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- PDB-6mqw: Crystal Structure of All-trans Retinal-Bound R111K:Y134F:T54V:R13... -

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Basic information

Entry
Database: PDB / ID: 6mqw
TitleCrystal Structure of All-trans Retinal-Bound R111K:Y134F:T54V:R132Q:P39Y:R59Y:L121E Human Cellular Retinoic Acid Binding Protein II Irradiated with 400 nm laser (30 seconds) and subsequently dark adapted (10 minutes) at 2.1 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 / 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: 2.09 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: 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
Revision 1.4Oct 16, 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)15,8792
Polymers15,5951
Non-polymers2841
Water97354
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)31,7584
Polymers31,1892
Non-polymers5692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_465y-1,x+1,-z1
Buried area3240 Å2
ΔGint-24 kcal/mol
Surface area13780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.586, 58.586, 100.178
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
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


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


Mass: 18.015 Da / Num. of mol.: 54 / 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: 3.18 Å3/Da / Density % sol: 61.35 % / Description: hexagonal
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 3350, DL-malic acid / PH range: 6.0-6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
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: 2.09→35.645 Å / Num. obs: 12273 / % possible obs: 99.9 % / Redundancy: 9.5 % / Rmerge(I) obs: 0.067 / Rrim(I) all: 0.093 / Net I/σ(I): 36.75
Reflection shellResolution: 2.09→2.12 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.677 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 1205 / Rrim(I) all: 0.754 / % possible all: 100

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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: 2.09→35.645 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 22.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2202 1086 8.85 %
Rwork0.1831 --
obs0.1865 12265 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.09→35.645 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1090 0 20 54 1164
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071187
X-RAY DIFFRACTIONf_angle_d0.8621618
X-RAY DIFFRACTIONf_dihedral_angle_d10.445988
X-RAY DIFFRACTIONf_chiral_restr0.052186
X-RAY DIFFRACTIONf_plane_restr0.004208
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0901-2.18520.28921340.19391359X-RAY DIFFRACTION100
2.1852-2.30040.25981330.20241361X-RAY DIFFRACTION99
2.3004-2.44450.25911340.22031378X-RAY DIFFRACTION100
2.4445-2.63320.28811300.22141386X-RAY DIFFRACTION100
2.6332-2.89810.29221370.2261384X-RAY DIFFRACTION100
2.8981-3.31720.23851340.19361397X-RAY DIFFRACTION100
3.3172-4.17830.19691420.16571422X-RAY DIFFRACTION100
4.1783-35.65030.17231420.15761492X-RAY DIFFRACTION100

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