[English] 日本語
Yorodumi
- PDB-9ppr: Zn- and Bi-bound structure of the H77C variant of TriCyt2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9ppr
TitleZn- and Bi-bound structure of the H77C variant of TriCyt2
ComponentsSoluble cytochrome b562
KeywordsMETAL BINDING PROTEIN / Bi- and Zn-binding protein / assembly
Function / homology
Function and homology information


electron transport chain / periplasmic space / electron transfer activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562
Similarity search - Domain/homology
Bismuth(III) ION / Soluble cytochrome b562
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsEng, V.H. / Tezcan, F.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM138884 United States
National Science Foundation (NSF, United States)DGE-2038238 United States
CitationJournal: J.Inorg.Biochem. / Year: 2025
Title: Design of a protein scaffold with a selective, Bi-containing heterodinuclear metal coordination motif.
Authors: Eng, V.H. / Gascon, M. / Kakkis, A. / Tezcan, F.A.
History
DepositionJul 21, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Soluble cytochrome b562
B: Soluble cytochrome b562
C: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,17812
Polymers35,6383
Non-polymers5409
Water7,512417
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.750, 70.860, 75.480
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 10 or resid 12...
d_2ens_1(chain "B" and (resid 1 through 10 or resid 12...
d_3ens_1(chain "C" and (resid 1 through 10 or resid 12...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ALAALALEULEUAA1 - 101 - 10
d_12ASPASPALAALAAA12 - 2412 - 24
d_13VALVALLEULEUAA26 - 7626 - 76
d_14LEULEUARGARGAA78 - 10678 - 106
d_21ALAALALEULEUBB1 - 101 - 10
d_22ASPASPALAALABB12 - 2412 - 24
d_23VALVALLEULEUBB26 - 7626 - 76
d_24LEULEUARGARGBB78 - 10678 - 106
d_31ALAALALEULEUCC1 - 101 - 10
d_32ASPASPALAALACC12 - 2412 - 24
d_33VALVALLEULEUCC26 - 7626 - 76
d_34LEULEUARGARGCC78 - 10678 - 106

NCS oper:
IDCodeMatrixVector
1given(-0.0475982227656, 0.0331853654824, -0.998315150996), (0.996293312677, 0.0732712345192, -0.0450661880619), (0.0716522456309, -0.99675977934, -0.0365499382518)-34.1049617275, 33.3357777423, 2.8806963231
2given(0.0536938369477, 0.996949832278, 0.0566392425413), (-0.0672330875473, 0.0602017486062, -0.995919405074), (-0.996291465292, 0.0496667029968, 0.0702604782274)-34.1122230046, 0.786683731328, -32.4442706427

-
Components

-
Protein , 1 types, 3 molecules ABC

#1: Protein Soluble cytochrome b562 / Cytochrome b-562


Mass: 11879.474 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Gene: cybC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0ABE7

-
Non-polymers , 5 types, 426 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-BS3 / Bismuth(III) ION


Mass: 208.980 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Bi / Feature type: SUBJECT OF INVESTIGATION
#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


Mass: 18.015 Da / Num. of mol.: 417 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 18% PEG 1500, 200 mM CaCl2, 100 mM HEPES (pH 8.5)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.278 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.278 Å / Relative weight: 1
ReflectionResolution: 1.57→44.84 Å / Num. obs: 79015 / % possible obs: 98.66 % / Redundancy: 12.6 % / Biso Wilson estimate: 20.96 Å2 / CC1/2: 1 / Net I/σ(I): 28.45
Reflection shellResolution: 1.575→1.631 Å / Mean I/σ(I) obs: 2.52 / Num. unique obs: 3916 / CC1/2: 0.607 / % possible all: 94.98

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.57→44.84 Å / SU ML: 0.1852 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 23.2432
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2252 3792 4.8 %
Rwork0.1851 75223 -
obs0.1871 79015 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.76 Å2
Refinement stepCycle: LAST / Resolution: 1.57→44.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2499 0 9 417 2925
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01252567
X-RAY DIFFRACTIONf_angle_d1.10853478
X-RAY DIFFRACTIONf_chiral_restr0.0643387
X-RAY DIFFRACTIONf_plane_restr0.0075458
X-RAY DIFFRACTIONf_dihedral_angle_d12.1458969
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.830283258444
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS1.14812980984
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.590.31291450.29452588X-RAY DIFFRACTION92.27
1.59-1.620.28051000.27162771X-RAY DIFFRACTION96.25
1.62-1.640.30411720.26362732X-RAY DIFFRACTION97.68
1.64-1.660.29581330.25822727X-RAY DIFFRACTION98.35
1.66-1.690.27491330.24082788X-RAY DIFFRACTION97.79
1.69-1.710.28121470.23312769X-RAY DIFFRACTION98.71
1.71-1.740.30561420.23862783X-RAY DIFFRACTION98.55
1.74-1.770.26191400.21792785X-RAY DIFFRACTION98.02
1.77-1.80.26471310.22522807X-RAY DIFFRACTION99.19
1.8-1.840.24661320.21312788X-RAY DIFFRACTION98.92
1.84-1.870.25831390.21562771X-RAY DIFFRACTION98.34
1.87-1.920.28841410.21462795X-RAY DIFFRACTION98.79
1.92-1.960.24831480.20012794X-RAY DIFFRACTION99.59
1.96-2.010.26651620.19932767X-RAY DIFFRACTION99.39
2.01-2.060.18761320.18622844X-RAY DIFFRACTION99.17
2.06-2.120.24151410.18672765X-RAY DIFFRACTION99.45
2.12-2.190.2381490.18532790X-RAY DIFFRACTION99.49
2.19-2.270.23441260.17672814X-RAY DIFFRACTION99.39
2.27-2.360.24181540.18532822X-RAY DIFFRACTION99.23
2.36-2.470.24981340.17932779X-RAY DIFFRACTION99.73
2.47-2.60.27131420.19232833X-RAY DIFFRACTION99.8
2.6-2.760.22081480.19222802X-RAY DIFFRACTION99.7
2.76-2.980.23361350.17552822X-RAY DIFFRACTION99.93
2.98-3.270.21431460.17282841X-RAY DIFFRACTION100
3.28-3.750.1691510.15712810X-RAY DIFFRACTION100
3.75-4.720.17271410.15332822X-RAY DIFFRACTION100
4.72-44.840.22711280.18152814X-RAY DIFFRACTION99.8

+
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