[English] 日本語
Yorodumi
- PDB-6rjv: The X-ray structure of the Gold/Serum Albumin adduct obtained upo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6rjv
TitleThe X-ray structure of the Gold/Serum Albumin adduct obtained upon reaction of the protein with AuL12, a gold(III) dithiocarbamate complex
ComponentsSerum albumin
KeywordsTRANSPORT PROTEIN
Function / homology
Function and homology information


cellular response to calcium ion starvation / enterobactin binding / negative regulation of mitochondrial depolarization / toxic substance binding / small molecule binding / cellular response to starvation / fatty acid binding / pyridoxal phosphate binding / blood microparticle / protein-containing complex ...cellular response to calcium ion starvation / enterobactin binding / negative regulation of mitochondrial depolarization / toxic substance binding / small molecule binding / cellular response to starvation / fatty acid binding / pyridoxal phosphate binding / blood microparticle / protein-containing complex / DNA binding / extracellular region / metal ion binding / cytoplasm
Similarity search - Function
Serum Albumin; Chain A, Domain 1 - #10 / 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 ...Serum Albumin; Chain A, Domain 1 - #10 / 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 / Serum Albumin; Chain A, Domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.21 Å
AuthorsMerlino, A. / Giorgio, A. / Ferraro, G.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Association for Cancer Research22587 Italy
CitationJournal: Inorg.Chem. / Year: 2019
Title: Structural Characterization of a Gold/Serum Albumin Complex.
Authors: Pratesi, A. / Cirri, D. / Fregona, D. / Ferraro, G. / Giorgio, A. / Merlino, A. / Messori, L.
History
DepositionApr 29, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serum albumin
B: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,5666
Polymers133,1242
Non-polymers4434
Water77543
1
A: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7833
Polymers66,5621
Non-polymers2212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7833
Polymers66,5621
Non-polymers2212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)214.380, 44.610, 142.610
Angle α, β, γ (deg.)90.00, 114.00, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 1 / Auth seq-ID: 3 - 583 / Label seq-ID: 3 - 583

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.813078, -0.015504, 0.581949), (0.013799, -0.999878, -0.007358), (0.581992, 0.002047, 0.813192)97.52197, 50.07998, -30.86524

-
Components

#1: Protein Serum albumin / BSA


Mass: 66561.969 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P02769
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Au
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 20% PEG3350 0.1 M Tris HCl pH 8.5 0.2 M MgCl2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 3.21→130.28 Å / Num. obs: 20541 / % possible obs: 98.6 % / Redundancy: 3.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.041 / Net I/σ(I): 13.3
Reflection shellResolution: 3.21→3.26 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 985 / CC1/2: 0.689 / Rpim(I) all: 0.377 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3v03

3v03


Resolution: 3.21→130.28 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.932 / SU B: 81.495 / SU ML: 0.571 / Cross valid method: THROUGHOUT / ESU R Free: 0.572 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25313 985 4.8 %RANDOM
Rwork0.18968 ---
obs0.19267 19556 98.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 115.46 Å2
Baniso -1Baniso -2Baniso -3
1--4.06 Å20 Å23.57 Å2
2---10.03 Å20 Å2
3---7.81 Å2
Refinement stepCycle: 1 / Resolution: 3.21→130.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9274 0 4 43 9321
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0129498
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6821.64712846
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.80151160
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.60723.525488
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.293151752
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.9641546
X-RAY DIFFRACTIONr_chiral_restr0.1220.21224
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027138
X-RAY DIFFRACTIONr_gen_planes_other
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_it2.3695.34646
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.9577.9495804
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.1575.5864851
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined7.94972.40814303
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCSNumber: 4637 / Type: tight thermal / Rms dev position: 3.98 Å / Weight position: 0.5
LS refinement shellResolution: 3.206→3.289 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 68 -
Rwork0.317 1402 -
obs--99.66 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.6629-0.60430.52272.5536-0.08312.3565-0.0282-0.47260.00110.24990.07090.116-0.02530.1302-0.04280.8041-0.06770.02780.608-0.02980.007938.115822.551141.3606
21.494-0.28820.29081.75540.20441.9559-0.0494-0.4960.00940.25480.1542-0.2191-0.02360.029-0.10490.794-0.0090.0540.6554-0.01290.068289.972428.601224.372
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 609
2X-RAY DIFFRACTION2B3 - 608

+
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