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- PDB-1iiu: Chicken plasma retinol-binding protein (RBP) -

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Basic information

Entry
Database: PDB / ID: 1iiu
TitleChicken plasma retinol-binding protein (RBP)
Componentsplasma retinol-binding protein
KeywordsTRANSPORT PROTEIN / RBP / retinol
Function / homology
Function and homology information


yolk plasma / The canonical retinoid cycle in rods (twilight vision) / Retinoid metabolism and transport / oocyte growth / yolk / retinol transport / retinol transmembrane transporter activity / maintenance of gastrointestinal epithelium / eye development / retinal binding ...yolk plasma / The canonical retinoid cycle in rods (twilight vision) / Retinoid metabolism and transport / oocyte growth / yolk / retinol transport / retinol transmembrane transporter activity / maintenance of gastrointestinal epithelium / eye development / retinal binding / response to vitamin A / retinol metabolic process / clathrin-coated vesicle / retinol binding / response to retinoic acid / gluconeogenesis / response to virus / positive regulation of insulin secretion / response to estrogen / glucose homeostasis / protein-containing complex assembly / protein domain specific binding / signaling receptor binding / extracellular space / extracellular exosome
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
: / RETINOL / Retinol-binding protein 4
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsZanotti, G. / Calderone, V. / Berni, R.
Citation
Journal: BIOCHIM.BIOPHYS.ACTA / Year: 2001
Title: Structure of Chicken plasma retinol-binding protein
Authors: Zanotti, G. / Calderone, V. / Beda, M. / Malpeli, G. / Folli, C. / Berni, R.
#1: Journal: J.Mol.Biol. / Year: 2001
Title: Crystal Structure of the Trigonal Form of Human Plasma Retinol-binding Protein at 2.5 A Resolution
Authors: Zanotti, G. / Ottonello, S. / Berni, R. / Monaco, H.L.
#2: Journal: Eur.J.Biochem. / Year: 1990
Title: The bovine plasma retinol-binding protein. Amino acid sequence, interaction with transthyretin, crystallization and preliminary X-ray data.
Authors: Berni, R. / Stoppini, M. / Zapponi, M.C. / Meloni, M.L. / Monaco, H.L. / Zanotti, G.
#3: Journal: J.Biol.Chem. / Year: 1993
Title: Crystal structure of liganded and unliganded forms of bovine plasma retinol-binding protein
Authors: Zanotti, G. / Berni, R. / Monaco, H.L.
#4: Journal: Proteins / Year: 1990
Title: Crystallographic Refinement of Human Serum Retinol Binding Protein at 2 Angstroms Resolution
Authors: Cowan, S.W. / Newcomer, M.E. / Jones, T.A.
History
DepositionApr 24, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: plasma retinol-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5043
Polymers20,1061
Non-polymers3992
Water1,71195
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.064, 53.560, 73.414
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein plasma retinol-binding protein / PRBP


Mass: 20105.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P41263
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-RTL / RETINOL


Mass: 286.452 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H30O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.25 Å3/Da / Density % sol: 45.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
28 %(v/v)MPD1reservoir
38 mMcadmium acetate1reservoir
420 mMsodium acetate1reservoir
540 mMsodium cacodylate1reservoirpH6.6

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER / Wavelength: 1.5418
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 22515 / % possible obs: 82 % / Observed criterion σ(F): 1 / Biso Wilson estimate: 10.9 Å2 / Rsym value: 0.15
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 6664 / % possible obs: 87.8 % / Num. measured all: 22515 / Rmerge(I) obs: 0.12
Reflection shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.66 Å / % possible obs: 68 % / Num. unique obs: 680 / Rmerge(I) obs: 0.32

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Processing

Software
NameVersionClassification
SAINTdata scaling
SAINTdata reduction
AMoREphasing
CNX2000.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→30.28 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 282522.35 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.266 438 7.5 %RANDOM
Rwork0.211 ---
obs-5851 87.8 %-
Solvent computationSolvent model: flat model / Bsol: 36.8295 Å2 / ksol: 0.289072 e/Å3
Displacement parametersBiso mean: 21.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å20 Å20 Å2
2--0.13 Å20 Å2
3---0.55 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 2.5→30.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1406 0 22 111 1539
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.021
X-RAY DIFFRACTIONc_angle_deg2.7
X-RAY DIFFRACTIONc_dihedral_angle_d25.6
X-RAY DIFFRACTIONc_improper_angle_d1.84
X-RAY DIFFRACTIONc_mcbond_it1.411.5
X-RAY DIFFRACTIONc_mcangle_it2.42
X-RAY DIFFRACTIONc_scbond_it1.972
X-RAY DIFFRACTIONc_scangle_it2.972.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.045 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.337 55 7.5 %
Rwork0.311 680 -
obs--67.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM
X-RAY DIFFRACTION4RETINOL.PAR
Software
*PLUS
Name: CNX / Version: 2000.1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 7.5 % / Rfactor obs: 0.21 / Rfactor Rfree: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 21.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_angle_deg2.8
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.84
X-RAY DIFFRACTIONc_mcbond_it1.411.5
X-RAY DIFFRACTIONc_scbond_it1.972
X-RAY DIFFRACTIONc_mcangle_it2.42
X-RAY DIFFRACTIONc_scangle_it2.972.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.337 / % reflection Rfree: 7.5 % / Rfactor Rwork: 0.311

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