[English] 日本語
Yorodumi
- PDB-3r8k: Crystal structure of human SOUL protein (hexagonal form) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3r8k
TitleCrystal structure of human SOUL protein (hexagonal form)
ComponentsHeme-binding protein 2
KeywordsAPOPTOSIS / HEBP family / SOUL protein
Function / homology
Function and homology information


azurophil granule lumen / heme binding / Neutrophil degranulation / mitochondrion / extracellular exosome / extracellular region / cytoplasm
Similarity search - Function
SOUL haem-binding protein / SOUL heme-binding protein / Multidrug-efflux Transporter 1 Regulator Bmrr; Chain A / Regulatory factor, effector binding domain / Regulatory factor, effector binding domain superfamily / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Heme-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsAmbrosi, E.K. / Capaldi, S. / Bovi, M. / Saccomani, G. / Perduca, M. / Monaco, H.L.
CitationJournal: Biochem.J. / Year: 2011
Title: Structural changes in the BH3 domain of SOUL protein upon interaction with the anti-apoptotic protein Bcl-xL.
Authors: Ambrosi, E. / Capaldi, S. / Bovi, M. / Saccomani, G. / Perduca, M. / Monaco, H.L.
History
DepositionMar 24, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 24, 2011Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Heme-binding protein 2
B: Heme-binding protein 2
C: Heme-binding protein 2
D: Heme-binding protein 2


Theoretical massNumber of molelcules
Total (without water)94,6534
Polymers94,6534
Non-polymers00
Water00
1
A: Heme-binding protein 2


Theoretical massNumber of molelcules
Total (without water)23,6631
Polymers23,6631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Heme-binding protein 2


Theoretical massNumber of molelcules
Total (without water)23,6631
Polymers23,6631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Heme-binding protein 2


Theoretical massNumber of molelcules
Total (without water)23,6631
Polymers23,6631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Heme-binding protein 2


Theoretical massNumber of molelcules
Total (without water)23,6631
Polymers23,6631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.919, 143.919, 242.120
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

-
Components

#1: Protein
Heme-binding protein 2 / Placental protein 23 / PP23 / Protein SOUL


Mass: 23663.248 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C6orf34, HEBP2, SOUL / Plasmid: pQE50 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 C41 / References: UniProt: Q9Y5Z4

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.82 Å3/Da / Density % sol: 67.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 2.0M ammonium sulphate, 0.1M Tris-HCl, 0.2M 1-butyl-3-methylimidazolium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 14, 2008
RadiationMonochromator: Channel cut ESRF monochromator, crystal type: Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.85→55.4 Å / Num. all: 35307 / Num. obs: 35245 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 20.5 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 25.7
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 20.4 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 8.3 / % possible all: 100

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3R8J

3r8j


Resolution: 2.85→55.4 Å / SU ML: 0.49 / σ(F): 1.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2683 1761 5 %Random
Rwork0.235 ---
all0.2367 35307 --
obs0.2367 35223 99.76 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.415 Å2 / ksol: 0.322 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.2102 Å20 Å20 Å2
2---0.2102 Å2-0 Å2
3---0.4204 Å2
Refinement stepCycle: LAST / Resolution: 2.85→55.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5631 0 0 0 5631
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085773
X-RAY DIFFRACTIONf_angle_d1.1697835
X-RAY DIFFRACTIONf_dihedral_angle_d15.6642151
X-RAY DIFFRACTIONf_chiral_restr0.074837
X-RAY DIFFRACTIONf_plane_restr0.0061019
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.95190.48751760.38523265X-RAY DIFFRACTION100
2.9519-3.07010.37681650.3523300X-RAY DIFFRACTION100
3.0701-3.20980.3661630.30883293X-RAY DIFFRACTION100
3.2098-3.3790.34561690.28163303X-RAY DIFFRACTION100
3.379-3.59070.3181710.2973306X-RAY DIFFRACTION100
3.5907-3.86780.28691780.25473325X-RAY DIFFRACTION100
3.8678-4.2570.25731970.21213324X-RAY DIFFRACTION100
4.257-4.87260.18181660.17023374X-RAY DIFFRACTION100
4.8726-6.13770.23731780.1953417X-RAY DIFFRACTION100
6.1377-55.41870.24141980.21473555X-RAY DIFFRACTION98

+
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