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- PDB-7mfx: The Crystal Structure of Q108K:K40H:T53A:R58L:Q38F:Q4F Mutant of ... -

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Basic information

Entry
Database: PDB / ID: 7mfx
TitleThe Crystal Structure of Q108K:K40H:T53A:R58L:Q38F:Q4F Mutant of HCRBPII Bound with FR1 Chromophore Showing Excited State Intermolecular Proton Transfer
ComponentsRetinol-binding protein 2
KeywordsLIPID BINDING PROTEIN / Domain Swapped Trimer / iLBP
Function / homology
Function and homology information


vitamin A metabolic process / retinoid binding / retinal binding / retinol binding / epidermis development / Retinoid metabolism and transport / fatty acid 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 domain / Lipocalin / cytosolic fatty-acid binding protein family / Calycin
Similarity search - Domain/homology
Chem-ZFJ / Retinol-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsGhanbarpour, A. / Geiger, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM101353 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: Design of Large Stokes Shift Fluorescent Proteins Based on Excited State Proton Transfer of an Engineered Photobase.
Authors: Santos, E.M. / Sheng, W. / Esmatpour Salmani, R. / Tahmasebi Nick, S. / Ghanbarpour, A. / Gholami, H. / Vasileiou, C. / Geiger, J.H. / Borhan, B.
History
DepositionApr 11, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 2.0May 18, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_src_gen / pdbx_contact_author / pdbx_distant_solvent_atoms / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_gen / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / struct_asym / struct_conn / struct_mon_prot_cis
Item: _entity.pdbx_number_of_molecules / _entity_src_gen.gene_src_common_name ..._entity.pdbx_number_of_molecules / _entity_src_gen.gene_src_common_name / _pdbx_struct_assembly_gen.asym_id_list / _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 / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_high / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine_hist.d_res_high / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_high / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.percent_reflns_obs / _reflns.B_iso_Wilson_estimate / _reflns_shell.Rmerge_I_obs / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_label_asym_id
Description: Atomic clashes
Details: side chain of LYS C 75, caused a clash and pushed the side chain of TRP D 109 out of density in the previous entry.
Provider: author / Type: Coordinate replacement
Revision 2.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)63,6009
Polymers62,2864
Non-polymers1,3145
Water3,927218
1
A: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8772
Polymers15,5711
Non-polymers3051
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8772
Polymers15,5711
Non-polymers3051
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9693
Polymers15,5711
Non-polymers3982
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8772
Polymers15,5711
Non-polymers3051
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.687, 54.515, 63.931
Angle α, β, γ (deg.)89.996, 86.630, 77.686
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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


Mass: 15571.499 Da / Num. of mol.: 4 / Mutation: Q4F, Q38F, K40H, T53A, R58L, Q108K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBP2, CRBP2
Production host: Bacterial expression vector pET-11a (others)
References: UniProt: P50120
#2: Chemical
ChemComp-ZFJ / (4aP)-N,N-diethyl-9,9-dimethyl-7-[(1E)-prop-1-en-1-yl]-9H-fluoren-2-amine


Mass: 305.456 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H27N / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2 Å3/Da / Density % sol: 38.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG4000, sodium acetate, ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97624 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 1.594→32.04 Å / Num. obs: 55438 / % possible obs: 86.8 % / Redundancy: 3.8 % / Biso Wilson estimate: 17.62 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 22.5
Reflection shellResolution: 1.594→1.651 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.12 / Num. unique obs: 5085

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2rct

2rct


Resolution: 1.59→32.04 Å / SU ML: 0.1901 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 25.6332 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2317 2003 3.62 %
Rwork0.198 53350 -
obs0.1992 55353 85.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.61 Å2
Refinement stepCycle: LAST / Resolution: 1.59→32.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4364 0 98 218 4680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00674643
X-RAY DIFFRACTIONf_angle_d0.87416297
X-RAY DIFFRACTIONf_chiral_restr0.0528669
X-RAY DIFFRACTIONf_plane_restr0.0043801
X-RAY DIFFRACTIONf_dihedral_angle_d5.97363744
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.59-1.630.35291210.24763395X-RAY DIFFRACTION76.53
1.63-1.680.27031530.22913765X-RAY DIFFRACTION85.3
1.68-1.730.25291450.22433785X-RAY DIFFRACTION85.85
1.73-1.780.28041270.23133616X-RAY DIFFRACTION81.3
1.78-1.850.30751260.22033218X-RAY DIFFRACTION72.26
1.85-1.920.21481270.21233687X-RAY DIFFRACTION83.37
1.92-2.010.25321580.20324095X-RAY DIFFRACTION91.78
2.01-2.110.24051500.20544087X-RAY DIFFRACTION92.23
2.11-2.250.2511550.2024073X-RAY DIFFRACTION91.75
2.25-2.420.23291520.20894002X-RAY DIFFRACTION90.76
2.42-2.660.22541470.20784032X-RAY DIFFRACTION90.18
2.66-3.050.26151440.20963806X-RAY DIFFRACTION85.7
3.05-3.840.20931310.17683471X-RAY DIFFRACTION78.75
3.84-32.040.19251670.17274318X-RAY DIFFRACTION96.95

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