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- PDB-1jyj: Crystal Structure of a Double Variant (W67L/W91H) of Recombinant ... -

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Basic information

Entry
Database: PDB / ID: 1jyj
TitleCrystal Structure of a Double Variant (W67L/W91H) of Recombinant Human Serum Retinol-binding Protein at 2.0 A Resolution
ComponentsPLASMA RETINOL-BINDING PROTEIN
KeywordsTRANSPORT PROTEIN / retinol binding protein / lipocalin family / beta barrel
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 / Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / uterus development / vagina development / positive regulation of immunoglobulin production / 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-binding protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGreene, L.H. / Chrysina, E.D. / Irons, L.I. / Papageorgiou, A.C. / Acharya, K.R. / Brew, K.
Citation
Journal: Protein Sci. / Year: 2001
Title: Role of Conserved Residues in Structure and Stability: Tryptophans of Human Serum Retinol-Binding Protein, a Model for the Lipocalin Superfamily
Authors: Greene, L.H. / Chrysina, E.D. / Irons, L.I. / Papageorgiou, A.C. / Acharya, K.R. / Brew, K.
#1: Journal: Proteins / Year: 1990
Title: Crystallographic refinement of human serum retinol-binding protein at 2 A resolution
Authors: Cowan, S.W. / Newcomer, M.E. / Jones, T.A.
#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: Zannotti, G. / Ottonello, S. / Berni, R. / Monaco, H.L.
History
DepositionSep 12, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PLASMA RETINOL-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4556
Polymers20,9951
Non-polymers4605
Water3,927218
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.762, 102.762, 72.725
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein PLASMA RETINOL-BINDING PROTEIN / PRBP


Mass: 20994.529 Da / Num. of mol.: 1 / Mutation: W67L, W91H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P02753
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 3.52 Å3/Da / Density % sol: 65.05 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 9.1
Details: Sodium Chloride, Tris/HCl buffer, beta-octyl-glucoside, pH 9.1, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.05 %beta-octylglucoside1drop
212 mg/mlprotein1drop
34.5 M1reservoirNaCl
450 mMTris-HCl1reservoirpH9.1
50.05 %beta-octylglucoside1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1.09 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.09 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 18890 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 18.8 Å2 / Rsym value: 0.102 / Net I/σ(I): 7.53
Reflection shellResolution: 2→2.07 Å / Mean I/σ(I) obs: 3.19 / Num. unique all: 1798 / Rsym value: 0.37 / % possible all: 92.7
Reflection
*PLUS
Num. measured all: 109525 / Rmerge(I) obs: 0.102
Reflection shell
*PLUS
Highest resolution: 2 Å / % possible obs: 92.7 % / Rmerge(I) obs: 0.37

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JYD

1jyd


Resolution: 2→19.66 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1659526.87 / Data cutoff high rms absF: 1659526.87 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.229 900 4.8 %RANDOM
Rwork0.205 ---
obs0.209 18890 97.8 %-
all-18890 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.44 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 22.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å21.44 Å20 Å2
2--0.94 Å20 Å2
3----1.89 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2→19.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1397 0 30 218 1645
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_improper_angle_d0.69
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.269 137 4.6 %
Rwork0.244 2851 -
obs--93.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4param.glyceroltop.glycerol
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 40 Å / Num. reflection obs: 27458 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.379

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