[English] 日本語
Yorodumi
- PDB-5ijf: Crystal structure of Human Serum Albumin in the presence of 0.5 m... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ijf
TitleCrystal structure of Human Serum Albumin in the presence of 0.5 mM zinc at pH 9.0
ComponentsSerum albumin
KeywordsTRANSPORT PROTEIN / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC
Function / homology
Function and homology information


cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / HDL remodeling / enterobactin binding / Heme biosynthesis / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / antioxidant activity ...cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / HDL remodeling / enterobactin binding / Heme biosynthesis / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / antioxidant activity / Aspirin ADME / 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; 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
Unknown ligand / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsHanding, K.B. / Shabalin, I.G. / Cooper, D.R. / Grabowski, M. / Almo, S.C. / Minor, W. / New York Structural Genomics Research Consortium (NYSGRC)
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM117325-01 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5U54GM094662-05 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM053163 United States
CitationJournal: Chem Sci / Year: 2016
Title: Circulatory zinc transport is controlled by distinct interdomain sites on mammalian albumins.
Authors: Handing, K.B. / Shabalin, I.G. / Kassaar, O. / Khazaipoul, S. / Blindauer, C.A. / Stewart, A.J. / Chruszcz, M. / Minor, W.
History
DepositionMar 2, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 13, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.3Oct 31, 2018Group: Data collection / Source and taxonomy / Structure summary
Category: entity / entity_src_gen / entity_src_nat / Item: _entity.src_method
Revision 1.4Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Apr 13, 2022Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.6Sep 27, 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)66,6374
Polymers66,5711
Non-polymers653
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.614, 121.560, 140.036
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Serum albumin /


Mass: 66571.219 Da / Num. of mol.: 1 / Fragment: residues 25-609 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: blood / References: UniProt: P02768
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 2 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.51 Å3/Da / Density % sol: 51.05 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 0.2 ul of 90 mg/ml protein in 20 mM K2HPO4 pH 7.5 buffer was mixed with 0.2 ul of the well condition (0.1 M MMT Buffer pH 9.0, 23 % PEG 1500, 1 mM ZnCl2) and equilibrated against well ...Details: 0.2 ul of 90 mg/ml protein in 20 mM K2HPO4 pH 7.5 buffer was mixed with 0.2 ul of the well condition (0.1 M MMT Buffer pH 9.0, 23 % PEG 1500, 1 mM ZnCl2) and equilibrated against well solution in 96 Well 3 drop Crystallization Plate (Swissci)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 16, 2013 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.65→50.01 Å / Num. obs: 19741 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 48.1 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/av σ(I): 28.724 / Net I/σ(I): 11.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.65-2.76.60.818188.4
2.7-2.7470.631194.6
2.74-2.87.20.628197.5
2.8-2.857.30.581199.1
2.85-2.927.40.5199.9
2.92-2.987.60.3591100
2.98-3.067.50.2821100
3.06-3.147.60.2261100
3.14-3.237.60.1651100
3.23-3.347.60.1331100
3.34-3.467.50.0991100
3.46-3.67.50.0761100
3.6-3.767.50.0621100
3.76-3.967.50.0551100
3.96-4.217.40.0441100
4.21-4.537.30.0411100
4.53-4.997.20.0391100
4.99-5.717.10.041199.9
5.71-7.196.90.0391100
7.19-506.30.07196.6

-
Processing

Software
NameVersionClassification
MD2data collection
HKL-3000data reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AO6

1ao6


Resolution: 2.65→50.01 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.917 / SU B: 49.517 / SU ML: 0.438 / SU R Cruickshank DPI: 1.0733 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.073 / ESU R Free: 0.383
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2924 949 4.9 %RANDOM
Rwork0.2131 ---
obs0.2171 18566 98.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 247.84 Å2 / Biso mean: 105.023 Å2 / Biso min: 46.15 Å2
Baniso -1Baniso -2Baniso -3
1--7.76 Å2-0 Å2-0 Å2
2--14.13 Å2-0 Å2
3----6.37 Å2
Refinement stepCycle: final / Resolution: 2.65→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4279 0 9 40 4328
Biso mean--92.21 84.98 -
Num. residues----572
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0194391
X-RAY DIFFRACTIONr_bond_other_d0.0020.023952
X-RAY DIFFRACTIONr_angle_refined_deg1.161.965974
X-RAY DIFFRACTIONr_angle_other_deg0.90639055
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2265570
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.35124.392189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.79815669
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6531522
X-RAY DIFFRACTIONr_chiral_restr0.0580.2683
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215051
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02985
X-RAY DIFFRACTIONr_mcbond_it8.2385.062286
X-RAY DIFFRACTIONr_mcbond_other8.2325.062285
X-RAY DIFFRACTIONr_mcangle_it11.4917.6032854
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.487 69 -
Rwork0.385 1252 -
all-1321 -
obs--91.74 %
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)
17.21690.4079-0.28831.39220.78595.9885-0.3026-0.1742-0.1889-0.4007-0.13140.12640.70071.31850.43410.69380.31740.15490.40930.21780.467614.0679.398-19.472
25.6861.35910.11911.24952.73657.9448-0.59850.3127-0.88430.2094-0.26270.10911.0294-1.00440.86120.5991-0.11730.16910.2052-0.01360.672-8.1197.884-22.514
32.4859-0.6513-1.97843.41150.46845.59140.0012-0.72770.00140.4705-0.04380.3368-0.15940.31970.04270.41780.04380.12090.27370.060.46740.02524.3616.082
49.5816-0.8244-0.27463.0765-4.09616.51460.3638-0.39460.07930.0970.57210.5925-0.2461-0.7721-0.9360.38630.13050.03270.5113-0.02340.5072-13.54837.014-14.249
56.6211-1.61080.87815.8589-4.9365.94780.46350.73810.93580.1246-0.5651-0.3146-0.64910.4780.10150.59280.01510.06920.261-0.10330.614-0.439.491-12.394
68.91553.38633.01551.40160.74056.83870.27480.53251.1640.0174-0.0170.6428-0.16740.1998-0.25780.40820.2982-0.09360.5792-0.30210.5855-16.23640.608-35.04
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 115
2X-RAY DIFFRACTION2A116 - 185
3X-RAY DIFFRACTION3A186 - 385
4X-RAY DIFFRACTION4A386 - 445
5X-RAY DIFFRACTION5A446 - 499
6X-RAY DIFFRACTION6A500 - 582

+
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