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- PDB-6wnf: The Crystal Structure of Apo Domain-Swapped Dimer Q108K:K40D:T53A... -

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Basic information

Entry
Database: PDB / ID: 6wnf
TitleThe Crystal Structure of Apo Domain-Swapped Dimer 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: 1.67 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 22, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,80911
Polymers31,0792
Non-polymers7309
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9140 Å2
ΔGint-43 kcal/mol
Surface area13780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.089, 63.849, 72.827
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

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
11THRTHRILEILE(chain 'A' and (resid 1 through 42 or resid 44...AA1 - 421 - 42
12GLNGLNLYSLYS(chain 'A' and (resid 1 through 42 or resid 44...AA44 - 7544 - 75
13LEULEUGLUGLU(chain 'A' and (resid 1 through 42 or resid 44...AA77 - 8977 - 89
14VALVALVALVAL(chain 'A' and (resid 1 through 42 or resid 44...AA9292
15VALVALLYSLYS(chain 'A' and (resid 1 through 42 or resid 44...AA94 - 10794 - 107
16TRPTRPLYSLYS(chain 'A' and (resid 1 through 42 or resid 44...AA109 - 114109 - 114
17TYRTYRPHEPHE(chain 'A' and (resid 1 through 42 or resid 44...AA116 - 130116 - 130
18LYSLYSLYSLYS(chain 'A' and (resid 1 through 42 or resid 44...AA133133
29THRTHRILEILE(chain 'B' and (resid 1 through 42 or resid 44...BB1 - 421 - 42
210GLNGLNLYSLYS(chain 'B' and (resid 1 through 42 or resid 44...BB44 - 7544 - 75
211LEULEUGLUGLU(chain 'B' and (resid 1 through 42 or resid 44...BB77 - 8977 - 89
212VALVALVALVAL(chain 'B' and (resid 1 through 42 or resid 44...BB9292
213VALVALLYSLYS(chain 'B' and (resid 1 through 42 or resid 44...BB94 - 10794 - 107
214TRPTRPLYSLYS(chain 'B' and (resid 1 through 42 or resid 44...BB109 - 114109 - 114
215TYRTYRPHEPHE(chain 'B' and (resid 1 through 42 or resid 44...BB116 - 130116 - 130
216LYSLYSLYSLYS(chain 'B' and (resid 1 through 42 or resid 44...BB133133

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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.: 2 / 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: Bacterial expression vector pBEN1-SGC (others)
References: UniProt: P50120
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.25 Å3/Da / Density % sol: 45.27 %
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-D / Wavelength: 0.97872 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.67→50 Å / Num. obs: 31490 / % possible obs: 100 % / Redundancy: 14.6 % / Biso Wilson estimate: 23.5 Å2 / Rmerge(I) obs: 0.087 / Rrim(I) all: 0.09 / Net I/σ(I): 43.84
Reflection shellResolution: 1.67→1.7 Å / Redundancy: 14.3 % / Rmerge(I) obs: 1.238 / Num. unique obs: 3092 / % possible all: 100

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Processing

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

2rct


Resolution: 1.67→46.35 Å / SU ML: 0.2324 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.2972 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2696 1998 6.06 %
Rwork0.2393 30947 -
obs0.2411 32945 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.52 Å2
Refinement stepCycle: LAST / Resolution: 1.67→46.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2147 0 48 132 2327
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062286
X-RAY DIFFRACTIONf_angle_d0.823089
X-RAY DIFFRACTIONf_chiral_restr0.0529334
X-RAY DIFFRACTIONf_plane_restr0.0043396
X-RAY DIFFRACTIONf_dihedral_angle_d19.84171352
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.710.3861410.37412136X-RAY DIFFRACTION98.66
1.71-1.760.38731390.34932191X-RAY DIFFRACTION99.83
1.76-1.810.33181410.32892189X-RAY DIFFRACTION99.79
1.81-1.870.33441380.30492201X-RAY DIFFRACTION99.87
1.87-1.940.35171430.28832193X-RAY DIFFRACTION99.83
1.94-2.010.33731470.29732167X-RAY DIFFRACTION99.7
2.01-2.110.28591390.26332193X-RAY DIFFRACTION99.96
2.11-2.220.25551460.25912194X-RAY DIFFRACTION99.87
2.22-2.360.30231410.25622210X-RAY DIFFRACTION99.7
2.36-2.540.31021440.24632212X-RAY DIFFRACTION99.83
2.54-2.790.26761370.24932239X-RAY DIFFRACTION99.92
2.79-3.20.28741460.22162239X-RAY DIFFRACTION99.96
3.2-4.030.22781430.19552273X-RAY DIFFRACTION99.88
4.03-46.350.21071530.20252310X-RAY DIFFRACTION97.2
Refinement TLS params.Method: refined / Origin x: -45.2761222384 Å / Origin y: -31.9802297987 Å / Origin z: 2.51152518496 Å
111213212223313233
T0.235043520193 Å2-0.0275388437681 Å20.0111985167849 Å2-0.196809727252 Å2-0.0203663846553 Å2--0.145160168432 Å2
L2.23247159351 °2-0.566542185655 °2-0.0920329239711 °2-1.4076751195 °2-0.0471316846645 °2---0.0757158283511 °2
S-0.024924580948 Å °-0.0788525898421 Å °-0.143680032188 Å °-0.334539639494 Å °0.0693789027336 Å °-0.0783004087438 Å °-0.00243221557195 Å °0.0565566249172 Å °-0.0457286670121 Å °
Refinement TLS groupSelection details: all

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