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- PDB-1qab: The structure of human retinol binding protein with its carrier p... -

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Basic information

Entry
Database: PDB / ID: 1qab
TitleThe structure of human retinol binding protein with its carrier protein transthyretin reveals interaction with the carboxy terminus of RBP
Components
  • PROTEIN (retinol binding protein)
  • PROTEIN (transthyretin)
KeywordsTRANSPORT PROTEIN / human serum retinol binding protein / transthyretin / prealbumin
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 / Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / thyroid hormone binding / uterus development / vagina development / purine nucleobase metabolic process / Non-integrin membrane-ECM interactions / response to retinoic acid / Retinoid metabolism and transport / visual perception / gluconeogenesis / lung development / positive regulation of insulin secretion / hormone activity / azurophil granule lumen / glucose homeostasis / heart development / Amyloid fiber formation / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
Retinol binding protein/Purpurin / Lipocalin, ApoD type / Transthyretin/hydroxyisourate hydrolase domain / Lipocalin family conserved site / Transthyretin, conserved site / Transthyretin signature 2. / Transthyretin, thyroxine binding site / Transthyretin signature 1. / Transthyretin / Transthyretin/hydroxyisourate hydrolase ...Retinol binding protein/Purpurin / Lipocalin, ApoD type / Transthyretin/hydroxyisourate hydrolase domain / Lipocalin family conserved site / Transthyretin, conserved site / Transthyretin signature 2. / Transthyretin, thyroxine binding site / Transthyretin signature 1. / Transthyretin / Transthyretin/hydroxyisourate hydrolase / Transthyretin/hydroxyisourate hydrolase domain / Transthyretin/hydroxyisourate hydrolase domain superfamily / HIUase/Transthyretin family / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Lipocalin signature. / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
RETINOL / Retinol-binding protein 4 / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.2 Å
AuthorsNaylor, H.M. / Newcomer, M.E.
CitationJournal: Biochemistry / Year: 1999
Title: The structure of human retinol-binding protein (RBP) with its carrier protein transthyretin reveals an interaction with the carboxy terminus of RBP.
Authors: Naylor, H.M. / Newcomer, M.E.
History
DepositionFeb 3, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: PROTEIN (transthyretin)
B: PROTEIN (transthyretin)
C: PROTEIN (transthyretin)
D: PROTEIN (transthyretin)
E: PROTEIN (retinol binding protein)
F: PROTEIN (retinol binding protein)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,5548
Polymers95,9816
Non-polymers5732
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10970 Å2
ΔGint-68 kcal/mol
Surface area37090 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)140.23, 140.23, 124.08
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number92
Cell settingtetragonal
Space group name H-MP41212

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Components

#1: Protein
PROTEIN (transthyretin) / PREALBUMIN


Mass: 13776.376 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02766
#2: Protein PROTEIN (retinol binding protein) / RBP


Mass: 20437.863 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02753
#3: Chemical ChemComp-RTL / RETINOL


Mass: 286.452 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H30O

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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: 3.2 Å3/Da / Density % sol: 61.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1Hepes11
2Li2SO411
Crystal grow
*PLUS
PH range low: 8 / PH range high: 7.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
117 mg/mlprotein1drop
21.8 M1reservoirLi2SO4
340 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.914
DetectorType: ADSC / Detector: CCD / Date: May 15, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.914 Å / Relative weight: 1
ReflectionHighest resolution: 3.2 Å / Num. obs: 26640 / % possible obs: 99.9 % / Observed criterion σ(I): 4.4 / Redundancy: 12.4 % / Biso Wilson estimate: 51.4 Å2 / Rmerge(I) obs: 0.117
Reflection
*PLUS
Num. measured all: 331570

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.4refinement
RefinementResolution: 3.2→6.2 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 10.1 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(I): 2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflectionSelection details
Rfree0.403 508 RANDOM
Rwork0.278 --
obs-11303 -
Displacement parametersBiso mean: 51.4 Å2
Refinement stepCycle: LAST / Resolution: 3.2→6.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6412 0 42 0 6454
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.91
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 3.2→3.32 Å / Total num. of bins used: 8 /
RfactorNum. reflection
Rfree0.423 67
Rwork0.325 1368
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2R
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.278
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 51.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg28.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.91
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shell
*PLUS
Rfactor Rfree: 0.423 / Rfactor Rwork: 0.325

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