[English] 日本語
Yorodumi
- PDB-7dl4: Crystal structure of human serum albumin and nitrosylruthenium co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7dl4
TitleCrystal structure of human serum albumin and nitrosylruthenium complex adduct
ComponentsSerum albumin
KeywordsTRANSPORT PROTEIN / Ruthenium complexes / NO donors / Photodynamic / human serum albumin
Function / homology
Function and homology information


cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME ...cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME / antioxidant activity / toxic substance binding / Scavenging of heme from plasma / Recycling of bile acids and salts / cellular response to starvation / platelet alpha granule lumen / fatty acid binding / Post-translational protein phosphorylation / Cytoprotection by HMOX1 / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / pyridoxal phosphate binding / Platelet degranulation / protein-folding chaperone binding / blood microparticle / copper ion binding / endoplasmic reticulum lumen / Golgi apparatus / endoplasmic reticulum / protein-containing complex / DNA binding / extracellular space / extracellular exosome / extracellular region / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Serum albumin/Alpha-fetoprotein/Afamin / ALB/AFP/VDB / Serum albumin, N-terminal / Serum albumin, conserved site / Serum albumin-like / Serum albumin family / Albumin domain signature. / Albumin domain profile. / serum albumin
Similarity search - Domain/homology
5-chloranylquinolin-8-ol / NITRIC OXIDE / PALMITIC ACID / RUTHENIUM ION / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsXie, L.L. / Wang, W.M. / Wang, H.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)21671125, 62075118 China
CitationJournal: To Be Published
Title: Structural and Photodynamic Studies on Nitrosylruthenium Complexed Serum Albumin
Authors: Xie, L.L. / Wang, W.M. / Wang, H.F.
History
DepositionNov 26, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 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: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,99023
Polymers66,5711
Non-polymers2,41922
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area420 Å2
ΔGint-19 kcal/mol
Surface area29890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.983, 38.494, 95.516
Angle α, β, γ (deg.)90.000, 105.530, 90.000
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Serum albumin /


Mass: 66571.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: ALB, GIG20, GIG42, PRO0903, PRO1708, PRO2044, PRO2619, PRO2675, UNQ696/PRO1341
Production host: Homo sapiens (human) / References: UniProt: P02768

-
Non-polymers , 8 types, 136 molecules

#2: Chemical ChemComp-RU / RUTHENIUM ION / Ruthenium


Mass: 101.070 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ru / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-HZQ / 5-chloranylquinolin-8-ol


Mass: 179.603 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H6ClNO
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide / Nitric oxide


Mass: 30.006 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#8: Chemical
ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C16H32O2
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.46 Å3/Da / Density % sol: 50.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 32% PEG3350, 50 mM pottasium phosphate buffer

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 25509 / % possible obs: 98.4 % / Redundancy: 4 % / Biso Wilson estimate: 56.7 Å2 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.058 / Rrim(I) all: 0.117 / Χ2: 1.089 / Net I/σ(I): 5 / Num. measured all: 101803
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.443.30.71912130.8980.4510.8540.44597.4
2.44-2.493.30.72512090.8540.4470.8570.47396.1
2.49-2.533.70.6512620.9010.3860.760.46197.6
2.53-2.594.10.58412930.9140.330.6740.48399.5
2.59-2.644.20.50412520.9490.2810.5790.49899.4
2.64-2.74.10.44612850.9540.2520.5140.50699.6
2.7-2.774.20.39312900.9560.2180.4520.53999.8
2.77-2.854.20.3212500.9690.1810.3690.57499.4
2.85-2.934.20.28813090.9760.1610.3310.62499.5
2.93-3.024.10.24312680.9810.1370.280.64498.8
3.02-3.1340.212670.9770.1160.2320.70499.1
3.13-3.263.70.1712360.9870.1010.1990.88495
3.26-3.414.30.14612820.9860.0810.1671.12298.9
3.41-3.584.30.12612690.9860.070.1441.3899.1
3.58-3.814.30.11213060.9870.0630.1291.78799.3
3.81-4.14.10.09312830.9920.0530.1072.0198.9
4.1-4.5240.07812900.9930.0460.0912.15798.5
4.52-5.173.80.07212790.9920.0430.0842.20997
5.17-6.514.20.06513300.9950.0370.0751.6499.3
6.51-503.70.06113360.9920.0360.0722.29996

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GIY

5giy


Resolution: 2.4→35.539 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 30.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2683 1235 4.84 %
Rwork0.2081 24265 -
obs0.211 25500 98.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.81 Å2 / Biso mean: 64.6739 Å2 / Biso min: 32.87 Å2
Refinement stepCycle: final / Resolution: 2.4→35.539 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4619 0 143 114 4876
Biso mean--65.8 63.58 -
Num. residues----581
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094861
X-RAY DIFFRACTIONf_angle_d0.9556512
X-RAY DIFFRACTIONf_chiral_restr0.047707
X-RAY DIFFRACTIONf_plane_restr0.005833
X-RAY DIFFRACTIONf_dihedral_angle_d20.0393056
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4-2.49610.37481330.3229255395
2.4961-2.60970.32571240.2969269599
2.6097-2.74720.33491460.26282719100
2.7472-2.91930.32231380.2553268999
2.9193-3.14450.31871260.2538270899
3.1445-3.46080.35181420.2349264997
3.4608-3.9610.25081440.1996272699
3.961-4.98820.22391500.175270298
4.9882-35.5390.23441320.1777282498

+
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