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- PDB-7mfy: The Crystal Structure of Q108K:K40L:T51V:T53S:R58W:Y19W:A33W:L117... -

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Basic information

Entry
Database: PDB / ID: 7mfy
TitleThe Crystal Structure of Q108K:K40L:T51V:T53S:R58W:Y19W:A33W:L117E Mutant of HCRBPII Bound with LizFluor
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 / 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 / Chem-ZFG / Retinol-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 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 / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3426
Polymers15,7501
Non-polymers5935
Water3,225179
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.918, 66.617, 63.262
Angle α, β, γ (deg.)90.000, 90.981, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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


Mass: 15749.622 Da / Num. of mol.: 1 / Mutation: Y19W, A33W, K40L, T51V, T53S, R58W, Q108K, L117E
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-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-ZFG / 4-{5-[(2E)-but-2-en-2-yl]thiophen-2-yl}-N,N-dimethylaniline


Mass: 257.394 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H19NS / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 1.93 Å3/Da / Density % sol: 36.41 %
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: Mar 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.258→33.31 Å / Num. obs: 32216 / % possible obs: 99.5 % / Redundancy: 7.2 % / Biso Wilson estimate: 12.96 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 35.46
Reflection shellResolution: 1.258→1.303 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.441 / Num. unique obs: 3049 / % possible all: 97.5

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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: 1.26→33.31 Å / SU ML: 0.1027 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.225 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1808 1998 6.21 %
Rwork0.1634 30200 -
obs0.1645 32198 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.53 Å2
Refinement stepCycle: LAST / Resolution: 1.26→33.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1108 0 40 179 1327
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611190
X-RAY DIFFRACTIONf_angle_d0.83781606
X-RAY DIFFRACTIONf_chiral_restr0.0891167
X-RAY DIFFRACTIONf_plane_restr0.0047203
X-RAY DIFFRACTIONf_dihedral_angle_d9.183700
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.26-1.290.26341310.25751947X-RAY DIFFRACTION91.7
1.29-1.320.26971380.22952166X-RAY DIFFRACTION98.84
1.32-1.360.25541470.21732147X-RAY DIFFRACTION99.31
1.36-1.410.22591440.20512162X-RAY DIFFRACTION99.65
1.41-1.460.25041440.19922184X-RAY DIFFRACTION99.61
1.46-1.520.21941420.18862172X-RAY DIFFRACTION99.78
1.52-1.580.19661400.16072157X-RAY DIFFRACTION99.91
1.58-1.670.17711460.16082177X-RAY DIFFRACTION99.96
1.67-1.770.18041410.15782171X-RAY DIFFRACTION99.87
1.77-1.910.17861480.15012191X-RAY DIFFRACTION99.91
1.91-2.10.18531440.14862167X-RAY DIFFRACTION99.87
2.1-2.410.16441460.15432194X-RAY DIFFRACTION99.96
2.41-3.030.18431450.1652183X-RAY DIFFRACTION99.7
3.03-33.30.15131420.15132182X-RAY DIFFRACTION98.52
Refinement TLS params.Method: refined / Origin x: 2.79143602525 Å / Origin y: 17.7260484779 Å / Origin z: 15.4445907663 Å
111213212223313233
T0.109045197741 Å2-0.00137822249351 Å2-0.00235424723047 Å2-0.104664152114 Å2-0.00442088721195 Å2--0.111558831887 Å2
L0.471228861705 °2-0.101237328071 °20.104019057414 °2-0.412898746159 °20.0333164039966 °2--0.960462149238 °2
S-0.00248065133731 Å °0.0234789265852 Å °-0.00800309337499 Å °-0.0823703662942 Å °-0.0164508748389 Å °0.0107700792366 Å °-0.0383909958175 Å °0.0209392638549 Å °3.23700047587E-5 Å °
Refinement TLS groupSelection details: all

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