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- PDB-7lhn: Crystal structure of Q108K:K40L:T51V:T53C:R58W:T29L:Y19W:Q4A muta... -

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Basic information

Entry
Database: PDB / ID: 7lhn
TitleCrystal structure of Q108K:K40L:T51V:T53C:R58W:T29L:Y19W:Q4A mutant of cellular retinol binding protein II complex with all-trans-retinal after exposure to visible light
ComponentsRetinol-binding protein 2
KeywordsCYTOSOLIC PROTEIN / hCRBPII / Q4A / isomerization / retinal / cis / trans / rhodopsin / bacteriorhodopsin / all-trans-retinal
Function / homology
Function and homology information


vitamin A metabolic process / triglyceride biosynthetic process / retinoid binding / retinal binding / molecular carrier activity / retinol binding / epidermis development / fatty acid transport / Retinoid metabolism and transport / fatty acid binding ...vitamin A metabolic process / triglyceride biosynthetic process / retinoid binding / retinal binding / molecular carrier activity / retinol binding / epidermis development / fatty acid transport / Retinoid metabolism and transport / fatty acid binding / nucleus / 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
Similarity search - Domain/homology
RETINAL / Retinol-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsEhyaei, N. / Geiger, J.H. / Borhan, B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Research Resources (NIH/NCRR) United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2026
Title: Photoisomerization detected in a fully wavelength-tunable rhodopsin mimic system.
Authors: Ehyaei, N. / Bingham, C. / Silva, K. / Nossoni, Z. / Gavgani, H.N. / Nosrati, M. / Eaves, J. / Akhdar, M. / Vasileiou, C. / Borhan, B. / Geiger, J.H.
History
DepositionJan 25, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.3Jun 10, 2026Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Retinol-binding protein 2
B: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8405
Polymers31,1792
Non-polymers6613
Water2,936163
1
A: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9663
Polymers15,5901
Non-polymers3772
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8742
Polymers15,5901
Non-polymers2841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.755, 35.773, 64.153
Angle α, β, γ (deg.)86.180, 86.478, 65.224
Int Tables number1
Space group name H-MP1
Space group name HallP1

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Components

#1: Protein Retinol-binding protein 2 / Cellular retinol-binding protein II / CRBP-II


Mass: 15589.603 Da / Num. of mol.: 2 / Mutation: Q108K,K40L,T51V,T53C,R58W,T29L,Y19W,Q4A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBP2, CRBP2 / Production host: Escherichia coli (E. coli) / References: UniProt: P50120
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.05 Å3/Da / Density % sol: 39.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 30% PEG 4000, 0.1 M sodium acetate, 0.1 M ammonium acetate , pH 4.6, EVAPORATION, temperature 298K
PH range: 4.0-4.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.11→29.48 Å / Num. obs: 12568 / % possible obs: 88.28 % / Redundancy: 3 % / Biso Wilson estimate: 21.27 Å2 / Rpim(I) all: 0.06 / Rrim(I) all: 0.107 / Net I/σ(I): 13
Reflection shellResolution: 2.11→2.185 Å / Mean I/σ(I) obs: 4.33 / Num. unique obs: 1254 / Rpim(I) all: 0.163 / Rrim(I) all: 0.291 / % possible all: 88.93

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
Cootmodel building
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QYN

4qyn


Resolution: 2.11→29.48 Å / SU ML: 0.2314 / Cross valid method: FREE R-VALUE / σ(F): 2.02 / Phase error: 26.3809
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.264 1265 10.07 %
Rwork0.1719 11303 -
obs0.1811 12568 88.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.92 Å2
Refinement stepCycle: LAST / Resolution: 2.11→29.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2180 0 46 163 2389
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00732269
X-RAY DIFFRACTIONf_angle_d0.8713061
X-RAY DIFFRACTIONf_chiral_restr0.0541322
X-RAY DIFFRACTIONf_plane_restr0.0041390
X-RAY DIFFRACTIONf_dihedral_angle_d12.19291316
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.11-2.190.28721410.18571231X-RAY DIFFRACTION87.11
2.19-2.290.29011460.18111306X-RAY DIFFRACTION91.96
2.29-2.410.27591440.18161337X-RAY DIFFRACTION92.16
2.41-2.560.28791460.19251309X-RAY DIFFRACTION90.99
2.56-2.760.27031510.18531278X-RAY DIFFRACTION91.02
2.76-3.040.33011470.18221240X-RAY DIFFRACTION87.51
3.04-3.480.25361240.16311132X-RAY DIFFRACTION79.7
3.48-4.380.24331250.14851157X-RAY DIFFRACTION80.12
4.38-29.480.22111410.171313X-RAY DIFFRACTION92.03

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