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- PDB-1jyd: Crystal Structure of Recombinant Human Serum Retinol-Binding Prot... -

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Basic information

Entry
Database: PDB / ID: 1jyd
TitleCrystal Structure of Recombinant Human Serum Retinol-Binding Protein at 1.7 A Resolution
ComponentsPLASMA RETINOL-BINDING PROTEIN
KeywordsTRANSPORT PROTEIN / retinol binding protein / lipocalin superfamily / beta barrel
Function / homology
Function and homology information


Retinoid metabolism disease events / urinary bladder development / vitamin A import into cell / 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 ...Retinoid metabolism disease events / urinary bladder development / vitamin A import into cell / 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 / detection of light stimulus involved in visual perception / retinal metabolic process / molecular carrier activity / eye development / retinal binding / heart trabecula formation / retinol metabolic process / cardiac muscle tissue development / retinol binding / positive regulation of immunoglobulin production / Defective visual phototransduction due to STRA6 loss of function / response to muscle activity / The canonical retinoid cycle in rods (twilight vision) / uterus development / vagina development / phototransduction, visible light / response to retinoic acid / Retinoid metabolism and transport / lung development / gluconeogenesis / response to insulin / positive regulation of insulin secretion / male gonad development / glucose homeostasis / heart development / response to ethanol / spermatogenesis / response to xenobiotic stimulus / protein-containing complex binding / protein-containing complex / extracellular space / extracellular exosome / extracellular region
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-binding protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 1.3Aug 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)21,6687
Polymers21,1161
Non-polymers5536
Water3,693205
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.336, 101.336, 71.978
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: 21115.645 Da / Num. of mol.: 1
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


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 3.37 Å3/Da / Density % sol: 63.47 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: Sodium cacodylate, sodium chloride, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
112 mg/mlprotein1drop
210 mMsodium cacodylate1drop
33.9 M1droppH6.8NaCl
420 mMsodium cacodylate1reservoir
54.5 M1reservoirpH6.8NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.9 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. obs: 28189 / % possible obs: 90.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 23.1 Å2 / Rsym value: 0.047 / Net I/σ(I): 7.68
Reflection shellResolution: 1.7→1.72 Å / Mean I/σ(I) obs: 2.59 / Num. unique all: 1163 / Rsym value: 0.405 / % possible all: 91
Reflection
*PLUS
Num. measured all: 67359 / Rmerge(I) obs: 0.047
Reflection shell
*PLUS
Highest resolution: 1.7 Å / % possible obs: 91 % / Rmerge(I) obs: 0.505

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Processing

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

1rbp


Resolution: 1.7→19.15 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2348999.04 / Data cutoff high rms absF: 2348999.04 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1380 5 %RANDOM
Rwork0.248 ---
obs0.251 28189 90.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.51 Å2 / ksol: 0.428 e/Å3
Displacement parametersBiso mean: 26.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å21.35 Å20 Å2
2--1.02 Å20 Å2
3----2.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.7→19.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1407 0 36 205 1648
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_improper_angle_d0.73
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.323 232 4.9 %
Rwork0.319 4513 -
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: 1.7 Å / Lowest resolution: 40 Å / Num. reflection obs: 27458 / % reflection Rfree: 5 % / Rfactor Rfree: 0.27
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.469
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.73

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