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- PDB-9bcb: Crystal structure of human cellular retinol binding protein 3 in ... -

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Basic information

Entry
Database: PDB / ID: 9bcb
TitleCrystal structure of human cellular retinol binding protein 3 in complex with C11 TopFluor MG
ComponentsRetinol-binding protein 5
KeywordsLIPID BINDING PROTEIN / Cellular-retinol binding protein / retinol / retinoids / lipid transport
Function / homology
Function and homology information


retinoid binding / retinal binding / retinol binding / fatty acid transport / fatty acid binding / extracellular exosome / nucleus / cytosol
Similarity search - Function
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
: / Retinol-binding protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsGolczak, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)EY023948 United States
CitationJournal: To Be Published
Title: Interactom of cellular retinol binding protein 3.
Authors: Golczak, M.
History
DepositionApr 8, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Retinol-binding protein 5
B: Retinol-binding protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4384
Polymers32,8402
Non-polymers5992
Water7,404411
1
A: Retinol-binding protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9262
Polymers16,4201
Non-polymers5061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Retinol-binding protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5122
Polymers16,4201
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.213, 46.257, 71.530
Angle α, β, γ (deg.)90.00, 92.10, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Retinol-binding protein 5 / Cellular retinol-binding protein III / CRBP-III / HRBPiso


Mass: 16419.840 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBP5 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE / References: UniProt: P82980
#2: Chemical ChemComp-A1ALJ / 1-[11-(dipyrrometheneboron difluoride)undecanoyl]-rac-glycerol / [(2~{S})-2,3-bis(oxidanyl)propyl] 11-[2,2-bis(fluoranyl)-4,6,10,12-tetramethyl-1$l^{4},3-diaza-2$l^{4}-boratricyclo[7.3.0.0^{3,7}]dodeca-1(12),4,6,8,10-pentaen-8-yl]undecanoate


Mass: 506.433 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H41BF2N2O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 411 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 40.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.2 M sodium malonate, pH 5.0 and 20% PEG 3350 (w/v)

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Data collection

DiffractionMean temperature: 85 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.45→19.6 Å / Num. obs: 47122 / % possible obs: 98.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 17.29 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.032 / Rrim(I) all: 0.059 / Χ2: 1 / Net I/σ(I): 12.2
Reflection shellResolution: 1.45→1.47 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2330 / CC1/2: 0.807 / Rpim(I) all: 0.535 / Rrim(I) all: 0.764 / Χ2: 1.02 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
XDSdata reduction
Aimlessdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→19.6 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2221 2340 4.97 %
Rwork0.1868 --
obs0.1885 47079 98.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.45→19.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2266 0 42 411 2719
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072389
X-RAY DIFFRACTIONf_angle_d1.1213237
X-RAY DIFFRACTIONf_dihedral_angle_d31.887330
X-RAY DIFFRACTIONf_chiral_restr0.073349
X-RAY DIFFRACTIONf_plane_restr0.006413
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.480.4181410.34662591X-RAY DIFFRACTION98
1.48-1.510.28791320.31152587X-RAY DIFFRACTION98
1.51-1.550.391100.30932639X-RAY DIFFRACTION98
1.55-1.590.29941520.27852621X-RAY DIFFRACTION98
1.59-1.630.29861430.27042569X-RAY DIFFRACTION98
1.63-1.680.27291510.27192579X-RAY DIFFRACTION97
1.68-1.730.28411480.25712616X-RAY DIFFRACTION98
1.73-1.790.25721280.22572625X-RAY DIFFRACTION98
1.79-1.860.26951270.21392634X-RAY DIFFRACTION99
1.86-1.950.23751380.19992666X-RAY DIFFRACTION99
1.95-2.050.22031260.19672647X-RAY DIFFRACTION99
2.05-2.180.21241510.18452629X-RAY DIFFRACTION99
2.18-2.350.20131380.18042644X-RAY DIFFRACTION99
2.35-2.580.20811730.17772667X-RAY DIFFRACTION100
2.58-2.960.22631230.17282672X-RAY DIFFRACTION99
2.96-3.720.2131090.15012665X-RAY DIFFRACTION98
3.72-19.60.17311500.152688X-RAY DIFFRACTION97

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