[English] 日本語
Yorodumi
- PDB-7emr: Crystal Structure of HasAp Capturing Cobalt Tetraphenylporphyrin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7emr
TitleCrystal Structure of HasAp Capturing Cobalt 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 / Co-5,10,15,20-Tetraphenylporphyrin / PHOSPHATE ION / Heme acquisition protein HasAp
Function and homology information
Biological speciesPseudomonas aeruginosa str. PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsShisaka, Y. / Sakakibara, E. / Sugimoto, H. / Shoji, O.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP18H02084 Japan
Japan Science and TechnologyJPMJCR15P3 Japan
Japan Society for the Promotion of Science (JSPS)JP18J15250 Japan
CitationJournal: Chembiochem / Year: 2022
Title: Tetraphenylporphyrin Enters the Ring: First Example of a Complex between Highly Bulky Porphyrins and a Protein.
Authors: Shisaka, Y. / Sakakibara, E. / Suzuki, K. / Stanfield, J.K. / Onoda, H. / Ueda, G. / Hatano, M. / Sugimoto, H. / Shoji, O.
History
DepositionApr 14, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)60,34218
Polymers56,7053
Non-polymers3,63715
Water4,684260
1
A: Heme acquisition protein HasAp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0636
Polymers18,9021
Non-polymers1,1615
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint-9 kcal/mol
Surface area8230 Å2
MethodPISA
2
B: Heme acquisition protein HasAp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4247
Polymers18,9021
Non-polymers1,5236
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-7 kcal/mol
Surface area8060 Å2
MethodPISA
3
C: Heme acquisition protein HasAp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8555
Polymers18,9021
Non-polymers9544
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area330 Å2
ΔGint-10 kcal/mol
Surface area8160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.060, 85.060, 84.087
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

-
Components

-
Protein , 1 types, 3 molecules ABC

#1: Protein Heme acquisition protein HasAp


Mass: 18901.535 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa str. PAO1 (bacteria)
Gene: hasAp, PA3407 / Plasmid: pQE30 / Production host: Escherichia coli M15 (bacteria) / References: UniProt: G3XD33

-
Non-polymers , 6 types, 275 molecules

#2: Chemical ChemComp-J83 / Co-5,10,15,20-Tetraphenylporphyrin


Mass: 671.653 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C44H28CoN4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID


Mass: 221.317 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.68 Å3/Da / Density % sol: 54.14 % / Mosaicity: 0.16 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 100mM CAPS/NaOH (pH 10.5), 1.2M Sodium phosphate monobasic/0.8M pottasium phosphate dibasic, 0.2M lithium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Dec 18, 2018
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→48.92 Å / Num. obs: 86763 / % possible obs: 100 % / Redundancy: 14.9 % / CC1/2: 1 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.019 / Rrim(I) all: 0.073 / Net I/σ(I): 22 / Num. measured all: 1295135 / Scaling rejects: 13
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
1.55-1.5811.81.6265073043170.5890.4931.7011.7100
8.49-48.9213.40.04173405480.9980.0120.0436297.5

-
Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.1data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ELL

3ell


Resolution: 1.55→20 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.695 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1635 4450 5.1 %RANDOM
Rwork0.1315 ---
obs0.1331 82230 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 83.97 Å2 / Biso mean: 24.251 Å2 / Biso min: 15.19 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å20 Å2
2--0.29 Å20 Å2
3----0.58 Å2
Refinement stepCycle: final / Resolution: 1.55→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3969 0 245 260 4474
Biso mean--34.46 37.35 -
Num. residues----547
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0134506
X-RAY DIFFRACTIONr_bond_other_d0.0010.0183763
X-RAY DIFFRACTIONr_angle_refined_deg1.431.6996212
X-RAY DIFFRACTIONr_angle_other_deg1.4381.6228769
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3755584
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.95424.375176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.99215573
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.473157
X-RAY DIFFRACTIONr_chiral_restr0.0630.2568
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025355
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02941
X-RAY DIFFRACTIONr_rigid_bond_restr1.6138269
LS refinement shellResolution: 1.55→1.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 360 -
Rwork0.235 6002 -
all-6362 -
obs--99.94 %

+
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