[English] 日本語
Yorodumi
- PDB-8gf4: Crystal structure of Domain Related to Iron (DRI) in complex with heme -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8gf4
TitleCrystal structure of Domain Related to Iron (DRI) in complex with heme
ComponentsSsr1698 protein
KeywordsMETAL BINDING PROTEIN / Heme binding protein / DRI-Heme complex / DUF2470 domain / Iron homeostasis
Function / homologyDomain of unknown function DUF2470 / Domain of unknown function (DUF2470) / Haem oxygenase HugZ-like superfamily / PROTOPORPHYRIN IX CONTAINING FE / Ssr1698 protein
Function and homology information
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsKumaran, D. / Blaby, E.C.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)Quantitative Plant Science Initiative, SFA United States
CitationJournal: Nat Commun / Year: 2024
Title: A hemoprotein with a zinc-mirror heme site ties heme availability to carbon metabolism in cyanobacteria.
Authors: Grosjean, N. / Yee, E.F. / Kumaran, D. / Chopra, K. / Abernathy, M. / Biswas, S. / Byrnes, J. / Kreitler, D.F. / Cheng, J.F. / Ghosh, A. / Almo, S.C. / Iwai, M. / Niyogi, K.K. / Pakrasi, H.B. ...Authors: Grosjean, N. / Yee, E.F. / Kumaran, D. / Chopra, K. / Abernathy, M. / Biswas, S. / Byrnes, J. / Kreitler, D.F. / Cheng, J.F. / Ghosh, A. / Almo, S.C. / Iwai, M. / Niyogi, K.K. / Pakrasi, H.B. / Sarangi, R. / van Dam, H. / Yang, L. / Blaby, I.K. / Blaby-Haas, C.E.
History
DepositionMar 7, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2024Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ssr1698 protein
B: Ssr1698 protein
C: Ssr1698 protein
D: Ssr1698 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,72110
Polymers45,2274
Non-polymers1,4956
Water543
1
A: Ssr1698 protein
B: Ssr1698 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3615
Polymers22,6132
Non-polymers7473
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-102 kcal/mol
Surface area9450 Å2
MethodPISA
2
C: Ssr1698 protein
D: Ssr1698 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3615
Polymers22,6132
Non-polymers7473
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-101 kcal/mol
Surface area9560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.976, 42.976, 379.484
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

-
Components

#1: Protein
Ssr1698 protein / Domain Related to Iron / DRI


Mass: 11306.716 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Gene: ssr1698 / Production host: Escherichia coli (E. coli) / References: UniProt: P73129
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.24 Å3/Da / Density % sol: 45.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 23% PEG3350, 100 mM Bis-Tris, pH 5.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 15, 2019
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 7898 / % possible obs: 92.6 % / Redundancy: 3.5 % / CC1/2: 0.98 / Rmerge(I) obs: 0.092 / Net I/σ(I): 6
Reflection shellResolution: 3→3.08 Å / Rmerge(I) obs: 0.504 / Num. unique obs: 830 / CC1/2: 0.969

-
Processing

Software
NameVersionClassification
ADSCdata collection
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
REFMAC5.8.0267refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→37.25 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.848 / SU B: 25.065 / SU ML: 0.448 / Cross valid method: THROUGHOUT / ESU R Free: 0.605 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27914 763 10.4 %RANDOM
Rwork0.20122 ---
obs0.20602 6550 92.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.834 Å2
Baniso -1Baniso -2Baniso -3
1-2.58 Å21.29 Å2-0 Å2
2--2.58 Å2-0 Å2
3----8.36 Å2
Refinement stepCycle: 1 / Resolution: 3→37.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2724 0 90 3 2817
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132860
X-RAY DIFFRACTIONr_bond_other_d0.0050.0152692
X-RAY DIFFRACTIONr_angle_refined_deg2.081.6973888
X-RAY DIFFRACTIONr_angle_other_deg1.2271.616216
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8885356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.48124.706136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.69715496
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1171512
X-RAY DIFFRACTIONr_chiral_restr0.0580.2388
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023274
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02588
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_it5.5667.011436
X-RAY DIFFRACTIONr_mcbond_other5.5697.011434
X-RAY DIFFRACTIONr_mcangle_it8.75810.5061788
X-RAY DIFFRACTIONr_mcangle_other8.75910.5051788
X-RAY DIFFRACTIONr_scbond_it5.377.041424
X-RAY DIFFRACTIONr_scbond_other5.3687.041425
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.22810.4012101
X-RAY DIFFRACTIONr_long_range_B_refined12.10680.7473178
X-RAY DIFFRACTIONr_long_range_B_other12.10880.7123176
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 67 -
Rwork0.253 535 -
obs--99.01 %

+
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://pdbjlvh1.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