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

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Basic information

Entry
Database: PDB / ID: 7lhj
TitleCrystal structure of Q108K:K40L:T51V:T53C:R58W:T29L:Y19W:Q4A mutant of cellular retinol binding protein II complex with 15-cis-retinal
ComponentsRetinol-binding protein 2
KeywordsTRANSPORT PROTEIN / hCRBPII / Q4A / isomerization / retinal / cis / trans / rhodopsin / bacteriorhodopsin / CYTOSOLIC PROTEIN
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: 1.26 Å
AuthorsEhyaei, N. / Geiger, J.H. / Borhan, B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Research Resources (NIH/NCRR) United States
CitationJournal: To Be Published
Title: Crystal structure of Q108K:K40L:T51V:T53C:R58W:T29L:Y19W:Q4A mutant of cellular retinol binding protein II complex with 15cis- retinal
Authors: Ehyaei, N. / Geiger, J.H. / Borhan, B.
History
DepositionJan 25, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 2.0Apr 14, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Experimental preparation / Non-polymer description / Other / Refinement description / Structure summary
Category: atom_site / cell ...atom_site / cell / chem_comp / diffrn / entity / exptl_crystal_grow / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / software / struct_asym / struct_conn / struct_sheet_range / struct_site / struct_site_gen / symmetry
Item: _cell.angle_alpha / _cell.angle_beta ..._cell.angle_alpha / _cell.angle_beta / _cell.angle_gamma / _cell.volume / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _diffrn.ambient_temp / _exptl_crystal_grow.pdbx_details / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.overall_SU_ML / _refine.pdbx_ls_cross_valid_method / _refine.pdbx_overall_phase_error / _refine.pdbx_stereochemistry_target_values / _refine_hist.cycle_id / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_residues_total / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_restr.type / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_free_error / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.number_reflns_all / _refine_ls_shell.pdbx_total_number_of_bins_used / _refine_ls_shell.percent_reflns_obs / _reflns.B_iso_Wilson_estimate / _struct_asym.entity_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_value_order / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _symmetry.space_group_name_Hall
Description: Ligand identity
Details: One acetate initially modeled in the binding pocket was determined to be ordered water molecules.
Provider: author / Type: Coordinate replacement
Revision 2.1Oct 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)31,9587
Polymers31,1792
Non-polymers7795
Water4,936274
1
A: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0254
Polymers15,5901
Non-polymers4363
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9333
Polymers15,5901
Non-polymers3432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.923, 36.038, 64.026
Angle α, β, γ (deg.)86.203, 86.555, 65.059
Int Tables number1
Space group name H-MP1
Space group name HallP1

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Components

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


Mass: 15589.603 Da / Num. of mol.: 2 / Mutation: Q4A, Y19W, T29L, K40L, T51V, T53C, R58W, Q108K
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


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


Mass: 284.436 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C20H28O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 2.07 Å3/Da / Density % sol: 40.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
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: 1.26→29.48 Å / Num. obs: 58186 / % possible obs: 88.28 % / Redundancy: 3.1 % / Biso Wilson estimate: 13.07 Å2 / Rpim(I) all: 0.06 / Rrim(I) all: 0.107 / Net I/σ(I): 13
Reflection shellResolution: 1.26→1.31 Å / Mean I/σ(I) obs: 4.33 / Num. unique obs: 1254 / Rpim(I) all: 0.163 / Rrim(I) all: 0.291 / % possible all: 88.93

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549refinement
HKL-2000data scaling
PHENIXphasing
PDB_EXTRACT3.27data extraction
Cootmodel building
HKL-2000data processing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QYN

4qyn


Resolution: 1.26→22.32 Å / SU ML: 0.1377 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 21.7323
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2171 1960 3.37 %
Rwork0.1886 56193 -
obs0.1895 58153 86.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.49 Å2
Refinement stepCycle: LAST / Resolution: 1.26→22.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2184 0 54 274 2512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00532279
X-RAY DIFFRACTIONf_angle_d0.74643071
X-RAY DIFFRACTIONf_chiral_restr0.0771322
X-RAY DIFFRACTIONf_plane_restr0.0038392
X-RAY DIFFRACTIONf_dihedral_angle_d14.5266824
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.26-1.290.26911410.21973756X-RAY DIFFRACTION79.91
1.29-1.330.23571410.21893993X-RAY DIFFRACTION86.63
1.33-1.370.23691390.21743988X-RAY DIFFRACTION86.34
1.37-1.410.26341320.21184039X-RAY DIFFRACTION85.72
1.41-1.460.22151500.20113974X-RAY DIFFRACTION85.7
1.46-1.520.23451360.20453948X-RAY DIFFRACTION84.55
1.52-1.590.20681240.19313609X-RAY DIFFRACTION78.16
1.59-1.670.20331470.19073859X-RAY DIFFRACTION83.27
1.67-1.780.23041510.18874250X-RAY DIFFRACTION91.23
1.78-1.910.22511310.18714256X-RAY DIFFRACTION90.4
1.91-2.110.22971460.18454188X-RAY DIFFRACTION90.14
2.11-2.410.21791440.18784093X-RAY DIFFRACTION88
2.41-3.040.21911240.19633695X-RAY DIFFRACTION79.33
3.04-22.320.19811540.17474545X-RAY DIFFRACTION97.83

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