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- PDB-7lhm: Crystal structure of Q108K:K40L:T51V:T53C:R58W:T29L:Y19W:Q4A:Q38L... -

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Basic information

Entry
Database: PDB / ID: 7lhm
TitleCrystal structure of Q108K:K40L:T51V:T53C:R58W:T29L:Y19W:Q4A:Q38L mutant of cellular retinol binding protein II complex with all-trans-retinal
ComponentsRetinol-binding protein 2
KeywordsCYTOSOLIC PROTEIN / hCRBPII / Q4A / Q38L / isomerization / retinal / all-trans-retinal / rhodopsin / bacteriorhodopsin
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 / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin
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: 1.5 Å
AuthorsEhyaei, N. / Geiger, J.H. / Borhan, B.
Funding support1items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Research Resources (NIH/NCRR)
CitationJournal: To Be Published
Title: Crystal structure of Q108K:K40L:T51V:T53C:R58W:T29L:Y19W:Q4A:Q38L mutant of cellular retinol binding protein II complex with all-trans-retinal
Authors: Ehyaei, N. / Geiger, J.H. / Borhan, B.
History
DepositionJan 25, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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)32,0208
Polymers31,1492
Non-polymers8716
Water3,081171
1
A: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0104
Polymers15,5751
Non-polymers4363
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0104
Polymers15,5751
Non-polymers4363
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.979, 36.479, 63.896
Angle α, β, γ (deg.)90.810, 93.400, 115.900
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: 15574.632 Da / Num. of mol.: 2 / Mutation: Q108K,K40L,T51V,T53C,R58W,T29L,Y19W,Q4A,Q38L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBP2, CRBP2 / Production host: Escherichia coli (E. coli) / References: UniProt: P50120
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.08 Å3/Da / Density % sol: 40.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 30% PEG 4000, 0.1 M sodium acetate, 0.1 M ammonium acetate , pH 4.6, EVAPORATION, temperature 298K
PH range: 4.0-4.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.401→32 Å / Num. obs: 42611 / % possible obs: 95.93 % / Redundancy: 4 % / Rpim(I) all: 0.05 / Rrim(I) all: 0.1 / Net I/σ(I): 13
Reflection shellResolution: 1.401→1.451 Å / Num. unique obs: 4469 / Rpim(I) all: 0.16 / Rrim(I) all: 0.3

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
Cootmodel building
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QYN

4qyn


Resolution: 1.5→31.86 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 24.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2223 2001 5.21 %
Rwork0.198 36380 -
obs0.1992 38381 95.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 60.07 Å2 / Biso mean: 29.1688 Å2 / Biso min: 14.13 Å2
Refinement stepCycle: final / Resolution: 1.5→31.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2186 0 82 172 2440
Biso mean--37.76 37.55 -
Num. residues----266
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152286
X-RAY DIFFRACTIONf_angle_d1.4823078
X-RAY DIFFRACTIONf_dihedral_angle_d23.969314
X-RAY DIFFRACTIONf_chiral_restr0.057324
X-RAY DIFFRACTIONf_plane_restr0.006382
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.540.27221150.26842374248987
1.54-1.580.27321460.24182605275195
1.58-1.630.27221440.23112563270795
1.63-1.680.22291330.22712590272395
1.68-1.740.3221410.23022632277396
1.74-1.810.26861440.22672598274296
1.81-1.890.25931360.21912610274696
1.89-1.990.22111560.20322611276796
1.99-2.110.25221360.21112639277596
2.11-2.280.23791520.20452644279697
2.28-2.510.22291540.20982596275097
2.51-2.870.24991460.20492668281498
2.87-3.610.20611550.18272650280597
3.61-31.860.1861430.17832600274396

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