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- PDB-6mox: Crystal Structure of the All-trans Retinal-Bound R111K:Y134F:T54V... -

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Basic information

Entry
Database: PDB / ID: 6mox
TitleCrystal Structure of the All-trans Retinal-Bound R111K:Y134F:T54V:R132Q:P39Q:R59Y:L121E Human Cellular Retinoic Acid Binding Protein II Mutant in the Dark at 2.18 Angstrom Resolution
ComponentsCellular retinoic acid-binding protein 2
KeywordsLIPID BINDING PROTEIN / iLBP / Rhodopsin mimic
Function / homology
Function and homology information


positive regulation of collateral sprouting / retinoid binding / retinal binding / retinoic acid 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 / retinal binding / retinoic acid 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 / cytosol / cytoplasm
Similarity search - Function
Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding 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: 2.18 Å
AuthorsGhanbarpour, A. / Geiger, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM101353 United States
CitationJournal: J. Am. Chem. Soc. / Year: 2019
Title: Mimicking Microbial Rhodopsin Isomerization in a Single Crystal.
Authors: Ghanbarpour, A. / Nairat, M. / Nosrati, M. / Santos, E.M. / Vasileiou, C. / Dantus, M. / Borhan, B. / Geiger, J.H.
History
DepositionOct 4, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)15,8442
Polymers15,5601
Non-polymers2841
Water45025
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Cellular retinoic acid-binding protein 2
hetero molecules

A: Cellular retinoic acid-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6884
Polymers31,1192
Non-polymers5692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_465y-1,x+1,-z1
Buried area3050 Å2
ΔGint-24 kcal/mol
Surface area13200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.546, 58.546, 99.525
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 15559.702 Da / Num. of mol.: 1 / Mutation: R111K, Y134F, T54V, R132Q, P39Q, R59Y, L121E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRABP2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P29373
#2: Chemical ChemComp-RET / RETINAL / Retinal


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 61.13 % / Description: Hexagonal
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, BTP, Sodium Fluoride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.18→45.18 Å / Num. obs: 10769 / % possible obs: 99.94 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 14.5
Reflection shellResolution: 2.18→2.22 Å / Rmerge(I) obs: 0.638 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1059 / Rpim(I) all: 0.294 / % possible all: 99.81

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YFP

4yfp


Resolution: 2.18→45.178 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2501 1080 10.03 %
Rwork0.2034 --
obs0.2083 10767 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.18→45.178 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1086 0 20 25 1131
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081152
X-RAY DIFFRACTIONf_angle_d0.9381558
X-RAY DIFFRACTIONf_dihedral_angle_d11.909968
X-RAY DIFFRACTIONf_chiral_restr0.05177
X-RAY DIFFRACTIONf_plane_restr0.004202
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1797-2.27890.31861290.23571160X-RAY DIFFRACTION100
2.2789-2.3990.32731340.23721200X-RAY DIFFRACTION100
2.399-2.54930.29371330.2341195X-RAY DIFFRACTION100
2.5493-2.74610.26521300.23071187X-RAY DIFFRACTION100
2.7461-3.02240.26391340.21531206X-RAY DIFFRACTION100
3.0224-3.45960.26341330.20431210X-RAY DIFFRACTION100
3.4596-4.35820.23191380.18581221X-RAY DIFFRACTION100
4.3582-45.18730.20581490.18181308X-RAY DIFFRACTION100

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