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- PDB-5fen: Crystal structure of the Q108K:K40L:T53C mutant of human Cellular... -

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Basic information

Entry
Database: PDB / ID: 5fen
TitleCrystal structure of the Q108K:K40L:T53C mutant of human Cellular Retinol Binding Protein II in complex with All-trans-Retinal after 24 hours of incubation at 1.55 Angstrom Resolution
ComponentsRetinol-binding protein 2
KeywordsTRANSPORT PROTEIN / all-trans retinal / retinal light absorbing pigment / wavelength regulation
Function / homology
Function and homology information


vitamin A metabolic process / retinoid binding / retinal binding / retinol binding / epidermis development / fatty acid transport / Retinoid metabolism and transport / fatty acid binding / nucleus / cytosol
Similarity search - Function
Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / RETINAL / Retinol-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsNossoni, Z. / Nosrati, M. / Geiger, J.H.
CitationJournal: To Be Published
Title: Crystal structure of the Q108K:K40L:T53C mutant of human Cellular Retinol Binding Protein II in complex with All-trans-Retinal after 24 hours of incubation at 1.55 Angstrom Resolution
Authors: Nossoni, Z. / Nosrati, M. / Wang, W. / Berbasova, T. / Vasileiou, C. / Borhan, B. / Geiger, J.H.
History
DepositionDec 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Retinol-binding protein 2
B: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8566
Polymers31,1692
Non-polymers6874
Water3,765209
1
A: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9283
Polymers15,5851
Non-polymers3432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9283
Polymers15,5851
Non-polymers3432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.947, 35.890, 63.866
Angle α, β, γ (deg.)91.01, 92.23, 113.59
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Retinol-binding protein 2 / Cellular retinol-binding protein II / CRBP-II


Mass: 15584.521 Da / Num. of mol.: 2 / Mutation: Q108K, K40L, T53C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBP2, CRBP2 / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P50120
#2: Chemical ChemComp-RET / RETINAL / Retinal


Mass: 284.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28O
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.02 Å3/Da / Density % sol: 38.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 30% PEG4000, 0.1M Ammonium Acetate, 0.1 M Sodium Acetate pH 4.5
PH range: 4-4.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 32791 / % possible obs: 92.8 % / Redundancy: 3.8 % / Net I/σ(I): 32.7
Reflection shellResolution: 1.55→1.6 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.2 / % possible all: 69

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Processing

Software
NameVersionClassification
PHENIX1.7.2_869refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RCT

2rct


Resolution: 1.55→28.796 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 25.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2413 1662 5.07 %
Rwork0.1994 --
obs0.2015 32791 92.8 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.052 Å2 / ksol: 0.423 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.0776 Å20.0051 Å2-0.2072 Å2
2--0.2777 Å2-0.1214 Å2
3----0.3553 Å2
Refinement stepCycle: LAST / Resolution: 1.55→28.796 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2185 0 48 209 2442
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072300
X-RAY DIFFRACTIONf_angle_d1.1353102
X-RAY DIFFRACTIONf_dihedral_angle_d15.674856
X-RAY DIFFRACTIONf_chiral_restr0.071330
X-RAY DIFFRACTIONf_plane_restr0.011414
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.59560.32611030.28421925X-RAY DIFFRACTION69
1.5956-1.64710.34881270.2772409X-RAY DIFFRACTION85
1.6471-1.7060.32171380.26022571X-RAY DIFFRACTION92
1.706-1.77430.28351510.25162640X-RAY DIFFRACTION94
1.7743-1.8550.30921470.23662616X-RAY DIFFRACTION95
1.855-1.95280.27121430.2182677X-RAY DIFFRACTION96
1.9528-2.07510.25431500.2082661X-RAY DIFFRACTION96
2.0751-2.23530.28141370.19482714X-RAY DIFFRACTION96
2.2353-2.46010.23141410.20472715X-RAY DIFFRACTION97
2.4601-2.81580.26081390.19922724X-RAY DIFFRACTION97
2.8158-3.54660.2181330.1882764X-RAY DIFFRACTION98
3.5466-28.80070.19741530.17372713X-RAY DIFFRACTION97

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