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- PDB-6wp1: The Crystal Structure of Apo Domain-Swapped Trimer Q108K:K40L:T51... -

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Basic information

Entry
Database: PDB / ID: 6wp1
TitleThe Crystal Structure of Apo Domain-Swapped Trimer Q108K:K40L:T51K 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
ACETATE ION / Retinol-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsGhanbarpour, A. / Geiger, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM101353 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 / 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
D: Retinol-binding protein 2
E: Retinol-binding protein 2
F: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,69519
Polymers93,6636
Non-polymers1,03213
Water68538
1
A: Retinol-binding protein 2
E: Retinol-binding protein 2
F: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9835
Polymers46,8323
Non-polymers1512
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10820 Å2
ΔGint-62 kcal/mol
Surface area20530 Å2
MethodPISA
2
B: Retinol-binding protein 2
C: Retinol-binding protein 2
D: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,71314
Polymers46,8323
Non-polymers88111
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14270 Å2
ΔGint-64 kcal/mol
Surface area20110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.831, 78.466, 178.887
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
31
41
51
61

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
11THRTHRSERSER(chain 'A' and (resid 1 or (resid 2 and (name...AA1 - 551 - 55
12PHEPHELYSLYS(chain 'A' and (resid 1 or (resid 2 and (name...AA57 - 13257 - 132
23THRTHRSERSER(chain 'B' and (resid 1 or (resid 2 and (name...BB1 - 551 - 55
24PHEPHELYSLYS(chain 'B' and (resid 1 or (resid 2 and (name...BB57 - 13257 - 132
35THRTHRSERSER(chain 'C' and (resid 1 or (resid 2 and (name...CC1 - 551 - 55
36PHEPHELYSLYS(chain 'C' and (resid 1 or (resid 2 and (name...CC57 - 13257 - 132
47THRTHRSERSER(chain 'D' and (resid 1 or (resid 2 and (name...DD1 - 551 - 55
48PHEPHELYSLYS(chain 'D' and (resid 1 or (resid 2 and (name...DD57 - 13257 - 132
59THRTHRSERSER(chain 'E' and (resid 1 or (resid 2 and (name...EE1 - 551 - 55
510PHEPHELYSLYS(chain 'E' and (resid 1 or (resid 2 and (name...EE57 - 13257 - 132
611THRTHRSERSER(chain 'F' and (resid 1 through 34 or (resid 35...FF1 - 551 - 55
612PHEPHELYSLYS(chain 'F' and (resid 1 through 34 or (resid 35...FF57 - 13257 - 132

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Components

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


Mass: 15610.558 Da / Num. of mol.: 6 / Mutation: Q108K, K40L, T51K
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.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.62 Å3/Da / Density % sol: 52.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG4000, 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 MX300HE / Detector: CCD / Date: Jun 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.986→47.48 Å / Num. obs: 20546 / % possible obs: 100 % / Redundancy: 13.6 % / Biso Wilson estimate: 44.76 Å2 / Rrim(I) all: 0.292 / Net I/σ(I): 13.1
Reflection shellResolution: 2.986→3.03 Å / Redundancy: 11.7 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1916 / Rrim(I) all: 1.18

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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: 2.99→47.48 Å / SU ML: 0.4401 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.5205 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.302 2000 9.74 %
Rwork0.2466 18541 -
obs0.252 20541 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.1 Å2
Refinement stepCycle: LAST / Resolution: 2.99→47.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6202 0 68 39 6309
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00196354
X-RAY DIFFRACTIONf_angle_d0.57788563
X-RAY DIFFRACTIONf_chiral_restr0.0441955
X-RAY DIFFRACTIONf_plane_restr0.0021101
X-RAY DIFFRACTIONf_dihedral_angle_d14.80133741
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.99-3.060.40211300.32891210X-RAY DIFFRACTION92.22
3.06-3.140.31521420.28951317X-RAY DIFFRACTION99.86
3.14-3.240.36141390.27871283X-RAY DIFFRACTION99.93
3.24-3.340.38631420.27181322X-RAY DIFFRACTION100
3.34-3.460.311400.27251298X-RAY DIFFRACTION99.93
3.46-3.60.28451430.25471314X-RAY DIFFRACTION99.86
3.6-3.760.31931420.23771323X-RAY DIFFRACTION100
3.76-3.960.33021420.25191311X-RAY DIFFRACTION100
3.96-4.210.311430.22451332X-RAY DIFFRACTION100
4.21-4.530.26411440.2071328X-RAY DIFFRACTION100
4.53-4.990.24941440.19821337X-RAY DIFFRACTION100
4.99-5.710.30061460.23681350X-RAY DIFFRACTION100
5.71-7.190.30641470.26871366X-RAY DIFFRACTION100
7.19-47.480.26911560.25451450X-RAY DIFFRACTION99.94
Refinement TLS params.Method: refined / Origin x: -1.88223875928 Å / Origin y: 82.1336320868 Å / Origin z: -19.5993943519 Å
111213212223313233
T0.316999278333 Å20.00581788082111 Å20.000701802588905 Å2-0.338850136245 Å2-0.0374285588985 Å2--0.261849513478 Å2
L1.36046359588 °20.118134830156 °2-0.0358137625525 °2-0.119321742521 °2-0.116743477272 °2--0.0846392091961 °2
S-0.0247782075664 Å °0.242106981601 Å °-0.0391817758735 Å °-0.120911214925 Å °-0.0201103039896 Å °-0.0273522580991 Å °0.019343601369 Å °0.0760377777065 Å °0.0421069061442 Å °
Refinement TLS groupSelection details: all

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