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- PDB-1kt3: Crystal structure of bovine holo-RBP at pH 2.0 -

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Basic information

Entry
Database: PDB / ID: 1kt3
TitleCrystal structure of bovine holo-RBP at pH 2.0
ComponentsPlasma retinol-binding protein
KeywordsTRANSPORT PROTEIN / RBP / retinol binding
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 / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
RETINOL / Retinol-binding protein 4
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsCalderone, V. / Berni, R. / Zanotti, G.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: High-resolution Structures of Retinol-binding Protein in Complex with Retinol: pH-induced Protein Structural Changes in the Crystal State
Authors: Calderone, V. / Berni, R. / Zanotti, G.
#1: Journal: 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.
#2: 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.
History
DepositionJan 15, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Revision 1.4Oct 9, 2024Group: Structure summary / Category: 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)21,3822
Polymers21,0961
Non-polymers2861
Water3,495194
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.839, 50.198, 77.782
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 / RBP


Mass: 21095.654 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P18902
#2: Chemical ChemComp-RTL / RETINOL


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


Mass: 18.015 Da / Num. of mol.: 194 / 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: 1.94 Å3/Da / Density % sol: 43.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 2
Details: 50 mM Na citrate, 100 mM NaCl, pH 2.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7 / Method: vapor diffusion / Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
130 mMsodium cacodylate1reservoirpH7.
220 mMsodium acetate1reservoir
38 %(v/v)MPD1reservoir
40.5 mM1reservoirCdCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 10, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 1.399→34.246 Å / Num. all: 32419 / Num. obs: 32419 / % possible obs: 87.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 5.7
Reflection shellResolution: 1.4→1.47 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 1 / Num. unique all: 1249 / Rsym value: 0.464 / % possible all: 42.7
Reflection
*PLUS
Highest resolution: 1.39 Å / Lowest resolution: 34.3 Å / Num. measured all: 334447
Reflection shell
*PLUS
Highest resolution: 1.39 Å / % possible obs: 42.7 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 1.1

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHELXmodel building
SHELXL-97refinement
CCP4(SCALA)data scaling
SHELXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HBP

1hbp


Resolution: 1.4→34.246 Å / Num. parameters: 14484 / Num. restraintsaints: 17663 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2491 1599 5.2 %RANDOM
Rwork0.1746 ---
obs0.1753 32419 82.8 %-
all-32419 --
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1609
Refinement stepCycle: LAST / Resolution: 1.4→34.246 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1418 0 21 194 1633
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.046
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.028
X-RAY DIFFRACTIONs_zero_chiral_vol0.041
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.051
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.012
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.003
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.068
X-RAY DIFFRACTIONs_approx_iso_adps0.086
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 26941 / Num. reflection Rfree: 1347 / % reflection Rfree: 5 % / Rfactor Rfree: 0.2435 / Rfactor Rwork: 0.1421
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg3.2
X-RAY DIFFRACTIONs_plane_restr0.028
X-RAY DIFFRACTIONs_chiral_restr0.041

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