[English] 日本語
Yorodumi
- PDB-8ki1: Crystal structure of the holo form of the hemophore HasA from Pse... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ki1
TitleCrystal structure of the holo form of the hemophore HasA from Pseudomonas protegens Pf-5
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 / PROTOPORPHYRIN IX CONTAINING FE / PHOSPHATE ION / Heme acquisition protein HasAp
Function and homology information
Biological speciesPseudomonas protegens Pf-5 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 1, 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)39,88310
Polymers38,0912
Non-polymers1,7918
Water4,089227
1
A: Heme acquisition protein HasAp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8494
Polymers19,0461
Non-polymers8043
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-18 kcal/mol
Surface area8110 Å2
MethodPISA
2
B: Heme acquisition protein HasAp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0336
Polymers19,0461
Non-polymers9885
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-18 kcal/mol
Surface area8090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.597, 99.597, 90.473
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

-
Components

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


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 3.4 Å3/Da / Density % sol: 63.83 % / Mosaicity: 0.14 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 100mM Sodium acetate/acetic acid (pH 4.5), 2.5M NaCl, 0.2M 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: 1.9→45.24 Å / Num. obs: 40219 / % possible obs: 100 % / Redundancy: 20.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.317 / Rpim(I) all: 0.071 / Rrim(I) all: 0.324 / Net I/σ(I): 11.7 / Num. measured all: 835293 / Scaling rejects: 31
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.9-1.9421.94.8235622025700.5841.0474.9361.7100
9.11-45.2416.20.07462263840.9980.0180.07633.199.3

-
Processing

Software
NameVersionClassification
Aimless0.7.1data scaling
REFMAC5.8.0230refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.031 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1928 1984 4.9 %RANDOM
Rwork0.1583 ---
obs0.16 38157 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.84 Å2 / Biso mean: 28.239 Å2 / Biso min: 9.62 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å2-0.06 Å20 Å2
2---0.12 Å20 Å2
3---0.37 Å2
Refinement stepCycle: final / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2646 0 120 227 2993
Biso mean--36.37 36.67 -
Num. residues----362
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0143086
X-RAY DIFFRACTIONr_bond_other_d00.0172572
X-RAY DIFFRACTIONr_angle_refined_deg1.2351.6944274
X-RAY DIFFRACTIONr_angle_other_deg0.9891.6896017
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5715417
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.65925.303132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.88115412
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.786154
X-RAY DIFFRACTIONr_chiral_restr0.0630.2393
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023727
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02629
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 142 -
Rwork0.266 2821 -
all-2963 -
obs--99.9 %

+
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