[English] 日本語
Yorodumi
- PDB-5nub: Structure of human amniotic fluid RBP4 saturated with laurate -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5nub
TitleStructure of human amniotic fluid RBP4 saturated with laurate
ComponentsRetinol-binding protein 4
KeywordsTRANSPORT PROTEIN / RBP4 / plasma retinol-binding protein / lipocalin / laurate
Function / homology
Function and homology information


Retinoid metabolism disease events / urinary bladder development / embryonic retina morphogenesis in camera-type eye / retinol transport / female genitalia morphogenesis / retinol transmembrane transporter activity / embryonic organ morphogenesis / maintenance of gastrointestinal epithelium / embryonic skeletal system development / negative regulation of cardiac muscle cell proliferation ...Retinoid metabolism disease events / urinary bladder development / embryonic retina morphogenesis in camera-type eye / retinol transport / female genitalia morphogenesis / retinol transmembrane transporter activity / embryonic organ morphogenesis / maintenance of gastrointestinal epithelium / embryonic skeletal system development / negative regulation of cardiac muscle cell proliferation / eye development / heart trabecula formation / cardiac muscle tissue development / retinal binding / retinol metabolic process / retinol binding / positive regulation of immunoglobulin production / Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / uterus development / vagina development / response to retinoic acid / Retinoid metabolism and transport / visual perception / gluconeogenesis / lung development / positive regulation of insulin secretion / glucose homeostasis / heart development / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Retinol binding protein/Purpurin / Lipocalin, ApoD type / Lipocalin family conserved site / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
LAURIC ACID / Retinol-binding protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsPerduca, M. / Monaco, H.L. / Galliano, M.
CitationJournal: Biochim. Biophys. Acta / Year: 2018
Title: Human plasma retinol-binding protein (RBP4) is also a fatty acid-binding protein.
Authors: Perduca, M. / Nicolis, S. / Mannucci, B. / Galliano, M. / Monaco, H.L.
History
DepositionApr 28, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Retinol-binding protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2564
Polymers20,9841
Non-polymers2713
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint-7 kcal/mol
Surface area9470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.610, 102.610, 73.134
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

-
Components

#1: Protein Retinol-binding protein 4 / Plasma retinol-binding protein / RBP


Mass: 20984.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02753
#2: Chemical ChemComp-DAO / LAURIC ACID / Lauric acid


Mass: 200.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H24O2
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 3.53 Å3/Da / Density % sol: 65.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 4.3 M NaCl, 100 mM Hepes, pH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→56.47 Å / Num. obs: 37622 / % possible obs: 99.3 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 12.8
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 2.6 / % possible all: 98.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
iMOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5NU6

5nu6


Resolution: 1.6→30 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.866 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.07
RfactorNum. reflection% reflectionSelection details
Rfree0.20495 1953 5.2 %RANDOM
Rwork0.17355 ---
obs0.1752 35652 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.874 Å2
Baniso -1Baniso -2Baniso -3
1-1.06 Å20.53 Å2-0 Å2
2--1.06 Å20 Å2
3----3.45 Å2
Refinement stepCycle: 1 / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1408 0 16 109 1533
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.021465
X-RAY DIFFRACTIONr_bond_other_d0.0050.021345
X-RAY DIFFRACTIONr_angle_refined_deg0.6781.9371979
X-RAY DIFFRACTIONr_angle_other_deg0.9823.0063088
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5895175
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.06423.67179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.20615244
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3471513
X-RAY DIFFRACTIONr_chiral_restr0.0420.2203
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021682
X-RAY DIFFRACTIONr_gen_planes_other00.02367
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_it6.0652.418698
X-RAY DIFFRACTIONr_mcbond_other6.062.422699
X-RAY DIFFRACTIONr_mcangle_it6.7823.62872
X-RAY DIFFRACTIONr_mcangle_other6.7743.62872
X-RAY DIFFRACTIONr_scbond_it7.662.876766
X-RAY DIFFRACTIONr_scbond_other7.6552.877767
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.5884.1641107
X-RAY DIFFRACTIONr_long_range_B_refined7.83220.9421719
X-RAY DIFFRACTIONr_long_range_B_other7.92120.851671
X-RAY DIFFRACTIONr_rigid_bond_restr13.5932807
X-RAY DIFFRACTIONr_sphericity_free15.48539
X-RAY DIFFRACTIONr_sphericity_bonded17.83352847
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 133 -
Rwork0.271 2621 -
obs--97.94 %
Refinement TLS params.Method: refined / Origin x: 29.6352 Å / Origin y: 19.3305 Å / Origin z: -0.6922 Å
111213212223313233
T0.0622 Å20.0489 Å2-0.0635 Å2-0.0689 Å2-0.0577 Å2--0.1594 Å2
L1.5755 °20.2064 °2-0.005 °2-1.4533 °20.4979 °2--1.5145 °2
S0.1041 Å °-0.0259 Å °-0.074 Å °-0.0217 Å °0.0975 Å °-0.0615 Å °0.1112 Å °0.2524 Å °-0.2016 Å °

+
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