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- PDB-6wp2: The Crystal Structure of Apo Zinc-Bound Domain Swapped-Trimer Q10... -

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Basic information

Entry
Database: PDB / ID: 6wp2
TitleThe Crystal Structure of Apo Zinc-Bound Domain Swapped-Trimer Q108K:K40D:T53A:R58L:Q38F:Q4F:F57H Variant of HCRBPII
ComponentsRetinol-binding protein 2
KeywordsLIPID BINDING PROTEIN / iLBP
Function / homology
Function and homology information


vitamin A metabolic process / molecular carrier activity / 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 / Retinol-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsGhanbarpour, A. / Geiger, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Research Resources (NIH/NCRR) United States
CitationJournal: Chembiochem / Year: 2020
Title: Human Cellular Retinol Binding Protein II Forms a Domain-Swapped Trimer Representing a Novel Fold and a New Template for Protein Engineering.
Authors: Ghanbarpour, A. / Santos, E.M. / Pinger, C. / Assar, Z. / Hossaini Nasr, S. / Vasileiou, C. / Spence, D. / Borhan, B. / Geiger, J.H.
History
DepositionApr 26, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: 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
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
C: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,53015
Polymers46,6183
Non-polymers91212
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13450 Å2
ΔGint-270 kcal/mol
Surface area20170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.513, 74.451, 94.345
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 15539.413 Da / Num. of mol.: 3 / Mutation: Q108K, K40D, T53A, R58L, Q38F, Q4F, F57H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBP2, CRBP2 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P50120
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.28 Å3/Da / Density % sol: 46.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: ammonium iodide, PEG 3350

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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: Apr 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.47→50 Å / Num. obs: 15764 / % possible obs: 100 % / Redundancy: 14.1 % / Biso Wilson estimate: 49.46 Å2 / CC1/2: 0.898 / Rmerge(I) obs: 0.11 / Rrim(I) all: 0.166 / Net I/σ(I): 27
Reflection shellResolution: 2.47→2.52 Å / Rmerge(I) obs: 1.1 / Num. unique obs: 3092

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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: 2.48→47.17 Å / SU ML: 0.3458 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.2664
RfactorNum. reflection% reflection
Rfree0.3124 1569 10 %
Rwork0.2222 --
obs0.2314 15695 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 57.93 Å2
Refinement stepCycle: LAST / Resolution: 2.48→47.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3227 0 40 13 3280
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093382
X-RAY DIFFRACTIONf_angle_d1.11654567
X-RAY DIFFRACTIONf_chiral_restr0.0572492
X-RAY DIFFRACTIONf_plane_restr0.0051582
X-RAY DIFFRACTIONf_dihedral_angle_d3.77242725
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.48-2.550.40771330.2871187X-RAY DIFFRACTION92.57
2.55-2.640.42261380.29331250X-RAY DIFFRACTION99.78
2.64-2.750.41061420.28981278X-RAY DIFFRACTION99.65
2.75-2.870.42281400.28041273X-RAY DIFFRACTION99.79
2.87-3.030.33181410.23751269X-RAY DIFFRACTION99.93
3.03-3.210.35661430.23351285X-RAY DIFFRACTION99.93
3.21-3.460.31211400.23641272X-RAY DIFFRACTION100
3.46-3.810.30091440.21921291X-RAY DIFFRACTION100
3.81-4.360.26421470.19761311X-RAY DIFFRACTION99.93
4.36-5.50.27451450.18571319X-RAY DIFFRACTION99.93
5.5-47.170.29421560.21461391X-RAY DIFFRACTION99.94

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