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- PDB-6mqy: Crystal Structure of the 13-cis Product of All-trans Retinal-Boun... -

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Basic information

Entry
Database: PDB / ID: 6mqy
TitleCrystal Structure of the 13-cis Product of All-trans Retinal-Bound R111K:Y134F:T54V:R132Q:P39Y:R59Y:L121E Mutant of Human Cellular Retinoic Acid Binding Protein II Irradiated with 400 nm Laser (30 seconds) at 1.9 Angstrom
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 / 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: 1.9 Å
AuthorsGhanbarpour, A. / Geiger, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI) 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 11, 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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)16,1555
Polymers15,5951
Non-polymers5614
Water75742
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)32,31110
Polymers31,1892
Non-polymers1,1218
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_465y-1,x+1,-z1
Buried area4520 Å2
ΔGint-27 kcal/mol
Surface area13330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.343, 58.343, 99.865
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: 15594.747 Da / Num. of mol.: 1 / Mutation: R111K, Y134F, T54V, R132Q, P39Y, R59Y, L121E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRABP2
Production host: Bacterial expression vector pBEN1-SGC (others)
References: UniProt: P29373
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.15 Å3/Da / Density % sol: 60.91 % / Description: Hexagonal
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 3350, D-Malic acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97911 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 1.9→29.171 Å / Num. obs: 16010 / % possible obs: 99.2 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 35.49
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 1552 / Rrim(I) all: 0.481 / % possible all: 98.66

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YFP

4yfp


Resolution: 1.9→29.171 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 21.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.217 973 6.08 %
Rwork0.1893 --
obs0.1911 15994 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→29.171 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1093 0 38 42 1173
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081164
X-RAY DIFFRACTIONf_angle_d0.8711570
X-RAY DIFFRACTIONf_dihedral_angle_d12.253971
X-RAY DIFFRACTIONf_chiral_restr0.053176
X-RAY DIFFRACTIONf_plane_restr0.004198
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.00020.26831410.22252100X-RAY DIFFRACTION99
2.0002-2.12540.22621360.18962096X-RAY DIFFRACTION100
2.1254-2.28950.22411380.17822121X-RAY DIFFRACTION100
2.2895-2.51980.24591390.2012136X-RAY DIFFRACTION100
2.5198-2.88410.24151350.2072148X-RAY DIFFRACTION100
2.8841-3.63260.21281370.18772154X-RAY DIFFRACTION99
3.6326-29.17490.19381470.17942266X-RAY DIFFRACTION100

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