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- PDB-1aqb: RETINOL-BINDING PROTEIN (RBP) FROM PIG PLASMA -

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Basic information

Entry
Database: PDB / ID: 1aqb
TitleRETINOL-BINDING PROTEIN (RBP) FROM PIG PLASMA
ComponentsRETINOL-BINDING PROTEIN
KeywordsRETINOL TRANSPORT / RETINOIDS / VITAMIN A / CADMIUM ION
Function / homology
Function and homology information


retinol transport / retinol transmembrane transporter activity / retinal binding / retinol binding / extracellular space
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 speciesSus scrofa domestica (domestic pig)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsZanotti, G. / Panzalorto, M. / Marcato, A. / Malpeli, G. / Folli, C. / Berni, R.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Structure of pig plasma retinol-binding protein at 1.65 A resolution.
Authors: Zanotti, G. / Panzalorto, M. / Marcato, A. / Malpeli, G. / Folli, C. / Berni, R.
#1: 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.
#2: Journal: J.Mol.Biol. / Year: 1993
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.
History
DepositionJul 28, 1997Processing site: BNL
Revision 1.0Jan 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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 1.4Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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.ptnr1_symmetry / _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.ptnr3_symmetry / _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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5833
Polymers21,1841
Non-polymers3992
Water2,234124
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.810, 53.137, 72.966
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 RETINOL-BINDING PROTEIN / RBP


Mass: 21183.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domestica (domestic pig) / Cellular location: PLASMA / Species: Sus scrofa / Strain: domestica / References: UniProt: P27485
#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.: 124 / 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: 2.1 Å3/Da / Density % sol: 41 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6.8
Details: SITTING DROP VAPOR DIFFUSION METHOD, AT A FINAL PROTEIN CONCENTRATION OF 8 MG/ML IN THE PRESENCE OF 8% 2-METHYL-2,4-PENTANEDIOL, 3 MM CADMIUM ACETATE, 0.1 M TRIS-ACETATE, PH=6.8, vapor diffusion - sitting drop
Crystal grow
*PLUS
Temperature: 277 K / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 mg/mlprotein1drop
28 %(v/v)MPD1reservoir
33 mMcadmium acetate1reservoir
40.1 MTris-acetate1reservoir

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE M18X / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Sep 1, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→55 Å / Num. obs: 20127 / % possible obs: 91 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 8
Reflection shellResolution: 1.65→1.72 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 4 / Rsym value: 0.19 / % possible all: 56
Reflection
*PLUS
Num. measured all: 84968

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Processing

Software
NameClassification
SAINTdata scaling
SAINTdata reduction
SHELXL-93model building
X-PLORmodel building
SHELXL-93refinement
X-PLORrefinement
SHELXL-93phasing
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HBP

1hbp


Resolution: 1.65→55 Å / Num. parameters: 6308 / Num. restraintsaints: 5678 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: NO RESTRAINTS WERE APPLIED ON THE PLANARITY OF RETINOL MOLECULE
RfactorNum. reflection% reflectionSelection details
Rfree0.2372 1001 5 %EVERY 20TH REFLECTION
all0.1942 20090 --
obs0.1844 -90.5 %-
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 3 / Occupancy sum hydrogen: 5272 / Occupancy sum non hydrogen: 6284
Refinement stepCycle: LAST / Resolution: 1.65→55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1428 0 22 124 1574
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.03
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0.03
X-RAY DIFFRACTIONs_from_restr_planes0.2
X-RAY DIFFRACTIONs_zero_chiral_vol0.2
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.2
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.01
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0
X-RAY DIFFRACTIONs_approx_iso_adps0

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