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- PDB-1rbp: CRYSTALLOGRAPHIC REFINEMENT OF HUMAN SERUM RETINOL BINDING PROTEI... -

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Basic information

Entry
Database: PDB / ID: 1rbp
TitleCRYSTALLOGRAPHIC REFINEMENT OF HUMAN SERUM RETINOL BINDING PROTEIN AT 2 ANGSTROMS RESOLUTION
ComponentsPLASMA RETINOL-BINDING PROTEIN PRECURSOR
KeywordsRETINOL TRANSPORT
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
RETINOL / Retinol-binding protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsJones, T.A. / Newcomer, M.E. / Cowan, S.W.
CitationJournal: Proteins / Year: 1990
Title: Crystallographic refinement of human serum retinol binding protein at 2A resolution.
Authors: Cowan, S.W. / Newcomer, M.E. / Jones, T.A.
History
DepositionApr 2, 1990Processing site: BNL
Revision 1.0Jul 15, 1991Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Remark 700SHEET THE SHEET PRESENTED AS *A* ON SHEET RECORDS BELOW IS ACTUALLY AN EIGHT-STRANDED BETA-BARREL. ...SHEET THE SHEET PRESENTED AS *A* ON SHEET RECORDS BELOW IS ACTUALLY AN EIGHT-STRANDED BETA-BARREL. THIS IS REPRESENTED BY A NINE-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PLASMA RETINOL-BINDING PROTEIN PRECURSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2712
Polymers20,9841
Non-polymers2861
Water2,756153
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.700, 48.700, 76.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: RESIDUES 1 AND 2 HAVE LITTLE OR NO DENSITY AND, THEREFORE, ARE NOT WELL DEFINED BY THE COORDINATES IN THIS ENTRY. RESIDUES 65 AND 66, WHICH ARE LOCATED IN A LOOP AT THE SURFACE OF THE MOLECULE, ...1: RESIDUES 1 AND 2 HAVE LITTLE OR NO DENSITY AND, THEREFORE, ARE NOT WELL DEFINED BY THE COORDINATES IN THIS ENTRY. RESIDUES 65 AND 66, WHICH ARE LOCATED IN A LOOP AT THE SURFACE OF THE MOLECULE, ALSO HAVE POOR DENSITY. NO DENSITY WAS OBSERVED FOR THE C-TERMINAL RESIDUES 175 - 182.

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Components

#1: Protein PLASMA RETINOL-BINDING PROTEIN PRECURSOR


Mass: 20984.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P02753
#2: Chemical ChemComp-RTL / RETINOL / Retinol


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


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.35 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
30.5-1.2 M1reservoirKCl
575 mM1reservoirNaCl
2PEG60001reservoir
4tris-(hydroxymethyl)aminomethane1reservoir
11reservoirCdCl2

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2 Å / % possible obs: 85 % / Num. measured all: 11088 / Rmerge(I) obs: 0.09

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 2→8 Å / Rfactor Rwork: 0.181
Details: RESIDUES 1 AND 2 HAVE LITTLE OR NO DENSITY AND, THEREFORE, ARE NOT WELL DEFINED BY THE COORDINATES IN THIS ENTRY. RESIDUES 65 AND 66, WHICH ARE LOCATED IN A LOOP AT THE SURFACE OF THE ...Details: RESIDUES 1 AND 2 HAVE LITTLE OR NO DENSITY AND, THEREFORE, ARE NOT WELL DEFINED BY THE COORDINATES IN THIS ENTRY. RESIDUES 65 AND 66, WHICH ARE LOCATED IN A LOOP AT THE SURFACE OF THE MOLECULE, ALSO HAVE POOR DENSITY.
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1408 0 21 153 1582
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg3.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 8 Å / Rfactor obs: 0.181
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.1

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