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- PDB-4psq: Crystal Structure of Retinol-Binding Protein 4 (RBP4) in complex ... -

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Basic information

Entry
Database: PDB / ID: 4psq
TitleCrystal Structure of Retinol-Binding Protein 4 (RBP4) in complex with a non-retinoid ligand
ComponentsRetinol-binding protein 4
KeywordsTRANSPORT PROTEIN / retinol binding / disease mutation / secreted / sensory transduction / vision / Vitamin A
Function / homology
Function and homology information


Retinoid metabolism disease events / embryonic retina morphogenesis in camera-type eye / vitamin A import into cell / urinary bladder development / retinol transport / female genitalia morphogenesis / retinol transmembrane transporter activity / maintenance of gastrointestinal epithelium / embryonic organ morphogenesis / negative regulation of cardiac muscle cell proliferation ...Retinoid metabolism disease events / embryonic retina morphogenesis in camera-type eye / vitamin A import into cell / urinary bladder development / retinol transport / female genitalia morphogenesis / retinol transmembrane transporter activity / maintenance of gastrointestinal epithelium / embryonic organ morphogenesis / negative regulation of cardiac muscle cell proliferation / embryonic skeletal system development / detection of light stimulus involved in visual perception / retinal metabolic process / eye development / retinal binding / heart trabecula formation / retinol metabolic process / molecular carrier activity / retinol binding / cardiac muscle tissue development / Defective visual phototransduction due to STRA6 loss of function / positive regulation of immunoglobulin production / response to muscle activity / The canonical retinoid cycle in rods (twilight vision) / uterus development / vagina development / phototransduction, visible light / response to retinoic acid / Retinoid metabolism and transport / lung development / gluconeogenesis / response to insulin / male gonad development / positive regulation of insulin secretion / glucose homeostasis / heart development / spermatogenesis / 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-2WL / PHOSPHATE ION / Retinol-binding protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWang, Z. / Johnstone, S. / Walker, N.
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
DepositionMar 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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
B: Retinol-binding protein 4
A: Retinol-binding protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,43426
Polymers49,2412
Non-polymers2,19324
Water2,558142
1
B: Retinol-binding protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,59311
Polymers24,6201
Non-polymers97210
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Retinol-binding protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,84115
Polymers24,6201
Non-polymers1,22114
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.531, 96.531, 118.072
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Retinol-binding protein 4 / Plasma retinol-binding protein / PRBP / RBP


Mass: 24620.477 Da / Num. of mol.: 2 / Fragment: UNP residues 19-201
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
#2: Chemical ChemComp-2WL / (1-benzyl-1H-imidazol-4-yl)[4-(2-chlorophenyl)piperazin-1-yl]methanone


Mass: 380.871 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H21ClN4O
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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

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Sample preparation

CrystalDensity Matthews: 3.23 Å3/Da / Density % sol: 61.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1 M ammonium phosphate dibasic, 0.1 M imidazole, pH 8.0, 200 mM sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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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 315r / 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: 2.4→83.63 Å / Num. all: 24454 / Num. obs: 24453 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1.8 / Redundancy: 6.8 % / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 9.6
Reflection shellHighest resolution: 2.4 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.42 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.8.0049refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.888 / SU B: 8.773 / SU ML: 0.2 / Cross valid method: THROUGHOUT / ESU R: 0.322 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28691 1243 5.1 %RANDOM
Rwork0.24184 ---
obs0.24409 23158 99.94 %-
all-24417 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.631 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20.35 Å2-0 Å2
2--0.7 Å2-0 Å2
3----2.28 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2830 0 144 142 3116
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.023054
X-RAY DIFFRACTIONr_bond_other_d0.0010.022796
X-RAY DIFFRACTIONr_angle_refined_deg1.0891.9674094
X-RAY DIFFRACTIONr_angle_other_deg0.6536410
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9745352
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.56423.75160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.40215492
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8871526
X-RAY DIFFRACTIONr_chiral_restr0.0610.2410
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023440
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02760
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_it1.2144.4231408
X-RAY DIFFRACTIONr_mcbond_other1.2144.4211407
X-RAY DIFFRACTIONr_mcangle_it2.1656.6261760
X-RAY DIFFRACTIONr_mcangle_other2.1656.6291761
X-RAY DIFFRACTIONr_scbond_it1.1274.5371646
X-RAY DIFFRACTIONr_scbond_other1.1274.5371646
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0256.7182335
X-RAY DIFFRACTIONr_long_range_B_refined4.25934.6613444
X-RAY DIFFRACTIONr_long_range_B_other4.21834.5893404
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 103 -
Rwork0.333 1693 -
obs--100 %

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