[English] 日本語
Yorodumi
- PDB-3d95: Crystal Structure of the R132K:Y134F:R111L:L121E:T54V Mutant of A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3d95
TitleCrystal Structure of the R132K:Y134F:R111L:L121E:T54V Mutant of Apo-Cellular Retinoic Acid Binding Protein Type II at 1.20 Angstroms Resolution
ComponentsCellular retinoic acid-binding protein 2
KeywordsTRANSPORT PROTEIN / CRABPII / RETINOIC ACID / RETINOIDS / BETA BARREL / HIGH RESOLUTION / MUTANT / Cytoplasm / Nucleus / Retinol-binding / Transport / Vitamin A
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
Cellular retinoic acid-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / RIGID BODY REFINEMENT / Resolution: 1.2 Å
AuthorsVaezeslami, S. / Geiger, J.H.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Structural analysis of site-directed mutants of cellular retinoic acid-binding protein II addresses the relationship between structural integrity and ligand binding.
Authors: Vaezeslami, S. / Jia, X. / Vasileiou, C. / Borhan, B. / Geiger, J.H.
#1: Journal: Thesis
Title: Determining Crystal Structures of Proteins and Protein Complexes by X-Ray Crystallography: X-Ray Crystallographic Studies of the Mutants of Cellular Retinoic Acid Binding Protein Type II ...Title: Determining Crystal Structures of Proteins and Protein Complexes by X-Ray Crystallography: X-Ray Crystallographic Studies of the Mutants of Cellular Retinoic Acid Binding Protein Type II Toward Designing a Mimic of Rhodopsin
Authors: Vaezeslami, S.
History
DepositionMay 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_residues / software
Revision 1.3Oct 20, 2021Group: Advisory / Database references
Category: database_2 / pdbx_unobs_or_zero_occ_residues / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
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


Theoretical massNumber of molelcules
Total (without water)31,0152
Polymers31,0152
Non-polymers00
Water7,080393
1
A: Cellular retinoic acid-binding protein 2


Theoretical massNumber of molelcules
Total (without water)15,5081
Polymers15,5081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cellular retinoic acid-binding protein 2


Theoretical massNumber of molelcules
Total (without water)15,5081
Polymers15,5081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.591, 36.897, 57.811
Angle α, β, γ (deg.)73.28, 75.91, 87.76
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 / Retinoic acid-binding protein II / cellular


Mass: 15507.735 Da / Num. of mol.: 2 / Mutation: R132K, Y134F, R111L, L121E, T54V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRABP2 / Plasmid: PET17-B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P29373
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 393 / 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: 2.21 Å3/Da / Density % sol: 44.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 20% (W/V) PEG 6000, 0.1 M SODIUM ACETATE, 5% ETHANOL, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 2, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→40 Å / Num. obs: 77347 / % possible obs: 93.8 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 18.17
Reflection shellResolution: 1.2→1.24 Å / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 2.55 / % possible all: 89.9

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005phasing
RefinementMethod to determine structure: RIGID BODY REFINEMENT / Resolution: 1.2→40 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.896 / SU ML: 0.018 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.043 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.176 7560 10 %RANDOM
Rwork0.138 ---
obs0.141 75296 90 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å2-0.09 Å2-0.21 Å2
2---0.23 Å20.15 Å2
3---0.69 Å2
Refinement stepCycle: LAST / Resolution: 1.2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2174 0 0 415 2589
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222206
X-RAY DIFFRACTIONr_bond_other_d0.0010.022052
X-RAY DIFFRACTIONr_angle_refined_deg1.6761.9562994
X-RAY DIFFRACTIONr_angle_other_deg0.87834799
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4595272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.90825.91898
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.715410
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6841510
X-RAY DIFFRACTIONr_chiral_restr0.1120.2364
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022400
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02404
X-RAY DIFFRACTIONr_nbd_refined0.2070.2329
X-RAY DIFFRACTIONr_nbd_other0.1870.21976
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21092
X-RAY DIFFRACTIONr_nbtor_other0.0860.21447
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2253
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.240.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2570.277
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.237
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3981.51774
X-RAY DIFFRACTIONr_mcbond_other0.9361.5560
X-RAY DIFFRACTIONr_mcangle_it2.77722252
X-RAY DIFFRACTIONr_scbond_it3.6773951
X-RAY DIFFRACTIONr_scangle_it4.8734.5742
X-RAY DIFFRACTIONr_rigid_bond_restr2.39735079
X-RAY DIFFRACTIONr_sphericity_free8.0283413
X-RAY DIFFRACTIONr_sphericity_bonded4.86534226
LS refinement shellResolution: 1.2→1.23 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.171 371 -
Rwork0.169 3725 -
obs--66.2 %

+
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