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- PDB-3fmz: Crystal Structure of Retinol-Binding Protein 4 (RBP4) in complex ... -

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Basic information

Entry
Database: PDB / ID: 3fmz
TitleCrystal Structure of Retinol-Binding Protein 4 (RBP4) in complex with non-retinoid ligand
ComponentsRetinol-binding protein 4
KeywordsTRANSPORT PROTEIN / retinol binding / Disease mutation / Retinol-binding / Secreted / Sensory transduction / Transport / Vision / Vitamin A
Function / homology
Function and homology information


Retinoid metabolism disease events / urinary bladder development / embryonic retina morphogenesis in camera-type eye / retinol transport / female genitalia morphogenesis / retinol transmembrane transporter activity / embryonic organ morphogenesis / maintenance of gastrointestinal epithelium / embryonic skeletal system development / negative regulation of cardiac muscle cell proliferation ...Retinoid metabolism disease events / urinary bladder development / embryonic retina morphogenesis in camera-type eye / retinol transport / female genitalia morphogenesis / retinol transmembrane transporter activity / embryonic organ morphogenesis / maintenance of gastrointestinal epithelium / embryonic skeletal system development / negative regulation of cardiac muscle cell proliferation / eye development / heart trabecula formation / retinal binding / cardiac muscle tissue development / retinol metabolic process / retinol binding / positive regulation of immunoglobulin production / Defective visual phototransduction due to STRA6 loss of function / The canonical retinoid cycle in rods (twilight vision) / uterus development / vagina development / response to retinoic acid / Retinoid metabolism and transport / visual perception / gluconeogenesis / lung development / positive regulation of insulin secretion / glucose homeostasis / heart development / extracellular space / 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-2T1 / Retinol-binding protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å
AuthorsWang, Z. / Johnstone, S. / Walker, N.P.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Identification and Characterization of a Non-retinoid Ligand for Retinol-binding Protein 4 Which Lowers Serum Retinol-binding Protein 4 Levels in Vivo.
Authors: Motani, A. / Wang, Z. / Conn, M. / Siegler, K. / Zhang, Y. / Liu, Q. / Johnstone, S. / Xu, H. / Thibault, S. / Wang, Y. / Fan, P. / Connors, R. / Le, H. / Xu, G. / Walker, N. / Shan, B. / Coward, P.
History
DepositionDec 22, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 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

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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)50,0264
Polymers49,2412
Non-polymers7852
Water19811
1
A: Retinol-binding protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0132
Polymers24,6201
Non-polymers3921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Retinol-binding protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0132
Polymers24,6201
Non-polymers3921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.802, 84.802, 119.557
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBP4, PRO2222 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02753
#2: Chemical ChemComp-2T1 / 2-[({4-[2-(trifluoromethyl)phenyl]piperidin-1-yl}carbonyl)amino]benzoic acid


Mass: 392.372 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H19F3N2O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.19 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 6.5
Details: 0.4M Mg formate, 0.1M GndHCl, 0.1M Bis-Tris 6.5, vapor diffusion, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.999 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 14, 2007 / Details: 3X3 CCD ARRAY
RadiationMonochromator: DOUBLE-CRYSTAL, SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2.9→73.521 Å / Num. obs: 10890 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 52.465 Å2 / Rmerge(I) obs: 0.125 / Rsym value: 0.125 / Net I/σ(I): 5.773
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.9-3.063.70.4021.9601216080.402100
3.06-3.243.70.282.7548214710.28100
3.24-3.473.70.1884523014000.188100
3.47-3.743.70.1335.6489213210.133100
3.74-4.13.70.1057447812040.105100
4.1-4.593.70.0749.8404210930.074100
4.59-5.293.60.0788.935769830.078100
5.29-6.483.60.0888.228948060.088100
6.48-9.173.50.06710.222596380.06799.8
9.17-119.563.60.04313.413123660.043100

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
MOLREPphasing
RefinementResolution: 2.9→50 Å / Cor.coef. Fo:Fc: 0.875 / Cor.coef. Fo:Fc free: 0.795 / WRfactor Rfree: 0.259 / WRfactor Rwork: 0.203 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.826 / SU B: 16.978 / SU ML: 0.331 / SU Rfree: 0.445 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.445 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.286 522 4.8 %RANDOM
Rwork0.223 ---
obs0.226 10853 99.96 %-
all-10895 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 45.52 Å2 / Biso mean: 25.789 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20.22 Å20 Å2
2--0.45 Å20 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2814 0 56 11 2881
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222944
X-RAY DIFFRACTIONr_angle_refined_deg1.1481.9553988
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6935346
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.2923.846156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.32415482
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6531524
X-RAY DIFFRACTIONr_chiral_restr0.0760.2408
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212306
X-RAY DIFFRACTIONr_mcbond_it0.3291.51728
X-RAY DIFFRACTIONr_mcangle_it0.63522774
X-RAY DIFFRACTIONr_scbond_it0.7231216
X-RAY DIFFRACTIONr_scangle_it1.2844.51214
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 48 -
Rwork0.27 746 -
all-794 -
obs--100 %

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