[English] 日本語
Yorodumi
- PDB-4ykm: Crystal structure of the R111K:Y134F:T54V:R132Q:P39Q:R59Y:A32W:F3... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ykm
TitleCrystal structure of the R111K:Y134F:T54V:R132Q:P39Q:R59Y:A32W:F3Q mutant of human Cellular Retinoic Acid Binding Protein II with Retinal at 1.58 angstrom resolution
ComponentsCellular retinoic acid-binding protein 2
KeywordsTRANSPORT PROTEIN / Photoswitchable protein / Rhodopsin mimic / Retinal isomerization / Retinal iminium pKa change / Protein engineering
Function / homology
Function and homology information


positive regulation of collateral sprouting / retinoid binding / retinoic acid binding / retinal binding / embryonic forelimb morphogenesis / retinoic acid metabolic process / retinol binding / Signaling by Retinoic Acid / epidermis development / fatty acid transport ...positive regulation of collateral sprouting / retinoid binding / retinoic acid binding / retinal binding / embryonic forelimb morphogenesis / retinoic acid metabolic process / retinol binding / Signaling by Retinoic Acid / epidermis development / fatty acid transport / cyclin binding / fatty acid binding / regulation of DNA-templated transcription / endoplasmic reticulum / signal transduction / extracellular exosome / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
RETINAL / Cellular retinoic acid-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsNosrati, M. / Geiger, J.H.
CitationJournal: J.Am.Chem.Soc. / Year: 2016
Title: A Photoisomerizing Rhodopsin Mimic Observed at Atomic Resolution.
Authors: Nosrati, M. / Berbasova, T. / Vasileiou, C. / Borhan, B. / Geiger, J.H.
History
DepositionMar 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2016Group: Database references
Revision 1.2Aug 3, 2016Group: Database references
Revision 1.3Sep 27, 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 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cellular retinoic acid-binding protein 2
B: Cellular retinoic acid-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8494
Polymers31,2802
Non-polymers5692
Water6,774376
1
A: Cellular retinoic acid-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9242
Polymers15,6401
Non-polymers2841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cellular retinoic acid-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9242
Polymers15,6401
Non-polymers2841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.692, 39.296, 58.431
Angle α, β, γ (deg.)87.15, 80.00, 70.54
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Cellular retinoic acid-binding protein 2 / Cellular retinoic acid-binding protein II / CRABP-II


Mass: 15639.833 Da / Num. of mol.: 2 / Mutation: R111K, Y134F, T54V, R132Q, P39Q, R59Y, A32W, F3Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRABP2 / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P29373
#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 20% PEG3350, 0.1M Bis Tris Propane pH=6.0, 0.2M Sodium Floride

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0781 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. obs: 41716 / % possible obs: 95.9 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.064 / Rsym value: 0.048 / Net I/σ(I): 31.2
Reflection shellResolution: 1.58→1.61 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.461 / Mean I/σ(I) obs: 2.6 / % possible all: 88.4

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G7B

2g7b


Resolution: 1.58→31.758 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 21.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2162 2025 5.06 %
Rwork0.1819 --
obs0.1837 40016 95.73 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.327 Å2 / ksol: 0.38 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.5091 Å20.0956 Å2-0.3281 Å2
2--0.4971 Å2-0.3455 Å2
3---0.012 Å2
Refinement stepCycle: LAST / Resolution: 1.58→31.758 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2192 0 40 376 2608
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072296
X-RAY DIFFRACTIONf_angle_d1.1293111
X-RAY DIFFRACTIONf_dihedral_angle_d15.402873
X-RAY DIFFRACTIONf_chiral_restr0.072356
X-RAY DIFFRACTIONf_plane_restr0.004402
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5766-1.61610.29441390.24192451X-RAY DIFFRACTION87
1.6161-1.65970.25641570.21982655X-RAY DIFFRACTION95
1.6597-1.70860.24131360.21042693X-RAY DIFFRACTION94
1.7086-1.76370.25121290.19912749X-RAY DIFFRACTION96
1.7637-1.82680.25361550.19312684X-RAY DIFFRACTION96
1.8268-1.89990.2281340.19352701X-RAY DIFFRACTION95
1.8999-1.98630.23511630.19482691X-RAY DIFFRACTION96
1.9863-2.09110.23811300.19172757X-RAY DIFFRACTION96
2.0911-2.2220.2261550.18212706X-RAY DIFFRACTION97
2.222-2.39350.19641490.17732766X-RAY DIFFRACTION97
2.3935-2.63430.2181470.19342770X-RAY DIFFRACTION97
2.6343-3.01520.26091480.20082778X-RAY DIFFRACTION98
3.0152-3.79790.20111480.1642782X-RAY DIFFRACTION99
3.7979-31.76480.16651350.15692808X-RAY DIFFRACTION98

+
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