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- PDB-9pn1: Crystal structure of Q108K:K40L:T51V:T53C:R58W:T29L:Y19W:Q4A muta... -

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Basic information

Entry
Database: PDB / ID: 9pn1
TitleCrystal structure of Q108K:K40L:T51V:T53C:R58W:T29L:Y19W:Q4A mutant of cellular retinol binding protein II complex with 15-cis-retinal
ComponentsRetinol-binding protein 2
KeywordsTRANSPORT PROTEIN / hCRBPII / Q4A / isomerization / retinal / cis / trans / rhodopsin / bacteriorhodopsin / CYTOSOLIC PROTEIN
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
ACETATE ION / RETINAL / Retinol-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 Å
AuthorsEhyaei, N. / Silva, K. / Bingham, C. / 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
DepositionJul 18, 2025Deposition site: RCSB / Processing site: RCSB
SupersessionJun 10, 2026ID: 7LHJ
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)31,9587
Polymers31,1792
Non-polymers7795
Water4,179232
1
B: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9333
Polymers15,5901
Non-polymers3432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0254
Polymers15,5901
Non-polymers4363
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.923, 36.038, 64.026
Angle α, β, γ (deg.)86.200, 86.560, 65.060
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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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:Y19W:T53C:R58W:T29L: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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.07 Å3/Da / Density % sol: 40.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
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: 1.127 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 1.26→22.32 Å / Num. obs: 58186 / % possible obs: 86.21 % / Redundancy: 3.1 % / Biso Wilson estimate: 13.75 Å2 / Rpim(I) all: 0.06 / Rrim(I) all: 0.107 / Net I/σ(I): 13
Reflection shellResolution: 1.26→1.31 Å / Mean I/σ(I) obs: 4.33 / Num. unique obs: 5523 / Rpim(I) all: 0.163 / Rrim(I) all: 0.291

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data scaling
PHASERphasing
PDB_EXTRACTdata extraction
Cootmodel building
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.26→22.32 Å / SU ML: 0.1488 / Cross valid method: FREE R-VALUE / σ(F): 1.95 / Phase error: 22.0545
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2205 1960 3.37 %
Rwork0.1937 56193 -
obs0.1946 58153 86.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.52 Å2
Refinement stepCycle: LAST / Resolution: 1.26→22.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2184 0 54 232 2470
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01582279
X-RAY DIFFRACTIONf_angle_d1.40413071
X-RAY DIFFRACTIONf_chiral_restr0.0788322
X-RAY DIFFRACTIONf_plane_restr0.0044384
X-RAY DIFFRACTIONf_dihedral_angle_d16.1521840
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.26-1.290.2811400.22553752X-RAY DIFFRACTION79.92
1.29-1.330.23551420.22363998X-RAY DIFFRACTION86.63
1.33-1.370.24291390.22873988X-RAY DIFFRACTION86.34
1.37-1.410.28021320.22124038X-RAY DIFFRACTION85.73
1.41-1.460.22351500.20543976X-RAY DIFFRACTION85.71
1.46-1.520.2331360.20633943X-RAY DIFFRACTION84.52
1.52-1.590.20241240.19563611X-RAY DIFFRACTION78.14
1.59-1.670.21661470.19723861X-RAY DIFFRACTION83.27
1.67-1.780.23791510.19264251X-RAY DIFFRACTION91.23
1.78-1.910.22221310.18954252X-RAY DIFFRACTION90.41
1.91-2.110.23291460.18584189X-RAY DIFFRACTION90.11
2.11-2.410.22531440.18914094X-RAY DIFFRACTION87.98
2.41-3.040.22011240.20333695X-RAY DIFFRACTION79.33
3.04-22.320.20141540.18344545X-RAY DIFFRACTION97.83

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