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- PDB-6vis: The Crystal Structure of Domain-Swapped Trimer Q108K:K40D:T53A:R5... -

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Basic information

Entry
Database: PDB / ID: 6vis
TitleThe Crystal Structure of Domain-Swapped Trimer Q108K:K40D:T53A:R58L:Q38F:Q4F:V62E Variant of HCRBPII
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
Retinol-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsGhanbarpour, A. / Geiger, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) 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
DepositionJan 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 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
C: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0126
Polymers46,7353
Non-polymers2763
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12400 Å2
ΔGint-66 kcal/mol
Surface area19950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.123, 101.031, 109.474
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
11THRTHRVALVAL(chain 'A' and (resid 1 through 20 or (resid 21...AA1 - 341 - 34
12LEULEULYSLYS(chain 'A' and (resid 1 through 20 or (resid 21...AA36 - 13236 - 132
23THRTHRVALVAL(chain 'B' and (resid 1 through 20 or (resid 21...BB1 - 341 - 34
24LEULEULYSLYS(chain 'B' and (resid 1 through 20 or (resid 21...BB36 - 13236 - 132
35THRTHRVALVAL(chain 'C' and (resid 1 through 25 or (resid 26...CC1 - 341 - 34
36LEULEULYSLYS(chain 'C' and (resid 1 through 25 or (resid 26...CC36 - 13236 - 132

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Components

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


Mass: 15578.421 Da / Num. of mol.: 3 / Mutation: Q108K, K40D, T53A, R58L, Q38F, Q4F, V62E
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 293 K / Method: vapor diffusion / 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: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.788→48.13 Å / Num. obs: 10793 / % possible obs: 99.24 % / Redundancy: 3.7 % / Biso Wilson estimate: 57.46 Å2 / Rmerge(I) obs: 0.148 / Rrim(I) all: 0.16 / Net I/σ(I): 17.14
Reflection shellResolution: 2.788→2.888 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.819 / Mean I/σ(I) obs: 2.11 / Num. unique obs: 1015 / Rrim(I) all: 0.886 / % possible all: 93.81

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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: 2.79→48.13 Å / SU ML: 0.5222 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.4608 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2985 1081 10.02 %
Rwork0.232 9711 -
obs0.2386 10792 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.82 Å2
Refinement stepCycle: LAST / Resolution: 2.79→48.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3233 0 18 36 3287
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00153318
X-RAY DIFFRACTIONf_angle_d0.48024470
X-RAY DIFFRACTIONf_chiral_restr0.0403480
X-RAY DIFFRACTIONf_plane_restr0.0015575
X-RAY DIFFRACTIONf_dihedral_angle_d16.34051947
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.79-2.920.46671330.33941137X-RAY DIFFRACTION94.99
2.92-3.070.42271280.2941201X-RAY DIFFRACTION100
3.07-3.260.3711420.27881184X-RAY DIFFRACTION100
3.26-3.510.35031270.26431193X-RAY DIFFRACTION99.92
3.51-3.870.2961320.21781219X-RAY DIFFRACTION100
3.87-4.420.25931310.19661221X-RAY DIFFRACTION99.93
4.42-5.570.23821380.19021244X-RAY DIFFRACTION99.86
5.57-48.130.27141500.23571312X-RAY DIFFRACTION99.52
Refinement TLS params.Method: refined / Origin x: 51.7405525202 Å / Origin y: 24.9915336269 Å / Origin z: 30.3394018303 Å
111213212223313233
T0.294789558602 Å2-0.0246442601756 Å2-0.0262707702324 Å2-0.360780359976 Å20.00666730273366 Å2--0.368695288756 Å2
L0.371080102915 °2-0.496964248072 °2-0.0340996492087 °2-0.942009183366 °2-0.32246484426 °2--0.778027458584 °2
S-0.0472244486636 Å °-0.00459608447726 Å °0.0427591484434 Å °0.164844196553 Å °0.0962842829442 Å °-0.0555172162054 Å °-0.0331927387091 Å °-0.00121247974396 Å °-0.0575846904998 Å °
Refinement TLS groupSelection details: all

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