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- PDB-7mfz: The Crystal Structure of Domain-Swapped Trimer Q108K:K40D:T53A:R5... -

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Basic information

Entry
Database: PDB / ID: 7mfz
TitleThe Crystal Structure of Domain-Swapped Trimer Q108K:K40D:T53A:R58L:Q38F:Q4F Mutant of HCRBPII Bound with LizFluor3 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
ACETATE ION / Chem-ZFP / Retinol-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 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 12, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Oct 9, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)47,75610
Polymers46,6453
Non-polymers1,1107
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13000 Å2
ΔGint-68 kcal/mol
Surface area19600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.932, 102.410, 108.478
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRLEULEU(chain 'A' and (resid 1 through 36 or resid 38...AA1 - 361 - 36
12PHEPHETHRTHR(chain 'A' and (resid 1 through 36 or resid 38...AA38 - 3938 - 39
13VALVALGLNGLN(chain 'A' and (resid 1 through 36 or resid 38...AA41 - 12441 - 124
14CYSCYSLYSLYS(chain 'A' and (resid 1 through 36 or resid 38...AA126 - 133126 - 133
21THRTHRLEULEU(chain 'B' and (resid 1 through 36 or resid 38...BB1 - 361 - 36
22PHEPHETHRTHR(chain 'B' and (resid 1 through 36 or resid 38...BB38 - 3938 - 39
23VALVALGLNGLN(chain 'B' and (resid 1 through 36 or resid 38...BB41 - 12441 - 124
24CYSCYSLYSLYS(chain 'B' and (resid 1 through 36 or resid 38...BB126 - 133126 - 133
31THRTHRLEULEU(chain 'C' and (resid 1 through 36 or resid 38...CC1 - 361 - 36
32PHEPHETHRTHR(chain 'C' and (resid 1 through 36 or resid 38...CC38 - 3938 - 39
33VALVALGLNGLN(chain 'C' and (resid 1 through 36 or resid 38...CC41 - 12441 - 124
34CYSCYSLYSLYS(chain 'C' and (resid 1 through 36 or resid 38...CC126 - 133126 - 133

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Components

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


Mass: 15548.438 Da / Num. of mol.: 3 / Mutation: Q4F, Q38F, K40D, 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 pBEN1-SGC (others)
References: UniProt: P50120
#2: Chemical ChemComp-ZFP / 1-(4-{5-[(2E)-but-2-en-2-yl]thiophen-2-yl}phenyl)azetidine


Mass: 269.404 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H19NS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#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.: 77 / 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: 2.2 Å3/Da / Density % sol: 44.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 4000, 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-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.49→34.96 Å / Num. obs: 15016 / % possible obs: 99.51 % / Redundancy: 8.5 % / Biso Wilson estimate: 49.99 Å2 / Rrim(I) all: 0.149 / Net I/σ(I): 18.88
Reflection shellResolution: 2.49→2.579 Å / Redundancy: 8.5 % / Mean I/σ(I) obs: 1.75 / Num. unique obs: 1406 / Rrim(I) all: 1.537 / % possible all: 96.04

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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: 2.49→34.96 Å / SU ML: 0.4135 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.7392 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2836 1496 9.96 %
Rwork0.2058 13520 -
obs0.2136 15016 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.86 Å2
Refinement stepCycle: LAST / Resolution: 2.49→34.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3279 0 68 77 3424
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813426
X-RAY DIFFRACTIONf_angle_d1.18934615
X-RAY DIFFRACTIONf_chiral_restr0.063488
X-RAY DIFFRACTIONf_plane_restr0.0066593
X-RAY DIFFRACTIONf_dihedral_angle_d14.33612000
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.49-2.570.40411310.29661142X-RAY DIFFRACTION95.43
2.57-2.660.38441350.27451204X-RAY DIFFRACTION100
2.66-2.770.38461240.26691214X-RAY DIFFRACTION100
2.77-2.890.36181450.25971201X-RAY DIFFRACTION99.93
2.89-3.050.35031270.23261237X-RAY DIFFRACTION100
3.05-3.240.26971340.23331202X-RAY DIFFRACTION100
3.24-3.490.30421460.21341217X-RAY DIFFRACTION99.93
3.49-3.840.26151310.19111244X-RAY DIFFRACTION100
3.84-4.390.22291430.17111241X-RAY DIFFRACTION99.93
4.39-5.530.24521330.17361273X-RAY DIFFRACTION99.86
5.53-34.960.29011470.20111345X-RAY DIFFRACTION99.87

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