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- PDB-4o9s: Crystal structure of Retinol-Binding Protein 4 (RBP4)in complex w... -

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Basic information

Entry
Database: PDB / ID: 4o9s
TitleCrystal structure of Retinol-Binding Protein 4 (RBP4)in complex with a non-retinoid ligand
ComponentsRetinol-binding protein 4
KeywordsPROTEIN BINDING / retinol binding / Disease mutation / Retinol-binding / Secreted / Sensory transduction / Transport / Vision / Vitamin A / TRANSPORT PROTEIN
Function / homology
Function and homology information


urinary bladder development / Retinoid metabolism disease events / female genitalia morphogenesis / embryonic retina morphogenesis in camera-type eye / retinol transport / retinol transmembrane transporter activity / uterus development / vagina development / embryonic skeletal system development / maintenance of gastrointestinal epithelium ...urinary bladder development / Retinoid metabolism disease events / female genitalia morphogenesis / embryonic retina morphogenesis in camera-type eye / retinol transport / retinol transmembrane transporter activity / uterus development / vagina development / embryonic skeletal system development / maintenance of gastrointestinal epithelium / embryonic organ morphogenesis / negative regulation of cardiac muscle cell proliferation / all-trans-retinol binding / retinol binding / eye development / heart trabecula formation / retinol metabolic process / cardiac muscle tissue development / response to muscle activity / molecular carrier activity / positive regulation of immunoglobulin production / Defective visual phototransduction due to STRA6 loss of function / The canonical retinoid cycle in rods (twilight vision) / lung development / response to retinoic acid / Retinoid metabolism and transport / gluconeogenesis / retinoid metabolic process / positive regulation of insulin secretion / heart development / glucose homeostasis / response to ethanol / response to xenobiotic stimulus / protein-containing complex binding / protein-containing complex / extracellular exosome / extracellular region
Similarity search - Function
Retinol binding protein/Purpurin / Lipocalin, ApoD type / Lipocalin family conserved site / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-2RY / DI(HYDROXYETHYL)ETHER / Retinol-binding protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWang, Z. / Johnstone, S. / Walker, N.P.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2014
Title: Structure-assisted discovery of the first non-retinoid ligands for Retinol-Binding Protein 4.
Authors: Wang, Y. / Connors, R. / Fan, P. / Wang, X. / Wang, Z. / Liu, J. / Kayser, F. / Medina, J.C. / Johnstone, S. / Xu, H. / Thibault, S. / Walker, N. / Conn, M. / Zhang, Y. / Liu, Q. / Grillo, M. ...Authors: Wang, Y. / Connors, R. / Fan, P. / Wang, X. / Wang, Z. / Liu, J. / Kayser, F. / Medina, J.C. / Johnstone, S. / Xu, H. / Thibault, S. / Walker, N. / Conn, M. / Zhang, Y. / Liu, Q. / Grillo, M.P. / Motani, A. / Coward, P. / Wang, Z.
History
DepositionJan 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 2.0Feb 19, 2020Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / struct_ref_seq_dif
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Revision 2.1Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Retinol-binding protein 4
B: Retinol-binding protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,63734
Polymers49,9182
Non-polymers2,71932
Water4,161231
1
A: Retinol-binding protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,38918
Polymers24,9591
Non-polymers1,43017
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Retinol-binding protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,24816
Polymers24,9591
Non-polymers1,28915
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Retinol-binding protein 4
hetero molecules

B: Retinol-binding protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,63734
Polymers49,9182
Non-polymers2,71932
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_455y-1,-x+y,z+1/61
Buried area6000 Å2
ΔGint7 kcal/mol
Surface area19200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.737, 85.737, 118.806
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Retinol-binding protein 4 / Plasma retinol-binding protein / PRBP / RBP / Plasma retinol-binding protein(1-182) / Plasma ...Plasma retinol-binding protein / PRBP / RBP / Plasma retinol-binding protein(1-182) / Plasma retinol-binding protein(1-181) / Plasma retinol-binding protein(1-179) / Plasma retinol-binding protein(1-176)


Mass: 24958.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBP4, PRO2222 / Production host: Escherichia coli (E. coli) / References: UniProt: P02753

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Non-polymers , 5 types, 263 molecules

#2: Chemical ChemComp-2RY / 1-[4-(7-thia-9,11-diazatricyclo[6.4.0.0^{2,6}]dodeca-1(12),2(6),8,10-tetraen-12-yl)piperazin-1-yl]-2-[2-(trifluoromethyl)phenyl]ethanone


Mass: 446.489 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H21F3N4OS
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.29 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1M ammonium phosphate dibasic, 0.1M imidazole, 0.2M sodium chloride, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 27, 2007
RadiationMonochromator: DOUBLE-CRYSTAL, SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→63 Å / Num. all: 22054 / Num. obs: 22050 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.8.0049refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.894 / SU B: 7.852 / SU ML: 0.186 / Cross valid method: THROUGHOUT / ESU R: 0.345 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26072 1128 5.1 %RANDOM
Rwork0.23116 ---
obs0.23265 20882 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.782 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20.18 Å2-0 Å2
2--0.35 Å2-0 Å2
3----1.15 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2822 0 176 231 3229
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.023053
X-RAY DIFFRACTIONr_bond_other_d0.0010.022809
X-RAY DIFFRACTIONr_angle_refined_deg1.1381.9744085
X-RAY DIFFRACTIONr_angle_other_deg0.62136442
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4295349
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.74523.885157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.48215484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.2331524
X-RAY DIFFRACTIONr_chiral_restr0.050.2410
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023401
X-RAY DIFFRACTIONr_gen_planes_other00.02737
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2883.1431399
X-RAY DIFFRACTIONr_mcbond_other0.2883.1421398
X-RAY DIFFRACTIONr_mcangle_it0.5414.7111747
X-RAY DIFFRACTIONr_mcangle_other0.5414.7121748
X-RAY DIFFRACTIONr_scbond_it0.1713.2041654
X-RAY DIFFRACTIONr_scbond_other0.1713.2041654
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.3374.7362339
X-RAY DIFFRACTIONr_long_range_B_refined2.1925.3253549
X-RAY DIFFRACTIONr_long_range_B_other2.1925.3253549
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 66 -
Rwork0.288 1548 -
obs--99.94 %

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