[English] 日本語
Yorodumi
- PDB-9ipl: A tetrapyrrole binding domain variant of CoaR in closed conformat... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9ipl
TitleA tetrapyrrole binding domain variant of CoaR in closed conformation at 2.28 angstrom resolution
ComponentsMercuric resistance operon regulatory protein precorrin isomerase
KeywordsMETAL BINDING PROTEIN / tetrapyrrole binding / CoaR / cobalt binding
Function / homology
Function and homology information


precorrin-8X methylmutase activity / cobalamin biosynthetic process / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Cobalamin biosynthesis precorrin-8X methylmutase CobH/CbiC / Precorrin-8X methylmutase CobH/CbiC superfamily / Precorrin-8X methylmutase / MerR HTH family regulatory protein / helix_turn_helix, mercury resistance / MerR-type HTH domain profile. / MerR-type HTH domain / Putative DNA-binding domain superfamily
Similarity search - Domain/homology
Mercuric resistance operon regulatory protein precorrin isomerase
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsLiu, X.C.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: To Be Published
Title: A tetrapyrrole binding domain variant of CoaR in closed conformation at 2.28 angstrom resolution
Authors: Liu, X.C.
History
DepositionJul 10, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mercuric resistance operon regulatory protein precorrin isomerase
B: Mercuric resistance operon regulatory protein precorrin isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,44810
Polymers46,6802
Non-polymers7698
Water1,946108
1
A: Mercuric resistance operon regulatory protein precorrin isomerase
hetero molecules

B: Mercuric resistance operon regulatory protein precorrin isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,44810
Polymers46,6802
Non-polymers7698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554y,-x+y,z-1/61
Buried area2890 Å2
ΔGint-117 kcal/mol
Surface area16990 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-108 kcal/mol
Surface area16430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.043, 96.043, 148.664
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

-
Components

#1: Protein Mercuric resistance operon regulatory protein precorrin isomerase


Mass: 23339.752 Da / Num. of mol.: 2 / Fragment: tetrapyrrole binding domain
Source method: isolated from a genetically manipulated source
Details: a variant designed by PROSS program
Source: (gene. exp.) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Gene: merR / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q55938
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.24 Å3/Da / Density % sol: 73.67 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: Bis-Tris, (NH4)2SO4, PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9788 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jun 9, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.28→49.57 Å / Num. obs: 35426 / % possible obs: 100 % / Redundancy: 20.1 % / Biso Wilson estimate: 48.17 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.095 / Net I/σ(I): 20.5
Reflection shellResolution: 2.28→2.34 Å / Rmerge(I) obs: 1.755 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2619 / CC1/2: 0.791 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
xia2data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.28→45.74 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.946 / SU B: 5.872 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22974 1733 4.9 %RANDOM
Rwork0.20884 ---
obs0.20987 33586 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.452 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20.1 Å20 Å2
2--0.2 Å2-0 Å2
3----0.64 Å2
Refinement stepCycle: 1 / Resolution: 2.28→45.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2943 0 40 108 3091
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0123034
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162935
X-RAY DIFFRACTIONr_angle_refined_deg1.271.7934156
X-RAY DIFFRACTIONr_angle_other_deg0.4611.7236744
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8075394
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.811514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.52810475
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0650.2518
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023492
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02604
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_it4.0735.1581582
X-RAY DIFFRACTIONr_mcbond_other4.0715.1581582
X-RAY DIFFRACTIONr_mcangle_it6.2469.2651974
X-RAY DIFFRACTIONr_mcangle_other6.2459.2671975
X-RAY DIFFRACTIONr_scbond_it4.8055.9221452
X-RAY DIFFRACTIONr_scbond_other4.5355.8421421
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.46410.4512135
X-RAY DIFFRACTIONr_long_range_B_refined10.18150.193210
X-RAY DIFFRACTIONr_long_range_B_other10.18950.253193
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.28→2.338 Å
RfactorNum. reflection% reflection
Rfree0.274 111 -
Rwork0.315 2463 -
obs--99.27 %

+
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