JSPS)JP21H04704 Japan
Japan Society for the Promotion of Science (JSPS)JP22H05129 Japan
Japan Society for the Promotion of Science (JSPS)JP18J15250 Japan
CitationJournal: Rsc Adv / Year: 2024
Title: Heme-substituted protein assembly bridged by synthetic porphyrin: achieving controlled configuration while maintaining rotational freedom.
Authors: Inaba, H. / Shisaka, Y. / Ariyasu, S. / Sakakibara, E. / Ueda, G. / Aiba, Y. / Shimizu, N. / Sugimoto, H. / Shoji, O.
History
DepositionAug 22, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Heme acquisition protein HasAp
B: Heme acquisition protein HasAp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1659
Polymers38,0912
Non-polymers2,0747
Water5,567309
1
A: Heme acquisition protein HasAp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1294
Polymers19,0461
Non-polymers1,0833
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8120 Å2
MethodPISA
2
B: Heme acquisition protein HasAp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0375
Polymers19,0461
Non-polymers9914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-7 kcal/mol
Surface area8050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.561, 158.717, 33.534
Angle α, β, γ (deg.)90.00, 97.58, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Heme acquisition protein HasAp


Mass: 19045.621 Da / Num. of mol.: 2 / Fragment: Residues 1-183
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas protegens Pf-5 (bacteria) / Gene: hasAp / Plasmid: pQE30 / Production host: Escherichia coli M15 (bacteria) / References: UniProt: Q4K5N8

-
Non-polymers , 5 types, 316 molecules

#2: Chemical ChemComp-MQP / [5,10,15,20-tetraphenylporphyrinato(2-)-kappa~4~N~21~,N~22~,N~23~,N~24~]iron / Fe-5,10,15,20-Tetraphenylporphyrin


Mass: 668.565 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C44H28FeN4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES / CHES (buffer)


Mass: 207.290 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 309 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100 mM Tris-HCl (pH 7.0), 1.0 M Potassium sodium tartrate, 200 mM Lithium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jan 30, 2019
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→39.68 Å / Num. obs: 59034 / % possible obs: 95.5 % / Redundancy: 6.54 % / CC1/2: 0.998 / Rmerge(I) obs: 0.076 / Rrim(I) all: 0.082 / Net I/σ(I): 16.08
Reflection shell

Diffraction-ID: 1

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.45-1.530.3744.3887840.9070.41487.7
1.53-1.640.2647.1188740.9660.28694.9
1.64-1.770.1859.9983610.9820.295.5
1.77-1.940.12614.1777330.990.13696.9
1.94-2.170.08819.9670610.9940.09697.2
2.17-2.50.07423.5162660.9940.0897.9
2.5-3.060.06327.354170.9960.06999
3.06-4.310.05633.441790.9970.06199.7
4.31-39.680.05533.4823580.9970.05999.7

-
Processing

Software
NameVersionClassification
XDSdata scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→39.68 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.475 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.013 / ESU R Free: 0.011 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15178 3011 5.1 %RANDOM
Rwork0.11899 ---
obs0.12065 55595 95.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.825 Å2
Baniso -1Baniso -2Baniso -3
1--2.44 Å20 Å2-1.43 Å2
2--4.4 Å20 Å2
3----1.96 Å2
Refinement stepCycle: 1 / Resolution: 1.45→39.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2624 0 144 309 3077
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132922
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182452
X-RAY DIFFRACTIONr_angle_refined_deg1.541.7044019
X-RAY DIFFRACTIONr_angle_other_deg1.4841.6245712
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0335376
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.42825.041121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.47815384
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.189154
X-RAY DIFFRACTIONr_chiral_restr0.0680.2369
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023469
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02601
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_it1.0681.2381483
X-RAY DIFFRACTIONr_mcbond_other1.061.2361482
X-RAY DIFFRACTIONr_mcangle_it1.3311.8631866
X-RAY DIFFRACTIONr_mcangle_other1.3311.8651867
X-RAY DIFFRACTIONr_scbond_it1.331.361439
X-RAY DIFFRACTIONr_scbond_other1.3291.361440
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.5461.9782154
X-RAY DIFFRACTIONr_long_range_B_refined2.08915.9593442
X-RAY DIFFRACTIONr_long_range_B_other1.94715.6153387
X-RAY DIFFRACTIONr_rigid_bond_restr0.96635374
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.45→1.486 Å
RfactorNum. reflection% reflection
Rfree0.233 186 -
Rwork0.164 3597 -
obs--84.24 %

+
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