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- PDB-5nty: Structure of non-fluorescent human plasma RBP4 -

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Basic information

Entry
Database: PDB / ID: 5nty
TitleStructure of non-fluorescent human plasma RBP4
ComponentsRetinol-binding protein 4
KeywordsTRANSPORT PROTEIN / RBP4 / plasma retinol-binding protein / lipocalin / fatty acid / signaling protein
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 / cardiac muscle tissue development / retinal binding / retinol metabolic process / retinol binding / positive regulation of immunoglobulin production / Retinoid cycle disease events / 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 / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PALMITIC ACID / Retinol-binding protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPerduca, M. / Monaco, H.L. / Galliano, M.
CitationJournal: Biochim. Biophys. Acta / Year: 2018
Title: Human plasma retinol-binding protein (RBP4) is also a fatty acid-binding protein.
Authors: Perduca, M. / Nicolis, S. / Mannucci, B. / Galliano, M. / Monaco, H.L.
History
DepositionApr 28, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Retinol-binding protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2763
Polymers20,9841
Non-polymers2922
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-5 kcal/mol
Surface area9270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.770, 103.770, 73.940
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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


Mass: 20984.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02753
#2: Chemical ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O

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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: 3.65 Å3/Da / Density % sol: 66.31 %
Crystal growTemperature: 279 K / Method: microdialysis / Details: 4.5M NaCl, 20mM Na cacodylate, pH 6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 19780 / % possible obs: 98.5 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 7.9
Reflection shellResolution: 2→2.11 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 2.5 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1brq

1brq


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.939 / SU B: 10.31 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.133
RfactorNum. reflection% reflectionSelection details
Rfree0.23031 990 5 %RANDOM
Rwork0.17198 ---
obs0.17501 18786 98.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 55.543 Å2
Baniso -1Baniso -2Baniso -3
1--1.17 Å2-0.59 Å2-0 Å2
2---1.17 Å20 Å2
3---3.81 Å2
Refinement stepCycle: 1 / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1408 0 19 78 1505
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.021460
X-RAY DIFFRACTIONr_bond_other_d0.0050.021341
X-RAY DIFFRACTIONr_angle_refined_deg0.6051.9381970
X-RAY DIFFRACTIONr_angle_other_deg1.1363.0083081
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.0965173
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.52423.84678
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.77315241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.751512
X-RAY DIFFRACTIONr_chiral_restr0.0320.2202
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021670
X-RAY DIFFRACTIONr_gen_planes_other00.02362
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_it12.6342.936696
X-RAY DIFFRACTIONr_mcbond_other12.6252.939697
X-RAY DIFFRACTIONr_mcangle_it13.6514.396869
X-RAY DIFFRACTIONr_mcangle_other13.6554.393869
X-RAY DIFFRACTIONr_scbond_it14.5553.652764
X-RAY DIFFRACTIONr_scbond_other14.5463.653765
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other15.8695.2711102
X-RAY DIFFRACTIONr_long_range_B_refined16.55826.1531660
X-RAY DIFFRACTIONr_long_range_B_other16.62626.1761641
X-RAY DIFFRACTIONr_rigid_bond_restr20.26732801
X-RAY DIFFRACTIONr_sphericity_free30.891530
X-RAY DIFFRACTIONr_sphericity_bonded34.55752816
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 49 -
Rwork0.274 1418 -
obs--98 %
Refinement TLS params.Method: refined / Origin x: 29.8371 Å / Origin y: 19.4109 Å / Origin z: -0.7074 Å
111213212223313233
T0.2071 Å20.0541 Å2-0.035 Å2-0.2136 Å2-0.0507 Å2--0.0676 Å2
L2.1684 °20.7618 °20.0179 °2-2.1427 °2-0.0772 °2--2.1865 °2
S0.2054 Å °-0.2283 Å °-0.2156 Å °-0.2643 Å °0.0655 Å °-0.1325 Å °0.2323 Å °0.3184 Å °-0.2709 Å °

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