[English] 日本語
Yorodumi
- PDB-4ot2: Crystal Structure of Equine Serum Albumin in complex with Naproxen -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ot2
TitleCrystal Structure of Equine Serum Albumin in complex with Naproxen
ComponentsSerum albumin
KeywordsTRANSPORT PROTEIN / Helical / Three-domain protein / Serum Albumin Superfamily / Fatty acids / metabolites and drugs / Naproxen / Plasma
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 / 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
ACETATE ION / MALONATE ION / (2S)-2-(6-methoxynaphthalen-2-yl)propanoic acid / SUCCINIC ACID / Albumin
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / RIGID BODY REFINEMENT OF THE NATIVE STRUCTURE / Resolution: 2.42 Å
AuthorsSekula, B. / Bujacz, A. / Zielinski, K. / Bujacz, G.
CitationJournal: Proteins / Year: 2014
Title: Structural studies of bovine, equine, and leporine serum albumin complexes with naproxen.
Authors: Bujacz, A. / Zielinski, K. / Sekula, B.
History
DepositionFeb 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,95910
Polymers65,8541
Non-polymers1,1059
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.770, 93.770, 142.410
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Serum albumin


Mass: 65854.203 Da / Num. of mol.: 1 / Fragment: UNP residues 25-607 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P35747

-
Non-polymers , 5 types, 119 molecules

#2: Chemical ChemComp-NPS / (2S)-2-(6-methoxynaphthalen-2-yl)propanoic acid / NAPROXEN


Mass: 230.259 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H14O3 / Comment: antiinflammatory*YM
#3: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H2O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.74 Å3/Da / Density % sol: 55.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 1.6 M Ammonium sulfate, 0.1 M acetate buffer pH 4.5, cocrystallization with Naproxen, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 22, 2011 / Details: Mirrors
RadiationMonochromator: Double crystal monochromator Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.42→50 Å / Num. all: 27053 / Num. obs: 26724 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.94 % / Biso Wilson estimate: 54.59 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.079 / Net I/σ(I): 17.57
Reflection shellResolution: 2.42→2.52 Å / Redundancy: 3.95 % / Rmerge(I) obs: 0.951 / Mean I/σ(I) obs: 2.05 / Num. unique all: 3061 / Rsym value: 0.01094 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.8.0049refinement
XDSdata reduction
XDSdata scaling
REFMAC5.8.0049phasing
RefinementMethod to determine structure: RIGID BODY REFINEMENT OF THE NATIVE STRUCTURE
Starting model: PDB ENTRY 4F5T

4f5t


Resolution: 2.42→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.929 / SU B: 23.698 / SU ML: 0.238 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.38 / ESU R Free: 0.263 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24737 1084 4.1 %RANDOM
Rwork0.17927 ---
all0.182 27053 --
obs0.182 25640 98.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.105 Å2
Baniso -1Baniso -2Baniso -3
1-1.2 Å20.6 Å2-0 Å2
2--1.2 Å2-0 Å2
3----3.91 Å2
Refinement stepCycle: LAST / Resolution: 2.42→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4584 0 78 110 4772
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0194790
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7531.9956472
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8445583
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.67624.885217
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.36515861
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9731522
X-RAY DIFFRACTIONr_chiral_restr0.1080.2701
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213620
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_it2.5243.7412325
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.855.6042903
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.564.0982465
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined8.22532.7797648
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.42→2.483 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 81 -
Rwork0.324 1902 -
obs-1902 99.35 %
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)
13.88460.17270.50212.70590.66672.29640.22670.02770.3117-0.25330.00260.1926-0.3548-0.1055-0.22930.2934-0.0944-0.03460.08030.0530.129340.774341.950270.3704
27.6810.0691-1.90152.5322-0.62632.91240.21630.45170.1379-0.61420.0319-0.1138-0.0910.3664-0.24820.4181-0.1121-0.01630.1545-0.02260.051749.501928.785657.0196
32.77210.81210.14862.3727-0.24042.2297-0.20360.2806-0.4322-0.58750.1285-0.4133-0.07910.64820.07510.2901-0.14870.08820.3737-0.06730.190954.127621.140262.9868
42.25721.40410.53061.90671.34462.8277-0.0357-0.27550.20680.1626-0.04530.2875-0.14580.12760.0810.1734-0.0218-0.03230.1529-0.040.182340.358719.3484.0716
53.23541.41071.31935.79630.55825.1225-0.0236-0.0871-0.13260.06840.2008-0.45740.03670.7067-0.17720.0405-0.05-0.00860.2577-0.0590.069954.839620.296183.8616
66.93552.1507-0.76440.9369-0.23941.50620.1062-0.34020.12350.3405-0.15250.1390.1099-0.02640.04630.44090.0020.01510.2571-0.05150.205236.65944.883297.3872
73.59970.7319-1.20671.1266-1.2525.86740.0217-0.1563-0.24370.1113-0.0150.24270.1991-0.4417-0.00670.129-0.03110.0110.0586-0.00830.126829.69312.246889.9179
81.9208-0.1533-3.3780.12260.68259.4137-0.15690.0007-0.27160.0417-0.07360.01330.4969-0.12690.23050.11630.0010.00940.0523-0.00880.074535.0876-5.476577.9875
95.6218-1.45651.77021.7706-1.86825.70010.1553-0.2239-0.3119-0.2497-0.12930.23760.13960.1765-0.0260.19160.0146-0.03770.0555-0.03610.096232.43063.087756.8226
101.5132-1.7451.46893.0011-0.56923.0757-0.020.01990.0745-0.04320.0009-0.10750.14370.19180.01910.15580.0389-0.03040.1096-0.01390.103137.77248.444865.254
115.50071.64762.50992.58810.96835.90470.1002-0.18150.35180.2764-0.20580.36310.3462-0.50690.10560.0507-0.04250.02940.0535-0.02480.057423.24586.975967.1982
120.6598-0.5605-0.44783.4568-1.64214.91220.27580.1861-0.0454-0.3989-0.21170.0516-0.0808-0.0646-0.06410.27720.0342-0.00510.0714-0.0250.020132.72837.325843.9755
131.65151.5386-1.29882.3395-1.23962.43340.01070.0429-0.1052-0.484-0.2633-0.14050.29390.05350.25260.50590.094-0.02480.2042-0.01110.159634.8205-0.593337.7506
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 106
2X-RAY DIFFRACTION2A107 - 147
3X-RAY DIFFRACTION3A148 - 198
4X-RAY DIFFRACTION4A199 - 250
5X-RAY DIFFRACTION5A251 - 295
6X-RAY DIFFRACTION6A296 - 336
7X-RAY DIFFRACTION7A337 - 366
8X-RAY DIFFRACTION8A367 - 398
9X-RAY DIFFRACTION9A399 - 417
10X-RAY DIFFRACTION10A418 - 468
11X-RAY DIFFRACTION11A469 - 497
12X-RAY DIFFRACTION12A498 - 537
13X-RAY DIFFRACTION13A538 - 583

+
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